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EXAM 1
CHAPTER 1: Studying Life
CHARACTERISTICS OF LIFE:
1. Cell theory:
•All living organisms are made up of cells.
•Cells are the smallest unit of life.
2. Reproduction: all living organisms contain DNA which is used to produce new organisms.
3. Growth and development: cells produce more cells growth and development. →
4. Energy use and metabolism: all living organisms acquire energy from the environment and use it to do
biological work.
5. Regulation and homeostasis: all living organisms regulate their bodies to maintain a stable environment
(homeostasis).
6. Response to environmental changes: all living organisms must be able to respond to environmental changes.
7. Biological evolution: populations of living organisms change over time, eventually new species and higher →
taxonomic categories. (Creationists disagree here.)
LEVELS OF ORGANIZATION:
Cells tissues organs multicellular organisms populations communities ecosystems biosphere → → → → → → →
- Two-part naming system devised by Carolus Linnaeus.
•First name is (generalgenus ).
•Second name is the within that genus (specific). species
THE 3 DOMAINS:
1. Bacteria
2. Archaea
3. Eukarya
•Protista
•Fungi
•Plantae
•Animalia
Domains are divided into smaller taxonomic units:
Kingdom phylum class order family → → → → → Genus species→
SCIENTIFIC METHOD:
1. Making observations
2. Asking questions
3. Forming hypotheses
4. Making predictions based on these hypotheses
5. Testing the predictions through additional observations or conducting experiments
6. Analyzing the results & drawing conclusions
Use (begins with some data or observation) to form hypothesisinductive logic: .
Use deductive logic: (start with a statement believed to be true) to make predictions based on the hypothesis.
- General specific→
Observation/question hypothesis→
Hypothesis prediction→
EXPERIMENTS:
-Controlled experiment: manipulates one or more of the factors being tested.
•Factor/variable of interest is manipulated experimental group→.
•Control group is unmanipulated.
-Comparative experiment: starts with the prediction that there will be a difference between multiple samples or
groups based on the hypothesis.
•Variables cannot be controlled b/c researcher is usually working with natural populations and settings.
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•Both variables are measured in a variety of samples and compared/correlated with one another.
CHARACTERISTICS OF A GOOD EXPERIMENT:
1. Testable hypothesis
2. Repeatability
Hypothesis: one possible explanation for an observation/answer to a question.
Theory: hypothesis that has been tested for its predictive power many times and has not yet been found incorrect.
Law: a theory that has been tested for its predictive power many times and has still not been found incorrect;
“universally” confirmed; frequently reduced to a mathematical formula.
CHAPTER 2: The Chemical Basis of Life I: Atoms, Molecules and Water
PERIODIC TABLE:
-Rows/periods = # electron shells.
-Columns/groups = # valence electrons.
Atomic number: number of protons (= number electrons); written as subscript before atomic symbol (6C).
Mass number/atomic mass: sum of neutrons and protons; written as subscript before atomic symbol (^12C)
Isotopes: atoms of the same element which have the same number of protons & electrons, but different number of
neutrons different forms of the same element. →
- Carbon 12 is the most common isotope atomic weight = 12 on periodic table→.
# of electrons how it will combine with other atoms. →
Chemical reactions usually involve changes in the distribution of electrons between atoms.
ORBITALS:
- 3D spaces around nuclei where e-s are found ( ). s, p, d, f
- Only 2 e-s may occupy same orbital.
- Arranged in e- shells/energy levels.
•Energy is required to move negatively charged e-s farther aways from positive protons in nucleus.
•E-s can pick up or lose energy.
oE-s gaining energy move farther from nucleus higher energy level→.
oE-s losing energy drop to lower energy levels closer to nucleus.
-First shell: 1 orbital; 2 e-
-Second shell: 4 orbitals; 8 e-
OCTET RULE: tendency for most atoms to need 8 e-s for stability.
BONDS:
-Chemical bonds: 2 or more atoms join together to form a molecule.
-Covalent bonds: results from the sharing of 1 or more pairs of e-s → STRONGEST.
-Hydrogen bonds: occur only with polar molecules; molecules have partial charges partial opposite charges →
attract one another H bond. →
•Very weak individually.
•Function in attractions between and within molecules.
•Play a major role in maintaining protein structure.
-Van der Waals interactions: atoms joined by nonpolar covalent bonds nonrandom distribution of e- one →s →
atom for a short amount of time could have more or less e-s than expected by chance electric charge. →
•Close together attracted. →
•Weak type of bond.
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-Ions and ionic bonds: form from the transfer rather than sharing of e-s between atoms.
•Transfer occurs due to very large differences in electronegativity (<2).
•One atom strips e-s from another.
•Have full + and – charges always form polar molecules. →
oNa, Cl,
-Hydrophobic interaction: nonpolar molecules in an aqueous solution will tend to draw together due to their
non-attraction to water.
•Weak type of chemical bond.
STRONGEST WEAKEST→: Covalent ionic hydrogen hydrophobic interactions van der Waals interactions. → → → →
•Sharing e-s equally in a covalent bond = covalent bonds (electronegativity = 0.2 – 0.5). nonpolar
•Atoms with different electronegativity will not share e-s equally; e-s will spend more time around the
more electronegative element areas of partial charges within molecule = covalent bonds →polar
(electronegativity difference = 0.5 – 1.6).
•For biologically important atoms (C, H, O, N), can tell how many covalent bonds they form from # of
e-s needed to fill outer energy level/shell.
oC:
▪4 valence e-s (6 total: 2 in 1 shell and 4 in 2 shell)
st nd
▪needs 4 more to fill 2 energy level .
nd
▪will form 4 covalent bonds with other atoms.
oN:
▪5 valence e-s (7 total: 2 in 1 shell and 5 in 2 shell)
st nd
▪Needs 3 more to fill 2 energy level.
nd
▪Will form 3 covalent bonds with other atoms.
oO:
▪Has 6 valence e-s (8 total: 2 in 1 shell and 6 in 2 shell)
st nd
▪Needs 2 more to fill 2 energy level.
nd
▪Will form 2 covalent bonds with other atoms.
oH:
▪Has 1 valence e- (1 total)
▪Will form one covalent bond to share its 1 e-.
COMPOUND: consists of 2 or more different elements (O2 is not a compound, only molecule; H2O is both).
- Molecular shape most important factor in determining function of molecules. →
ELECTRONEGATIVITY: at atom’s attraction to electrons; depends on # of protons in the atom’s nucleus
and their distance from the e-s in chemical bonds.
-O and N have a high electronegativity, H is low.
- E-s shared between O and H are not shared equally.
- STRONGEST WEAKEST:→
•O → N → C → H.
CHEMICAL REACTIONS:
-Endergonic: if energy has to be put in larger/more complex molecules.→
-Exergonic: if energy is given off in breaking down large complex molecules smaller less →
complex ones.
-Calorie: unit of energy in chemical reactions.
•1 calorie = amount of heat energy needed to raise temperature of 1 g of pure H2O
from 14.5 degrees C 15.5 degrees C.→
ACIDS, BASES, AND pH:
- H+ ions form normally by the dissociation of H2O
- O retains 1 of H’s e-s but expels the proton as a H ion.
- Reversible, but rare.
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- Gives off H+s → acid (proton donors).
•Adding protons (H+) increasing H+ ion concentration decreasing the pH→ → .
- Accepts protons (H+) → base (proton acceptor).
•Decreases the H+ ion concentration increasing the pH. →
CHAPTER 3: Chemical Basis of Life —Organic MoleculesII
MOLECULES:
-Organic molecules are those with a chain or ring of carbon atoms.
▪to this chain/ring are attached a variety of other atoms or groups of atoms determine the shape →
and function of the molecule functional groups covalently bonded to carbon skeletons.: :
1. Amino groups: consists of a N atom bound to 2 H atoms.
-N atom is bound to carbon skeleton of organic molecules.
-Can and do ionize.
-N has 2 unpaired electrons (- functions as a base, accepting H+ ions. ) →
-b/c of full + charge amino groups are polar→.
oAmino acids have an amino group as
well as a carboxyl group.
oMany nitrogenous bases in
nucleotides also have amino groups.
2. Carbonyl groups: include a double bonded O attached to the carbon skeleton.
-Polar (partially – and +) b/c of electronegativity differences between C and O.
-Carbonyl groups are subdivided depending on where the O is attached:
-Aldehyde group: O is attached to a terminal/end C.
▪Such as glucose
-Ketone/keto group: O is attached to an
internal/middle C.
▪Such as fructose.
-Organic molecules with carbonyl groups are called
carbohydrates, such as glucose.
3. Hydroxyl group: a H bonded to an O ( ) which is then bound to a carbon skeleton.OH
-b/c O is more – than H, hydroxyl groups are polar.
-Organic molecules containing only hydroxyl groups are called alcohols.
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4. Carboxyl groups: include both a hydroxyl and a carbonyl group bound to the same
carbon atom.
-Compounds with carboxyl groups are acids.
-Carbon compounds with carboxyl groups are called organic acids.
-Polar (b/c of full – charge).
5. Methyl groups: consist of 3 H atoms bound to a C.
-Similar electronegativity between C and H nonpolar →.
6. Phosphate groups: consist of a phosphorus bonded to 3 hydroxyls and 1 carbonyl.
-Bound to the carbon skeleton or organic molecules by one of the hydroxyl
groups after a condensation reaction.
-Polar for same reason as carboxyl &
sulfate.
-Found in all nucleic acids and
carbohydrates.
7. Sulfate groups: resemble phosphate groups.
-Central S atom covalently bound to 4 Oxygens.
-Full – charge polar.→
-Can be found in carbohydrates, proteins, and lipids.
8. Sulfhydryl groups: consist of a H bonded to a S atom.
-S is bound to the carbon skeleton.
-Molecules with sulfhydryl groups are called . thiols
-2 amino acids contain a sulfhydryl.
-Nonpolar due to similar electronegativity of S and H.
-The hydrogens can be removed to link 2 sulfhydryl
groups together disulfide bridge. →
-Can play important role in stabilizing the three-
dimensional shape of organic molecules, particularly proteins, by forming
these disulfide bridges.
ISOMERS: chemical compounds with the same chemical/molecular formula but different
arrangements of the atoms (structural or optical).
▪Optical isomers:
oOnly L-amino acids are found in the proteins of living organisms;
enzymes responsible for protein synthesis do not
recognize/process D-amino acids.
oOnly D-monosaccharides are found in the carbohydrates of living
organisms; enzymes responsible for carbohydrate synthesis do not recognize/process L-sugars.
POLYMERS: large and complex molecules made of many similar subunits (monomers).
oConstructed using the condensation reaction.
•Water is removed from the 2 monomers (usually 2 hydroxyl); remaining O holds the 2
monosaccharides together with an oxygen bridge (or C-N bond in proteins) → Disaccharide.
•Oxygen bridge = ester bonds.
oHydrolytic reaction: reverse ^ reaction occurs.
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•Water is inserted, breaking the oxygen bridge 2 monosaccharides from the disaccharide. →
CLASSES OF ORGANIC MOLECULES & THEIR SUBUNITS:
POLYMER
MONOMER
Lipids (fats and oils)
Fatty acids
carbohydrates
Monosaccharides
proteins
Amino acids
Nucleic acids
Nucleotides
CARBOHYDRATES:
oSugars and starches.
oC(H2O)n
oEach middle C contains a H atom and a hydroxyl group, rather than water itself.
oShort-term energy storage.
oCellulose→plant walls (structural function)
oChitin→arthropod exoskeletons & fungal cell walls
oDerived carbohydrates: have additional functional groups attached.
•Sugar phosphates have phosphate groups attached.
•Important in metabolic pathways.
AMINO SUGARS: amino groups are attached (cartilage, chitin).
FUNCTIONAL GROUPS:
o1 carbonyl
oMany hydroxyls
oSometimes a phosphate
MONOSACCHARIDES:
oCan form either straight chains or ring structures if they have 5 or more carbons; rings predominate.
•2 versions of the ring structures, differing in the
orientation of the hydrogen and hydroxyl groups
at carbon #1.
oCan be connected together via hydroxyl groups using the
condensation reaction water is removed and the . →
monosaccharides are connected with a glycosidic linkage:
a bond between simple sugars).
oAlpha-glycosidic linkage: bond projects below the plane of the ring.
oBeta-glycosidic linkage: bond projects above the plane of the ring.
SACCHARIDES:
1. Monosaccharide = 1 subunit
2. Disaccharide = 2 subunits
3. 12Oligosaccharide = -20 units (w/ additional side groups special characteristics; covalently bond to →
proteins→glycoproteins or lipids→glycolipids).
4. Polysaccharide = (extensive branching; each mono has sites for glycosidic linkages).many subunits
LIPIDS (FATS AND OILS):
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oFrequently called hydrocarbons b/c usually have only H atoms attached to most of the carbon chain.
oNonpolar
oSaturated fatty acid: carbon chain has only single covalent bonds; cannot hold any more H atoms
•Chain straight.
•Can pack more tightly together allowing more hydrophobic interactions more solid→ → .
oUnsaturated fatty acids: at least 1 C- double bond in the chain.C
•Chain is bent.
•More spread out allowing less hydrophobic interactions more liquid→ → .
GLYCERIDES: liquid polymers
oBuilt with the molecule glycerol: a 3-carbon molecule with each C containing a hydroxyl
group.
•Hydroxyl groups are important in building large polymers because they participate
in condensation reactions.
oOne, two, or three fatty acids can be attached to glycerol to glyceride. →
1. Monoglycerides: glycerol with a single fatty acid attached.
2. Diglycerides: glycerol with two fatty acids attached.
3. Triglycerides: Glycerol with three fatty acids attached.
•The major form of long-term energy storage
in fat (adipose tissue).
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PHOSPHOLIPIDS: modified diglycerides; contain the following:
oN containing region
oPhosphate group
oTwo fatty acids.
oOne fatty acid saturated and the other unsaturated.
oAll components connected with condensation reactions.
oAmphipathic (some parts polar, some parts nonpolar).
CAROTENOIDS: pigments broken into 2 molecules of Vitamin A, from which cis-retinal for vision is →
derived.
STEROIDS: family of lipid molecules which contain a series of four rings.
oCholesterol is the starting point for the synthesis of other steroids (many of which are
hormones).
VITAMINS:
omany are coenzymes: helping enzymes carry out important metabolic reactions in many biochemical
pathways.
oVitamins A, D, E and K are lipids.
•Waxes are lipids produce skin/coat hair/feathers/leaves to keep them water-proof. by
PROTEINS: polymers built from amino acids; contain the following:
oAmino group
oCarboxyl group
oHydrogen atom
oSide (R) group→gives amino acids their different properties.
•Amino acids are polymerized with condensation reactions (dehydration) direct C-N covalent bond →
(peptide bond).
PROTEIN STRUCTURES:
oPrimary: linear sequence of amino acids; depends on covalent bonds.
oSecondary: repeated patterns of hydrogen bonding between adjacent amino and carboxyl groups.
•Alpha helix
oForms when primary structure of the chain forms a right-handed coil; stabilized by hydrogen
bonds between the amino and carboxyl groups of adjacent amino acids.
•Beta pleated sheet
oForms when the primary structure of the protein’s chain bends back and hydrogen bonds
form between adjacent rows; flat, sheet-like.
oTertiary: overall 3D shape of a larger polypeptide. Maintained by:
•Covalent (peptide) between amino acids
•Covalent disulfide bridges between specific cysteine side groups
•Hydrogen bonds between various side groups
•Hydrophobic interactions between nonpolar amino acids
•Van der waals forces
•Ionic bonds between charged amino acids
oQuaternary: found only in those proteins composed of multiple polypeptides; overall 3D shape of the mature
protein. Maintained by:
•Hydrophobic interactions
•Van der waals forces
•Hydrogen bonds
•Ionic bonds
oThese weak bonds allow small changes in the structure to aid the protein’s function.
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-Domains: distinct regions of proteins; repeated in other proteins; same
function in all proteins where it is found.
-Each domain is encoded by a distinct gene: exon.
-Ligand-binding domain: required for hormone to bind and activate protein.
-Nuclear localization domain: required to transport protein to nucleus of cell.
-DNA-binding domain: required for protein to bind to specific gene(s).
-Activation domain: required for protein to activate the target gene.
-Chaperone proteins: attach to proteins as they form to help them assume
their correct shape.
NUCLEIC ACIDS: composed of nucleotides.
2 types:
-DNA: encodes the info necessary for life and passes it from generation to generation.
•Hydrogen bonding between complementary bases holds the 2 strands together.
•Purine: (2 rings); always pairs with a pyrimidine (1 ring).
oCytosine Guanine
→
→
→
→→ in both DNA & RNA with 3 hydrogen bonds.
oAdenine Thymine / Uracil
→
→
→
→→ (DNA) (RNA) with 2 hydrogen bonds.
▪can reproduce itself exactly during replication.
▪Can copy its info into RNA during transcription.
-RNA: used to take the info in DNA and make proteins.
•Using info from DNA, orders specific sequence of amino acids in proteins during translation.
•4 dif types of RNA (mRNA, rRNA, snRNA (small nuclear), and tRNA).
Nucleotides are composed of 3 parts:
1. A pentose sugar (ribose or deoxyribose: differ in functional groups at
carbon atom #2).
2. At least one phosphate group.
3. A nitrogen-rich (nitrogenous) base.
-Nucleotides are connected together with condensation reactions by connecting the phosphate group from
carbon #5 to the hydroxyl group on carbon #3.
•Meaning sugars are connected to the phosphate groups above and below by oxygen bridges.
•Sugar-phosphate backbone with bases projecting to the center.
•ATP: energy intermediary in many biochemical pathways.
•GTP: energy intermediary during translation.
•cAMP: a second messenger important in transferring the signal from a hormone to the interior of a cell.
CLARIFICATIONS:
Condensation reaction covalently bond monomers together to form polymers.
Carbohydrates
Glycosidic linkage
Oxygen bridge
Lipids
Ester bond
Oxygen bridge
Nucleic Acids
Phosphodiester linkage
Oxygen bridges
between phosphate
and hydroxyl
Proteins
Peptide bond
Direct C-N bond
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EXAM 2
CHAPTER 4: General Features of Cells
-as cells increase in volume surface area also increases, but at a lower rate→.
oSurface area : volume ratio: 3:1, 0.3:1, 0.03:1, etc.
Why are cells so small?
-Cell’s volume determines its metabolic activity.
-Cell’s determines the surface area rate of transport into and out of the cell.
-As a cell grows its metabolic activity increases, but at a rate faster than the increase in surface area (and →
therefore, its ability to keep up with internal demands).
Light microscope: uses light passing through the sample resolving power = (2 x 10^-4 mm) as long as cells are ; 200 nm
at least 200 nm apart, one can tell that they are 2 different cells.
Transmission electron microscope uses an electron beam passing through the sample; resolving power (2 x 10^-= 0.2 nm
7 mm).
-Cells must be killed and stained with heavy metals to block/scatter the e- beam.
-Those that pass through are focused.
-Subcellular (organelle level)
Scanning electron microscope: coats the surface of sample with heavy metal stains and uses electron beam to scan
surface; 3D view of the surface.
-2 million x
-No splitting
Prokaryotic cells: domain bacteria and archaea.
-Lack membrane-bound organelles (ex. nucleus)
-Relatively simple in structure
-Generally smaller than eukaryotic cells
STRUCTURE
FUNCTION
PLASMA MEMBRANE
Single membrane
Regulate transport
CELL WALL
Peptidoglycan membrane
Protection/support
CAPSULE
Polysaccharides
Protection/hydration
NUCLEOID
Aqueous
Heredity/DNA
CYTOPLASM
Aqueous
Biochemical reactions
RIBOSOMES
Solid—RNA and proteins
Protein synthesis
FLAGELLA
Solid—Proteins
Movement
Eukaryotic cells: , kingdoms Protista Plantae, Fungi, and Animalia.
-Possess membrane-bound organelles.
-Are complex in structure with many organelles.
-Larger in size
Cytoplasm: aqueous mixture containing a wide variety of proteins.
-Many proteins are enzymes, controlling a host of reactions.
-Many of these reactions are the first reactions in important metabolic pathways like and glycolysis fatty acid
synthesis.
The cytoskeleton: series of fibrous organelles which provide an internal skeleton to cells
and perform some other functions.
-Each of these 3 types of fibers are constructed of many protein monomers.
1. Microtubules Tubulin: largest fiber in cytoskeleton; long hollow tubes of
contributing to the cytoskeleton.
oHave 2 differently charged ends→helps them grow and shrink.
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oCentrioles and basal bodies control their from one growth
point to another.
oForm cellular “roads” along which vesicles and chromosomes
move using molecular “motors”: Kinesin.
•Motor protein “walks” along microtubule from – end → +
end carrying cargo in vesicle.
oForm Cilia and Flagella for cellular locomotion.
oForm the for moving chromosomes during Mitotic Spindle
nuclear division ( ). mitosis
•Cilia = hairs locomotion→
•Flagella = tail locomotion→
2. Intermediate filaments: more than 50 types; many found only in specialized cells.
oStructure: thin rods of Keratin.
oMore than other parts of cytoskeleton (not constantly growing and stable
shrinking).
oFunction: maintain cellular shape and provide mechanical strength to cells.
oLine inside of nuclear membrane to anchor nuclear pores (in form of nuclear
lamina).
oMedium size
3. Microfilaments structure Actin: : smallest; thin rods of .
oCan exist as single filaments, in bundles or in
networks.
oFunctions:
1. Cellular movement: muscle
contraction, cytoplasmic streaming,
pseudopod formation.
2. Cytoplasmic division (cytokinesis): divide a cell into 2 daughter cells mitosis and following
meiosis.
3. Tend to occur near plasma membrane and anchor other proteins.
4. Support the plasma membrane & provide shape and strength to the cell.
The nucleus and endomembrane system:
-Nucleus
-Structure: double membrane
-Function: stores DNA
-Membranes form compartments!
Nucleus: nuclear membran contains thousands of small pores which regulate transport between the nucleus and the e
cytoplasm.
-Pores are surrounded by a complex of 8 large protein granules.
-Proteins targeted for the nucleus have a short peptide Nuclear Localization Signal (“tagged” for import through
pores) needed to enter or leave.
-Double membrane (2 lipid bilayers).
-Nucleolus: consists of the gene(s) which code for ribosomal RNA.
•rRNAs needed for ribosomes construction.
-The outer of the two nuclear membranes is in places continuous with the Endoplasmic Reticulum.
Organelles that process information:
-Ribosomes: no membrane not technically an “organelle”. →
•Large and small solid subunits, each composed of 1-3 rRNAs and -30+ proteins (prokaryotes20 )
(eukaryotes have 30-50 proteins per subunit).
•Function = protein synthesis.
•Location = 3 possible locations: free in cytoplasm, attached to ER inside mitochondria and , or
chloroplasts.
Endomembrane system: group of functionally interrelated organelles. Includes the:
-Nuclear envelope
-Endoplasmic reticulum:
•single membrane surrounding central : hollow part of tube. lumen
•Tubes and flattened sacs
•Can compose up to 10% cell’s volume.
•Many folds in membrane much more surface area than plasma membrane. →
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•Rough ER: studded w/ ribosomes
oFunction: synthesize/modify glycoproteins, membrane-bound proteins, and proteins destined
for various organelles.
oRibosomes synthesize proteins transported into lumen of ER (segregating them from →
cytoplasm).
oProteins in the rough ER can be chemically modified to alter functions.
oAlso “tagged” w/ short peptide to mark for delivery to various organelles via vesicles.
oSome of these proteins have oligosaccharide chain attached and form→glycoproteins.
•Smooth ER lacks ribosomes and is more tubular than flattened sacs. :
NO RIBOSOMES = NOT WORKING W/ PROTEINS!!!!
oContinuous with sections of the rough ER.
oFunctions:
1. Detoxification: of various poisons taken into the body, by modifying them to be
more polar and easier to excrete from the cell.
2. Contains enzymes necessary for glycogen and calcium metabolism.
3. Synthesize phospholipids for membranes, and other lipids including steroid
hormones.
-Golgi apparatus:
FURTHER MODIFYING PROTEINS FROM THE ROUGH ER
•Structure: flattened sacs (single membrane surrounding central lumen).
•Vesicles transport proteins from the ER cis→ →medial→trans regions of the golgi.
•Functions:
1. Add and/or modify carbohydrate portion of glycoproteins.
2. Proteolysis: proteases cut large proteins into smaller, functional proteins.
3. Secretion: packages materials into secretory vesicles to be released from the cell.
•Concentrate, package, and sort proteins.
-Lysosomes:
•Structure: large vesicles containing digestive enzymes (glycoproteins) surrounded by a single
membrane.
•Function: digestion via hydrolytic reactions.
•Primary lysosomes: formed by vesicles containing hydrolytic enzymes forming from the golgi.
•Secondary lysosomes: formed by the fusion of a and a primary lysosome food vacuole (phagosome).
-Peroxisomes
-Vacuoles: structures similar to large vesicles.
•Functions:
1. Storage of food or waste.
2. Maintain turgor pressure.
•Contractile vacuoles: freshwater protists use them to excrete excess water.
▪Water diffuses in CV contracts forcing water out via pores. → →
-Plasma membrane part of the : endomembrane system: membrane transport cell signaling, and cell adhesion, .
•Surrounds cell and divides it from external environment.
•Functions:
1. Membrane transport everything leaving and entering must pass through (: protein
transporters fill this role).
2. Cell signaling: communicate with each other and the environment (hormones fill this role).
3. Cell adhesion: multicellular organisms need a way to hold cell together and recognize each
other (many types of fill this role).proteins
-Vesicles: . (shuttle materials between these)
-Microbodies:
•Structure: vesicle-like
•Function: contain enzymes for specific functions.
•Includes peroxisomes glyoxysomes and .
oPeroxisomes: contain catalase to degrade hydrogen peroxide.
▪hydrogen peroxide is formed as a byproduct of many types of reactions, but in high
levels is toxic.
▪Are synthesized as vesicles from the ER.
oGlyoxysomes: also contain enzymes for specific reactions.
▪Found primarily in plant seeds.
▪Convert stored lipids into carbohydrates for growth.
▪LIPIDS→
→
→
→→CARBS
Semiautonomous organelles:
-Mitochondria: cellular respiration
•Structure: double membrane (two spaces).
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•Function: convert energy in organic molecules (ex. glucose) into ATP (aerobic respiration).
•Cellular respiration begins in the cytoplasm with glycolysis continues in the mitochondria with Krebs →
cycle and electron transport end product is ATP, a modified nucleotide which has a high energy →
content and is used to do most types of cellular work.
-Chloroplast: photosynthesis
•Structure: 3 membranes (inner outer, and thylakoid, ).
•Function: photosynthesis.
•Plastids: photosynthetic pigments embedded within the thylakoids; 10% phospholipid content; liquid
surrounding the thylakoids = the stroma.
oChromoplasts: . plastids, but NOT semiautonomous
▪Function: produce and store various producing redcarotenoid pigments , yellow,
and orange colors in flower and fruit (color).
oLeukoplasts: also plastids, also NOT semiautonomous.
▪Function: store food (starch and fats).
Both of these can divide independently of the cell and contain their own DNA & ribosomes.
Endosymbiont Theory for the origin of mitochondria, chloroplasts, and eukaryotic cells:
1. Prokaryotic cells, some of which had aerobic respiration and others photosynthesis.
2. Engulfment stage: large prokaryotic cells engulfed smaller ones but didn’t digest them.
3. Evolution into “organelles” with double membrane (mitochondria & chloroplasts.
-Only organelles that contain DNA like prokaryotic cells.
-Contain ribosomes like prokaryotic cells.
-Both double-membraned.
Extracellular structures: cell walls and extracellular membrane included.
Plant cell wall:
-Structure: thin mat of fibers. cellulose
-Function: support the cell
•Limits volume of the cell to help maintain turgor pressure.
•Forms a barrier to prevent infection by fungi/bacteria.
Extracellular matrix:
-Structure: interwoven mat of fibrous proteins such as collagen, a matrix of glycoproteins (proteoglycans),
proteins which link the others together into a continuous unit.
-Function: help connect adjacent cells together.
Protein sorting to organelles:
-Advantage if eukaryotic cells large # of organelles. →
-Each organelle has own set of proteins which carry out functions.
-Most proteins synthesized on ribosomes in the cytoplasm.
-Synthesized in the cytoplasm and many stay in the cytoplasm to perform their various roles.
-Other proteins destined for an organelle will be transported to it after synthesis.
•Cotranslational sorting: (ER)
oMany proteins take the first step in being sorted to organelles
when they are being translated.
o1 12
st -20 amino acids are nonpolar (hydrophobic) and form
an ER signal sequence.
oA special protein, the signal recognition protein (SRP) finds
and binds the signal sequence (hydrophobic amino acids).
oSRP drags the ribosome to the ER and attaches to the SRP
receptor.
oWhen SRP docks with the receptor, the protein chain is
threaded through a channel protein embedded in ER
membrane.
oProtein then threaded through the ER membrane so it will end up in the lumen of the ER.
oThe SRP is now finished and leaves. (cuts of ER signal sequence)
oProtein synthesis continues, the signal sequence is removed, and the entire protein will end
up in the lumen of the ER.
o4 TOTAL PROTEINS HERE→
→
→
→→
oafter proteins are translated→packaged into vesicles for transport to organelles.
14
oVesicles destined for an organelle have specific protein (receptors) embedded in
membrane to help concentrate the proteins being carried and to help vesicle fuse with
proper target organelle.
•Post-translational sorting: proteins destined for the nucleus, microbodies, mitochondria,
and chloroplasts are synthesized on ribosomes in the cytoplasm and sorted they are after
made.
o1 12
st -20 amino acids on these proteins are special sequences which act as a
transit sequence or sorting signals.
oThe transit sequence (matrix-targeting sequence for mitochondria) is bound and
transported by “chaperones” to a receptor protein on the outer mitochondrial
membrane.
oOnce bound, the protein is threaded
through a channel protein.
oProtein delivered to matrix, signal
sequence removed, and becomes active
in the duties of mitochondria.
oOther signal/transit sequences deliver
proteins to the nucleus, chloroplast, and
microbodies.
oNuclear proteins are unique: signal/transit
sequences not removed.
oPosition of the nucleus keeps changing with each cell division and nuclear
proteins must be gathered and redelivered to new Nuclei continually.
Chapter 5: Membrane Structure, Synthesis, and Transport
Fluid mosaic model: double layer of phospholipids
-Phospholipids are amphipathic, fatty acid tails =
nonpolar, phosphate heads = polar.
-Each phospholipid layer = a leaflet.
-Phospholipids in the membrane are not covalently
bound to each other; free to move within the membrane;
can move from one end of prokaryotic cell to the other in
less than a second; 5-10 seconds in eukaryotic cells.
-Phospholipids are free to move between leaflets NOT
(flip-flop).
•Special protein Flippase is needed to do this using ATP.
-Lipid content of membrane can vary.
-Most common phospholipids have an even number of carbons
(18-20 in the tails).
-Because flip-flop is rare the 2 layers may have different lipid content/ratios. →
-Up to 25% of lipids in animal cell may be cholesterol.
Selective permeability:
-Polar molecules cannot pass hydrophobic membrane center.
-Nonpolar molecules can generally diffuse.
-Proteins: proteins are embedded in bilayer (mosaic)
Membrane proteins: protein ratio of membranes varies from -70x more lipid molecules than protein molecules15 .
-Proteins usually determine function do most of membrane’s work.→
-Peripheral membrane proteins are less closely associated with the membrane loosely ;
bound to the membrane.
•Bound by hydrogen or ionic bonds to transmembrane proteins or the heads of
phospholipids.
•Exposed proteins of peripheral proteins are usually polar for binding.
•Typically occur only on one leaflet of membrane membranes may be asymmetric →
with different functions.
-Integral membrane proteins are more closely associated with membrane.
•Often transverse (span the membrane).
•Exposed portions are usually nonpolar for binding.
•2 types:
oTransmembrane
▪Transverse the membrane with domains forming -helices. a
15
▪Regions occur on both sides of the membrane and may be bound to the
cytoskeleton.
oLipid-anchored
▪Have a lipid covalently attached to the protein.
▪Lipid is inserted into phospholipid bilayer to anchor protein.
Factors affecting membrane fluidity:
-Fewer hydrophobic interactions higher fluidity:→
1. Shorter hydrocarbon chains.
2. More unsaturated hydrocarbon chains (more kinks in the
chains).
3. More cholesterol will make membrane more fluid at low
temperature and less fluid at higher temperature.
-Membrane proteins, like phospholipids, can diffuse/move
throughout the membrane; because of their polarity, they do
not flip-flop.
•Some proteins exposed to the cytoplasm attach to
elements of the cytoskeleton, anchoring them in one
position, restricting their movements.
Membrane carbohydrates:
-Carbohydrates in membranes occur only as glycoproteins and
glycolipids.
•May function as antigens, identifying the cells of organisms
(cell surface recognition).
•Or may label proteins w/ signals for cellular destinations.
-Also only occur in the exterior (extracellular) leaflet of the plasma
membrane.
-Some cells have a thick layer of carbohydrates outside the plasma
membrane ( ): can shield the cell from the immune system glycocalyx
of other cells.
Membrane synthesis:
-Phospholipids are synthesized by the
smooth ER and inserted into the
membrane(s).
-After insertion into the cytosol leaflet, ic
Flippase moves some to the exterior
leaflet.
-Phospholipids can be spread
throughout the endomembrane
system by lateral diffusion.
-The membranes of the nucleus, ER, golgi, plasma membrane, mitochondria, and chloroplast are either directly
connected, or by vesicles.
-Lipid exchange proteins can extract a lipid from one membrane, diffuse through the cytoplasm, and insert it
into any other membrane.
-The mitochondria and chloroplast both synthesize various types of lipids which are then
transferred to other organelles by lipid exchange proteins.
-Most membrane proteins are synthesized in the rough ER.
-Hydrophobic helices are left in the ER membrane as they are synthesized, forming a
transmembrane proteins.
-From the ER, proteins can be moved to other membranes by vesicles.
-Glycosylation of proteins occurs in the rough ER with modifications in the golgi.
-Oligosaccharides are synthesized in the lumen of the ER on a dolichol lipid then
transferred as a unit to the R/side group of an asparagine amino acid on the protein.
-In the golgi, an oligosaccharide chain can also be synthesized and transferred to the oxygen of a serine or
threonine amino acid.
16
-These proteoglycans (types of glycoproteins) are often secreted from the cell to help form the extracellular
matrix.
-Proteoglycans are also components of mucus.
Membrane transport:
-b/c of biological membrane hydrophobic interior selectively permeable.→
-Molecules are passed through membranes by either of 2 processes:
1. Passive transport: simple/passive facilitated diffusion; molecules move with the concentration gradient. &
•Does not require energy but depends on the kinetic energy of the solute (dissolved) molecule. (all
molecules are in constant motion)
•Molecules in motion will tend to evenly distribute themselves with time.
Simple/passive diffusion is the net movement of a substance from an area of high concentration to an area of low
concentration.
- It can occur for nonpolar molecules or small uncharged particles) diffusing directly through the phospholipid
bilayer.
- Diffusion of repiratory gases ( ) = simple/passive. O, N, CO2
- Due to kinetic energy.
- High→low concentration.
- Directly through membrane.
-Rate of diffusion depends on:
oElectrical charge
oTemperature
oConcentration
oMolecular size
- Diffusion over short distances = very effective.
- Molecule can diffuse from one end of cell to other in millisecond.
- Nonpolar molecules can diffuse throughout cell, but polar molecules need special means to transport.
Facilitated diffusion: still passive: the diffusion of macromolecules and polar molecules through membranes using proteins
(with conc grad).
- Proteins may be channel or carrier/transporter proteins.
•Channel proteins transmembrane proteins that form channels through the membrane through which :
certain molecules can diffuse.
oMay be gated and only transport when the gate is open.
oLigand-gated channels open when a signal molecule (ligand) is bound.
oVoltage-gated channels open when a membrane is depolarized, by a change in the
electrical charge across the membrane.
oTransporter proteins bind the solute which is then carried through the membrane, usually by
a conformational change in the protein.
oOnce transported, the solute is released on the opposite side of the membrane.
oThe solute can diffuse in either direction according to its concentration gradient.
oTypes of transporters:
▪Uniports: transports one solute molecule in one direction.
▪Symport: transports 2 in same direction.
▪Antiport: transports 2 in different directions (1 AT A TIME).
2. Active transport: molecules move against concentration gradient required ATP. →
•Primary AT: the transport of a substance, with a pump, against its concentration gradient with the
direct expenditure of energy.
oATP is often the energy source used.
oThe is a classic example. sodium potassium pump
▪Pumping 2 cations at uneven rates electrical →
charge across membrane.
▪Voltage difference→variety of purposes in
cells.
17
•Secondary AT: uses active transport of one molecule (against
gradient) to drive the transport of a 2 molecule (against gradient)
nd
to drive the transport of a 2 molecule (also against gradient
nd
through channels or transporters).
oNo ATP expended directly (at least not for 2 molecule).
nd
oUses pre-existing gradient of 1 molecule (kinetic energy)
st
to drive active transport (against gradient) of 2
nd
molecule.
Osmosis: the diffusion of water through a semipermeable membrane; water sometimes diffuses through special pores in
membranes (aquaporins) of some cells.
- Aquaporins are found in plant cells, and kidney cells and RBCs of animals.
- Water molecules pass single file through the pore, which excludes other molecules.
- Water can also hitchhike, bound to cations (Na+) when they pass through pores (other kinds of pores/channels
as well).
3 conditions (solutions) into which a cell may be placed:
- Isotonic: no volume change.
- Hypertonic: cell loses volume; higher concentration in solution.
- Hypotonic: cell gains volume; lower concentration in solution.
Endocytosis: brings large sized materials into cells using vesicle formation.
- After the vesicle imports material from outside the cell, it can fuse with a
primary lysosome.
- Macromolecules are digested to monomers before they are transported to
the cytoplasm.
- Receptor-mediated endocytosis: uses receptors to concentrate materials
before bringing them in.
Exocytosis: also discards materials from cells using vesicles.
- Adds phospholipids to plasma membrane.
Cell junctions: cells produce an extracellular matrix for strength and support.
- Multicellular organisms also use cell junctions to hold adjacent cells
together.
- Most cell junctions are composed of proteins and play a variety of roles
in cells.
•Anchoring junctions: cadherin & integrin.
oDepend on integral proteins passing through the cell
membrane and connecting to elements of the
cytoskeleton of adjacent cells.
oCadherins are fibrous proteins connected to actin microfilaments in the
cytoplasm; they extend into the extracellular matrix where Ca+ ions help
them bind to each other.
oIntegrins are composed of 2 subunits (blue) that bind other proteins
(pink) which then bind to actin microfilaments in the cytoplasm.
oIn the extracellular matrix, integrin binds to fibronectin
(wishbone) which then binds to elements of the matrix such as
collagen fibers.
•Tight junctions: occluding & claudin
18
oForm seals between cells
1. Limit movement of materials through intercellular spaces.
2. Limit movement of proteins within the membrane.
•Gap junctions: connexon
oConnexon proteins from channels connecting the cytoplasm of
2 adjacent cells.
oAllow passage of ions and small molecules for communication
between cells.
CHAPTER 6: Metabolism
Metabolism: total chemical activity of a living organism.
2nd law of thermodynamics: in any energy conversion, some energy is lost (becomes less usable) from doing
work→entropy increases (measure of disorder).
Metabolic pathways:
Catabolic reactions: larger molecules are broken down into smaller ones with the release of potential chemical energy
(exergonic).
Anabolic reactions: smaller molecules are built into larger ones with the input of potential chemical energy
(endergonic).
METABOLISM = CATABOLISM + ANABOLISM
Exergonic reactions release energy (catabolic/breaking down); occur spontaneously.
Endergonic reactions require the input of energy (anabolic/building); do not occur spontaneously.
Enthalpy (H): total chemical energy of a molecule.
H = G + TS
-T = absolute temp in Kelvin.
- Free energy ( ): the usable energy available for cellular work. G
- Entropy ( ): the unusable energy in a molecule. S
In a chemical reaction, one molecule with one enthalpy another molecule with a different enthalpy. →
(reactants→products).
Enthalpy: Gibbs Free Energy (change in G): difference in enthalpy between a reactions products and reactants.
-EnthalpyProducts – EnthalpyReactants
- Determines whether reactions will occur spontaneously.
- Determines direction of reaction.
- Change in G < 0 = exergonic
Chemical equilibrium: point in reversible reaction at which there is no net change
in the concentration of reactants or products. (arrow in both directions)
- Chemical equilibrium constant (Ke): Ke = [Products] / [Reactants]. [ ] =
concentration of
- Ke > 1 = exergonic (spontaneous = lots of products)
Exergonic reactions (spontaneous):
Endergonic reactions (not spontaneous):
19
Glucose 1-Phosphate Glucose 6-Phosphate
→
→
→
→→
- Change in G = -1.7 kcal/mole, K = 19e
•Endergonic b/c it has a – change in G (gives off 1.7
kcal/mole)
ATP: Transferring energy in cells:
- ATP/ADP cycle: ATP + H2O ADP + PO4 ^-→
- Change in G = -7.3 kcal/mole (prod-rct at bottom)
Why is there so much energy in ATP?
- -- phosphate groups repel one another.
- Enormous amt of energy needed to hold together.
- All that energy released when bonds broken.
- Major function of ATP: couple exergonic to endergonic reactions
20
Enzymes: biological catalysts (protein catalysts); orient molecules to facilitate
the rxn.
Catalyst: substance that speeds up chemical rxn without being used up.
Activation energy: small amount of energy which must be supplied before
chemical reactions will occur.
Active site: site where substrate is bound and the reaction is catalyzed.
Factors affection enzyme function:
- Competitive inhibition occurs when inhibitor :
molecule is shaped very much like the
substrate.
•Binds to and blocks the active site.
- Noncompetitive inhibition: occurs when an inhibitor binds to separate
(inhibition/allosteric) site, changing the shape of the e=enzyme to an
inactive conformation (shape).
•More than one shape (conformation) depending
upon whether a ligand (substrate inhibitor activator) is
bound.
- Prosthetic groups small molecules permanently attached to :
enzymes that aid in catalysis.
- Cofactors: inorganic ions (Fe3+ or Zn2+ that bind to enzymes
temporarily and promote chemical reactions.
•Usually act as temporary electron acceptors/donators.
- Coenzyme: organic molecules that bind enzymes temporarily
and participate in/enhance the reaction.
•Many are derived from the vitamins necessary in our
diet.
•Coenzyme NAD+ is used to pick up electrons from one
enzyme and store them temporarily before giving them
to another enzyme.
Metabolic pathway: series of chemical reactions where the product of
one reaction is the reactant for the next.
Rate-limiting reaction: the slowest reaction; limits the overall rate of the metabolic pathway, usually located at front of
the pathway.
Feedback inhibition: occurs when product from end of a metabolic pathway acts as a noncompetitive inhibitor,
inactivating an enzyme early in the pathway (enzyme #1).
Enzymatic (protein) denaturation: shape of an enzyme is permanently altered destroy catalytic ability. →
- Heat
- Strong acids
- Strong bases
- Highly charged ions
CHAPTER 8: Photosynthesis
Photosynthesis: the conversion of light energy to chemical energy.
Heterotrophs: organisms which cannot manufacture their own food from simple carbon compounds.
Autotrophs: organisms which can manufacture their own food from simple carbon compounds.
Reactants: CO2, H2O, light (energy)
Products: food (carbohydrates), oxygen
H2O + CO2 C6H12O6 + O2
→
→
→
→→
- Water enters the plant through the roots. DIFFUSION
- CO2 enters the plant from the atmosphere (0.3%) through microscopic pores (stomata) on the underside of
leaves. DIFFUSION
- Light comes in particles termed photons. Light travels in waves.
Electromagnetic radiation: all forms of radiant energy, including the visible light spectrum.
21
Relationship between wavelength and energy: inverse relationship—longer wavelengths have less energy.
The visible spectrum: wavelengths 400-700 nm (nm = 10^-9 m or one-billionth of a meter).
- Violet = lowest WL = most energy
red = longest WL = least energy
Pigments: molecules capable of absorbing some wavelengths (colors) of light but not others.
- Only the wavelengths not absorbed by pigment are reflected or transmitted so they can be seen.
Absorption spectrum: graph for pigment; plots amount of light absorbed vs. wavelength.
Action spectrum: graph for entire plant, plotting photosynthetic activity (action) vs. wavelength.
- Compare these 2 ^^ to determine which of the many pigments in a plant are the major ones used
for photosynthesis.
- Light absorbed used for photosynthesis. →
Structure of chlorophyll:
- hydrophobic, hydrocarbon “tail” inserts chlorophyll into the thylakoid membrane.
- “head” has alternating double bonds and single bonds—useful for picking up and giving off extra electrons.
Photosystems I and II: groups/clusters of many (250-400) of chlorophyll a and b; and carotene and xanthophyll as
accessory pigments.
- Arranged in such a way that light is passed from pigments that absorb shorter wavelengths to those energy
that absorb longer wavelengths.
- A special pair of Chlorophyll a molecules occur in each photosystem and ultimately receive the
energy/electrons from all the other pigments. Chlorophyll passes to e- acceptor. a
- Pass high energy e-s generate by photosystem absorbing light to molecules outside the photosystem.
-Photosystem I: chlorophyll ais P700.
-Photosystem II: chlorophyll ais P680.
Reactions of photosynthesis divided into 2 major processes:
1. Energy-transduction reactions: light-dependent; energy transfer.
•Noncyclic photophosphorylation (energy/electron
transfer NADPH→).
oWater + light NADPH + oxygen + ATP
→
→
→
→→
•Photolysis (splitting water) ultimate source of e-s. =
oLight absorbed by photosystem II is also used to split
water, generating O2 gas (diffuses out through
stomata); e-s are passed to photosystem II then the ET
chain; H+ ions added to those pumped into the
thylakoid lumren.
•Chemiosmosis (making ATP)
•Step 1: light hits photosystem I, transferring the energy in the photon to an e- in one pf the
pigment molecules.
oElectrons energized: energy passed to P700 (reaction center) which passes its e-s to
Feridoxin then NADP+ Reductase then NADP+ reducing it to NADPH.
oProblem: photosystem I will eventually run out of e-s and shut down.
•Step 2: light hits photosystem II transferring the energy in the photon to an electron in a pigment.
oElectrons energized: energy passed to P680 (reaction center) which passes its e-s to the
redox chain (photosynthetic electron transport chain) and then to photosystem I.
Chemiosmotic theory: e-s passing through redox chain used to pump H+ ions
from stomata into thylakoid lumen.
•H+ ions diffuse down concentration gradient and pass through ATP synthase, making ATP.
o
•Cyclic photophosphorylation (energy/e- transfer)
oPhotons energize e-s in P700 (PSI).
oDifference: e-s not passed to NADP+, but to the redox chain (backwards) to make extra ATP
only; no NADPH or oxygen.
•Step 1: light hits photosystem I, transferring the energy in the photon to an e- in one pf the pigment
molecules.
oElectrons energized: energy passed to P700 (reaction center) which passes its e-s to Feridoxin
then NADP+ Reductase then NADP+ reducing it to NADPH.
oProblem: photosystem I will eventually run out of e-s and shut down.
•Step 2: light hits photosystem II transferring the energy in the photon to an electron in a pigment.
oElectrons energized: energy passed to P680 (reaction center) which passes its e-s to the
redox chain (photosynthetic electron transport chain) and then to photosystem I.
22
Chemiosmotic theory: e-s passing through redox chain used to pump H+ ions from
stomata into thylakoid lumen.
•H+ ions diffuse down concentration gradient and pass through ATP synthase, making ATP.
•Major products of light-dependent reactions: , . ATP NADPH, and Oxygen
ATP synthase: H+ ions diffuse back into the stroma through ATP synthase making ATP.
- Multimeric protein
- Rotates as H+ ions pass, coupling with H+ flow with ADP phosphorylation.
- Consists of a base embedded in the thylakoid membrane, a rotating shaft, and a
stationary head.
- Shaft rotates as H+ ions pass between the a and c subunits in the base.
- The 120 degree rotation causes conformational changes in the head.
- In the 1 conformation, the subunit binds ADP and phosphate.
st
- In the 2 , ADP and phosphate are forced together
nd →ATP
- In the 3 , ATP is released.
rd
- H+ ion flow is coupled to ATP synthesis
2. Carbon-fixation reactions: light-independent; CO2 covalently bonded to RuBP.
23
CHAPTER 8: Photosynthesis
-Calvin Benson cycle: C3 photosynthesis light-INDEPENDENT reactions (AKA b/c of the 3PG) ( ):
1. STEP 1 CO2 added to RuBP: → 2 molecules of 3PG.
•Enzyme here = ribulose biphosphate carboxylase-oxygenase
•Happening in the STROMA
•Phosphate groups at C #1 and #5
2. STEP 2: phosphorylation and reduction of (3PG is phosphorylated).3PG G3P
→
→
→
→→
•Uses ATP and NADPH (from non. cyc. phos.)
3. STEP 3 Regeneration of RuBP: from G3P to continue the cycle.
•via pentose phosphate pathway
NET YIELD every 6 CO2 6 net carbons of carbohydrate 1 glucose: → OR .
oOther organic molecules are synthesized from the carbohydrates produced in photosynthesis.
-Photorespiration Ribulose (a reaction): (in the absence of CO2) adds oxygen to RuBP (instead of CO2).
•Product: 1 molecule of 1 molecule of Glycolate3PG +
oGlycolate is respired (broken down using oxygen) but produces no ATP (expensive).
oThis process is essentially undoing the Calvin Benson cycle
o6 CO2s from Calvin Benson join with 6 RuBPs 12 G3Ps glucose. → →
•Conditions for photorespiration:
oHot, dry ,or still conditions = most vulnerable to photorespiration
oFavored if O2 levels are high
oPlants have closed stomata to prevent water loss, which → low CO2 conditions as
well
oC4 photosynthesis is the solution for photorespiration: a special type of light-
independent reaction (LD still occurs).
-C-4 basic reactions: CO2 is added to PEP by PEP carboxylases Oxaloacetate/Malate -carbon →(4
compounds)
•Oxaloacetate/Malate break down Pyruvate + CO2(first detectable chemical) →
→
→
→→ (which is
then used in C3 photosynthesis (Calvin Cycle).
oPEP Carboxylase = reliable
oPyruvate is phosphorylated PEP (with ATP) →
→
→
→→ to continue the cycle.
oCellular locations:
▪CO2 “capture” occurs in Mesophyll cells.
▪Oxaloacetate/Malate is transferred to Bundle Sheath Cells, where it
generates CO2 for C3 photosynthesis.
oNet effect:
▪CO2 is pumped into bundle sheath cells increases local concentration→;
occurs in low O2 location (LD occurs in mesophyll).
▪Mesophyll cells = O2 production = light dependent.
-Crassulacean Acid Metabolism (CAM): another type of light INDEPENDENT
•Found in desert plants (hotter & drier than photorespiration)
•Modification from C4
oNight: (cooler temps at night time) CO2 fixed and stored as Oxaloacetate/Malate
until the next day
•Day & night in mesophyll
oDay: CO2 released for C3 (CB) photosynthesis in same cell.
▪Advantage: stomata can be open at night to capture CO2 without losing
much water vapor.
▪During the day, stomata are closed to prevent desiccation.
▪NO BUNDLE
24
CHAPTER 7: Cellular Respiration, Fermentation, and Secondary Metabolism
What was added to CO2 to carbohydrates during photosynthesis (Calvin-Benson)?: →
-Energy (ATP) and electrons (NADPH).
This will basically be the opposite of photosynthesis (convert sugar ATP). →
Overall Reaction in Aerobic Respiration:
-Glucose + 6O2 6CO2 + 6H2O
→
→
→
→→
- Breakdown of glucose = catabolic
- Delta G = -686 kcal/mole (exergonic)
- This is a reversible reaction!!
Steps in the breakdown of glucose for energy:
-Glycolysis (in the cytoplasm) = sugar cutting
-Glucose is split into 2 molecules of pyruvate (6 carbon) (each 3 carbon)
•→
→
→
→→ 2 ATP directly
•NOTE: breaking down glucose 2 NADH + 2 ATP. 2 pyruvate broken down = 1 carbon from each →
→ Acetyl-CoA (and another NADH from each pyruvate).
- The Krebs cycle breaks Aceyl-CoA to CO2 and electrons (NADH and FADH2).
- The energy in the electrons of NADH and FADDH2 is converted to the energy of ATP by electron
transport (oxidative phosphorylation).
-Glycolysis = glucose→pyruvate
•Cellular location: glycolytic enzymes are all cytoplasmic.
•1st half of glycolysis: energy is invested: 2 ATP are added to glucose fructose 1,6-→
biphosphate split into 2 molecules of G3P. ; REQUIRES ENERGY→ENDERGONIC
•2nd half of glycolysis: ^these 2 G3Ps 2 molecules pyruvate 4 ATP + 2 NADH→ → . EXERGONIC,
DOES NOT REQUIRE ENERGY.
•Essentially, G3P is oxidized (forming NADH) and dephosphorylated (forming ATP)
•Substrate-level phosphorylation high-energy phosphates are transferred directly from a :
substrate (like PEP) ADP. →
oMaking ATP without pumping H ions and using ATP synthase (made w/
chemiosmosis).
•End products of glycolysis:
o2 Pyruvate
o4 ATP (-2 invested)
o2 NADH
•Energy yield: Net (via substrate-level phosphorylation) and 2 ATP 2 NADH
•Control of glycolysis:
oPhosphofructokinase = rate-limiting enzyme.
oATP = noncompetitive inhibitor → inactivates Phosphofructokinase where there is
enough ATP so more is not produced.
•Possible fates of pyruvate from glycolysis:
oAerobic respiration: If oxygen and the Krebs cycle are present, complete oxidation
of pyruvate occurs to CO2 and H2O.
▪Pyruvate oxidation (respiration): pyruvate Acetyl-CoA using 3 reactions →
by the pyruvate dehydrogenase complex:
1. Decarboxylated: splitting off CO2
2. Oxidized: passing electrons to NAD+
3. The remaining 2-carbon compound (Acetate) is added to CoA,
making Acetyl-CoA.
oAnaerobic respiration: If oxygen or the Krebs cycle are NOT present, pyruvate is
reduced by NADH to a waste product and then discarded (fermentation).
-The citric acid (Krebs) cycle
•8 enzymes convert Acetyl-CoA to CO2 and NADH.
•Cellular location: Krebs enzymes all occur in the mitochondrial matrix.
25
•Decarboxylation: steps 3
and 4 remove 2 CO2 per
Acetyl-CoA.
•Oxidation: steps 3, 4, and
8 pass es- to NAD+; step 6
passes them to FAD.
•Substrate-level
phosphorylation: step 5
uses energy from
rearranging Succinyl CoA
to succinate to add a
PO4- to ADP ATP.→
•Electron yield per glucose:
o2 NADH from
glycolysis
o2 NADH from
pyruvate
oxidation
o6 NADH and from Krebs cycle2 FADH2
•Control of the Krebs cycle:
oIn mammals and humans, Isocitrate Dehydrogenase is the rate-limiting enzyme.
oBoth NADH and ATP act as non-competitive inhibitors, slowing the rate of the
process so that more ATP and NADH are not produced.
-The respiratory chain: respiratory electron transport (oxidative phosphorylation):
•Cellular location: cytochromes located in the inner mitochondrial membranes respiratory →
enzyme complexes (e- transport chain). (Inner mitochondrial membrane)
•Electron transport:
1. NADH passes e- NADH Dehydrogenases →
2. NADH Dehydrogenase passes e- Ubiquinone and pumps H+ to intermembrane s →
space.
oUbiquinone accepts e-s from FADH2 via Succinate reductase.
oUbiquinone does not accept protons/H+ (these are pumped from
matrix→intermembrane space by other links in the chain).
3. Ubiquinone passes e- cytochrome b-s →c1
4. Cytochrome b-c1 passes e- Cytochrome c (and pumps H+ into intermembrane s →
space)
oCytochrome c does not accept protons/H+ (these are pumped from matrix to
intermembrane space by other links in the chain.
5. Cytochrome c passed e- Cytochrome Oxidases →
6. Cytochrome oxidase passes e- Oxygen (and pumps H+ to intermembrane space)s →
oOxygen is the “final e- acceptor”
oOxygen w/ e-s combines w/ protons (H+) H2O (where vapor on your breath →
comes from).
-Chemiosmotic theory: as NADH Dehydrogenase, Cytochrome b-c1, and Cytochrome Oxidase pass e-
s, they also pass H+s from matrix intermembrane space, which establishes an electrochemical →
gradient.
-ATP Synthase: ^These H+ ions diffuse back into the matrix through ATP synthase making ATP by →
oxidative phosphorylation.
•ADP FADH2=phosphorylated; NADH and =oxidized
•ATP synthase = a multimeric protein.
•Consists of a base embedded in the inner mitochondrial membrane
•Rotating shaft
•Stationary head
•Same process as in photosynthesis.
•The shaft rotates as H+ ions pass between the a and c subunits in the base.
•The 120 degree rotation conformational changes in the head. →
•In one conformation, the beta subunit binds ADP and phosphate.
•In the second conformation, ADP and phosphate are forced together ATP→
•In the third conformation, ATP is released.
•H+ flow is coupled to ATP synthase.
-Metabolic water: water produced comes from oxygen, the e-s from carbohydrates, and H+s; this
water is produced metabolically.
26
-Aerobic respiration: the oxygen used here ^ is
what makes this process AEROBIC.
•O2 is pulling e-s out of the chain b/c it is so
electronegative.
•Energy yield: oxidative phosphorylation of
aerobic respiration: 30-34 additional ATP (max) are
produced for every glucose that is broken down.
oMay be less since reducing power of NADH
and FADH2 can be used for other reactions like glycerol
and lactic acid synthesis.
oSome intermediates may be used to produce
other types of molecules.
o34-38 ATP per glucose (including the
additional 4 from earlier).
•Control of electron transport:
oATP is a noncompetitive inhibitor of cytochrome oxidase (one of the links in the chain)
oWhen ATP levels are high, it bonds to Cytochrome Oxidase, inhibiting it. And slowing
down electron transport and the additional production of ATP.
-Respiration of other organic molecules (other than glucose):
•Carbohydrates
1. Starch and glycogen: broken down (digested) glucose subunits which then enter → →
glycolysis.
2. Fructose: converted to G3P which then enters glycolysis.
3. Lactose: converted glucose + galactose glucose 1-phosphate enters glycolysis.→ → →
4. Proteins:
1. Digestion to amino acid subunits→
2. Deamination (amino groups removed) to organic acids which enter pyruvate → →
oxidation / Krebs)
o^these organic acids are either the organic acid intermediates of pyruvate
oxidation or Krebs, or are easily converted to them.
5. Lipids (triglycerides):
1. Digestion glycerol + fatty acids→
2. Glycerol enters glycolysis.→
3. Fatty acids split into Acetyl groups→
4. Acetyl groups enter Krebs→
-Comparative energy yields:
•Proteins and carbohydrates have about = energy per unit weight.
•Lipids have about 2x the energy of either protein or carbohydrate.
oNo oxygen or Krebs enzymes → → cannot do aerobic respiration fermentation!!
oNADH cannot be used for anything without electron
transport, and can be harmful at high concentrations.
oFermentation = no e- transport chains!
-Lactate fermentation (anaerobic): pyruvate is directly reduced →
NADH lactate, but the NADH is also oxidized back to NAD+.→
•NADH NAD+ is the whole point!→
oHappens naturally in oxidative phosphorylation
(e- transport).
-Ethanol fermentation: pyruvate is decarboxylated acetaldehyde, →
reduced (using NADH) ethanol, again oxidizing NADH back to → →
NAD+.
-Purpose of fermentation: must convert NADH back to NAD+ so glycolysis can continue.→
•Energy yield: 2 net ATP per glucose (glycolysis).
27
-Anaerobic respiration: no cytochrome oxidase in inner mitochondrial matrix. Instead, they produce
nitrate reductase.
•Nitrate reductase is inserted into cytoplasmic/cell membrane and functions IN PLACE of
cytochrome oxidase to accept e-s from cytochrome b, reducing nitrate ( to nitrite NO3 -) →
(NO2 -).
•Nitrate reductase is the last link in this chain.
•When working hard, muscle cells will ALSO do lactate fermentation to get extra ATP lactic →
acid = “the burn”.
•Both NADH Dehydrogenase and Ubiquinone pump H+ ions from the cytoplasm into
periplasmic space (between membrane & cell wall)
•^These flow back through ATP synthase to make ATP, but without O2 as an e- acceptor.
•Uses No3 – (nitrite) instead.
CHAPTER 9: Cell Communication
Cell signaling involves both incoming and outgoing signals:
- A signal = an agent that can influence the properties of a cell.
- Receptors cellular response (shape/activity altered due to binding of a signal).→
-Basic types of cell signaling:
•Direct intercellular signaling:
oCell junctions may allow signals to pass directly
between cells.
oAn example: gap junctions.
•Contact-dependent signaling:
oOne cell has a membrane-bound signal recognized by a receptor on another cell.
•Autocrine signaling:
oCell secretes a signal/chemical that binds to
receptors on their own surface and also surfaces
of neighboring cells of the same type, stimulating
both.
•Paracrine signaling:
oCell secretes a signal that binds receptors & influences target cell in close proximity
(but not themselves).
•Endocrine signaling:
oCell secretes a hormone into
bloodstream that affects cells far
from the source of the signal.
-Cellular responses to signals (3 step response to signals):
1. Receptor activation:
•Signaling molecule binds to the receptor →
conformational change in the receptor →
activates function.
•Ligands = signals that bind non-covalently and
temporarily to receptors.
•Binding changes the receptor and activates its ability
to initiate the cellular response.
•Binding is temporary and reversible.
•When ligand is released, receptor is no longer activated.
•Cell surface receptors are necessary because most signals are hydrophilic (or large)
molecules that will not diffuse.
•Many cells need surface (membrane-bound) receptors to bind signals.
•Cells contain large numbers of difference types of receptors (A-E):
28
a. enzyme-linked receptors: have a receptor in the extracellular matrix where the signal
(often a hormone) binds.
•Intracellular domain has a catalytic function.
•When extracellular domain is bound, the intracellular domain is activated.
•Most have a protein kinase function in the intracellular domain.
•When bound by a signal, this kinase function leads to the phosphorylation of
other proteins.
•Protein kinases remove a phosphate from ATP and attach it to a protein.
•The phosphorylated protein is usually activated to cause a cellular response.
b. G protein-coupled receptors:
•G proteins are named for their ability to bind
GTP as a substrate.
•The receptors typically have 7 transmembrane
segments which embed them in the plasma
membrane.
•G proteins have 2 subunits, an alpha and a
beta/gamma subunit.
•When bound by a signal, the receptor’s intracellular domain contacts and
causes the G protein to release GPD and bind GTP.
•When bound to GTP, the alpha subunit dissociates from the beta/gamma
subunit.
•Alpha subunit is then activated and free to initiate a cellular response.
•When the original signal dissociates from the receptor, the process is reversed.
The alpha subunit splits GTP to GDP, which allows alpha to re-bind the
beta/gamma subunit, inactivating the G protein, and ending the cellular
response.
c. Ligand-gated ion channels:
•when the signal (ligand) binds the receptor, it changes conformation and
opens the channel for ions to flow.
d. Intracellular receptors:
•Some signals are steroids (hormones) and can
pass through the membrane. Their receptors
are intracellular and bind the signal to cause
a conformational change in the receptor →
activates it.
•The active signal/receptor complex is found in
the nucleus and binds specific genes (acting
as transcription factors) to activate them.
e. Receptor tyrosine kinases:
•Epidermal growth factor is a hormone which activates a receptor tyrosine
kinase.
•EGF is a hormone which stimulates cell divisions throughout the body.
•EGF is secreted by endocrine cells into the blood and is carried throughout the
body.
•2 EGFs each bind a receptor, which then phosphorylate each other on
tyrosines (amino acids).
•The now activated receptor activates Grb, which then binds and activates
Sos.
•Activated Sos causes Ras to release GDP and bind GTP activates Ras. →
•Ras is the first kinase in an enzyme/protein kinase cascade.
•Ras binds and phosphorylates Raf which binds and phosphorylates Mek.
•Mek binds and phosphorylates Erk.
•Erk enters the nucleus and phosphorylates transcription factors (Myc and Fos)
•Myc and Fos bind genes (approx.. 100) which then produce proteins that
stimulate cell division.
- Since most signals can’t enter the cell, they depend on second messengers to carry the signal and
produce quick and short cellular responses.
-Second messengers typically produce quick and short cellular responses.
-Hormones: chemical secreted in minute quantities into the bloodstream which have effects in distant
parts of the body.
•Can produce a diverse set of responses throughout the body.
29
•Hormones can either be steroid and enter directly through membranes, or proteins and bind
receptors to second messengers. →
•Divergent effects are produced because:
1. only cells w/ receptors for that hormone can respond to the hormone.
2. different receptors may recognize the same hormone, and different receptors different →
effects in cells.
3. different receptors have different affinities/sensitivities for a hormone, so depending on
concentration, some will respond, and others won’t.
4. different cells have different transduction pathways so they respond differently.
5. different cell types may not express certain proteins, even if stimulated.
2. Signal transduction (conversion):
•most are hydrophilic and cannot enter cells through the membrane.
•Initial signal is transduced/converted to a 2 signal inside the cell.
nd
•When G protein receptors activate G proteins, the alpha subunits are freed up activate a →
variety of other proteins.
•One common enzyme activated by alpha subunits is Adenylyl Cyclase.
•Adenylyl Cyclase is a membrane bound enzyme, attached to the interior of the plasma
membrane.
•The function of adenylyl cyclase = remove phosphate from ATP cyclic AMP ( ). →cAMP
•cAMP is a common second messenger.
•Common effect of cAMP = activate protein kinase A (PKA).
•PKA has 2 catalytic subunits which phosphorylate and activate other proteins.
•cAMP binds the regulatory subunits which frees them from the catalytic subunits.
•Once freed, the catalytic subunits are active.
•Active PKA uses PO4 groups from ATP to phosphorylate and activate other proteins, causing
the cellular responses.
•Second messengers have short durations.
•Phosphodiesterase. Hydrolyzes cAMP to AMP, removing it from the regulatory subunits of
PKA.
•The regulatory subunits then rebind the catalytic subunits of PKA, inactivating them.
•G proteins can also activate enzymes other than adenylyl cyclase.
oSignal binds G protein-coupled receptor
oActivated G protein alpha subunit activates Phospholipase C.
•Phospholipase C cleaves Phosphatidylinositol releasing Diacylglycerol ( ) and Inositol →DAG
Phosphate ( ), both of which are second messengersIP3 .
•IP3 will bind to a ligand-gated Ca 2+ channel in the ER membrane, opening the channel.
•Ca 2+ has been actively transported into the ER; when channel opens Ca 2+ flows out. →
•Ca 2+ is another second messenger.
•In conjunction w/ DAG, Ca 2+ binds and activates protein kinase C.
•PKC phosphorylates other proteins.
•Ca 2+ by itself can also bind and activate the protein Calmodulin, which in turn alters the
function of still other cellular proteins.
•Advantages of second messengers:
oAmplify the signal so that each successive step in the pathway more and more →
messengers.
oGenerally small and hydrophobic allows them to rapidly diffuse throughout the →
cell to quick response. →
3. Cellular response cells respond to signals in variety of ways. :
a. Many activate enzymes inside the cell.
b. Some alter the function of structural proteins in the cell.
c. Some affect the function of transcription factors: proteins that bind to and regulate the
activity of genes directly.
-Apoptosis: cellular death (some during development is normal and helps form the organs of the body
(chicken vs. duck feet)
•BMP4 causes cells to die via apoptosis.
•Gremlin inhibits the function of BMP4 and allows cellular survival.
•Duck limbs produce gremlin in the webbing.
•Other cells experiencing extensive damage are programmed to die rather than damage
other cells and the life of the whole organism.
30
•Intrinsic=beginning inside the cell.
•Extrinsic = beginning on outer surface of cell
•Intrinsic and extrinsic signal transduction pathways lead to apoptosis.
•Internal cell damage (like DNA damage) can internal signals leading to apoptosis. →
•Surface proteins on the mitochondria play a key role in this intrinsic pathway leading to
apoptosis.
•Extracellular signals can also apoptosis (extrinsic). Example: there are death receptors in →
the cell membranes of cells. When bound by a signal (BMP4) they initiate a cellular response
→ programmed cell death.
•Another example of extrinsic pathway: cells infected with a virus may be signaled (triggered)
to die in order to remove the virus from the organism rather than spreading it.
CHAPTER 11: Nucleic Acid Structure, DNA Replication, and Chromosome Structure:
Genetic material MUST:
1. Contain info to build and run an entire organism.
2. Be copied accurately
3. Be transmitted, or passed from parent to offspring and cell to cell.
4. Account for the known variation within and between species.
- Most scientists believed it would be proteins since they were known to be much more variable than
nucleic acids (20 amino acids and only 4 nucleotides).
- Griffith (1928) set the stage for showing what the genetic material would be.
•Worked w/ 2 strains of Streptococcus pneumoniae.
•S strain = and killed mice. virulent
•R strain = and mouse’s immune system would kill it. not virulent
1. Injected with S mice died live S in the blood. → →
2. Injected with R mice lived dead R in blood.→ →
3. Heat killed S and injected it mice lived dead SS in blood.→ →
4. Mixed live R and heat-killed S and injected it mice died live S in blood. → →
•Something in dead S was transferred to live R live S strain (this something = genetic →
material)…
- Oswald Avery (1944)
•Took live R and mixed it w/ heat killed S, but first treated it with enzymes to destroy some class
of organic molecules.
•When treated heat killed S w/ protease to destroy proteins and added live R, mice still died.
So if genes in heat-killed S were proteins, should have been destroyed and not able to
transform R S. … genes could not be proteins!!→
•When treated heat-killed S w/ nucleases to destroy nucleic acids and added live R, mice
lived. …genes must consist of nucleic acids! Since when they are destroyed, so is the ability
to transform R→S.
•This was the 1 demonstration that genes were nucleic acids. People were doubtful b/c
st
wondered if small amounts of contaminating molecules could have been altering results.
- Hershey and Chase (1952): the 2 & definitive demonstration of the nature of genes.
nd
•Used radioactive isotopes in viruses.
•Of all organic molecules, only proteins have sulfur, so if they grow viruses in radioactive 35S,
only proteins will be “labeled”.
•Only nucleic acids have phosphorus, so viruses grown in radioactive 32P will be “labeled".
•Grew viruses in these 2 separate mixtures.
•BTW… viruses (bacteriophages) inject their genes into bacteria and the genes use the
bacterial cell to produce more viruses. So whatever genes are, they should be found inside
the bacterial cells after infection.
•Bacteria did NOT contain 35S (proteins) genes must not consist of proteins. →
•The bacteria DID contain 32P (nucleic acids) → genes must consist of nucleic acids.
- Watson and Crick (1953):
•(Using info from Rosalind Franklin, Erwin Chargaff, and Maurice Wilkins) first described the
correct molecular structure of DNA.
31
•Described a double helix with a sugar-phosphate backbone and the nitrogenous basses
projecting inward in complementary pairs.
-The structure of nucleic acids (described by Watson and Crick):
•Monomeric subunits = , which are made up of: nucleotides
oPentose sugar
oNitrogenous bases
oPhosphate group
•DNA backbone composed of alternating and sugars
phosphates.
•4 nitrogenous bases:
1. In DNA: A C G and T
2. In RNA: A C G and U
oPurines: A and G
(double ring)
oPyrimidines: C, U and T
(single ring)
-Antiparallel structure: the two strands run in
opposite directions.
-Differences between DNA and RNA:
32
EXAM 4
CHAPTER 11: Nucleic Acid Structure, DNA Replication, and Chromosome Structure (continued):
- Replication of DNA: 3 possible modes suggested by Watson & Crick’s structure:
1. Conservative: 2 old strands come back together after replication. Entire old molecule is
conserved in 1 of the 2 new molecules.
2. Semiconservative: 1 new and 1 old strand from new molecule. HALF of the old molecule
is conserved in each of the new molecules.
3. Dispersive: a patchwork of new and old forms of the new molecule. Old strand is
dispersed into new strand.
- Meselson and Stahl: first to demonstrate semiconservative DNA replication using density
gradient centrifugation.
•Grew bacteria in heavy 15N, then transferred them to normal 14N.
•After one generation in 14N medium, all DNA was half 15N and half 14N (all
intermediate)→ ruling out conservative replication.
•After two generations, half the DNA was 14N/14N (light) and half was 15N/14N (intermediate) ruling →
out dispersive replication.
- DNA Replication: 2 strands open out, new nucleotides line up
opposite the old complementary bases, DNA polymerase
catalyzes their addition to the new strand.
•DNA polymerase = large molecule.
•Most cells have at least 15 polymerases.
•Only 1 or 2 replicate chromosomes, the rest are involved in DNA repairs.
- The mechanism of DNA replication:
1. Helicase: initiates replication by denaturing (unzipping) DNA using energy from ATP.
2. Topoisomerase: travels in front of helicase, relieving the supercoiling caused by
helicase.
3. Single strand binding proteins: coat single-stranded DNA to keep it from renaturing (reforming double
helix).
4. Nucleoside triphosphate precursors b/c of base-pairing relationships, nucleoside triphosphates line up :
across from complementary bases in old strand, which is the template for the new strand.
5. DNA polymerase III splits off last 2 high-energy phosphates polymerizing the nucleotide the new DNA : → →
strand. DNA polymerase III has 2 limitations:
1. Can’t start new strands.
•To overcome this, replicates the first 12-20 nucleotides with RNA (making the RNA primase
primer chain), on which DNA polymerase III can then build.
2. Can’t add new nucleotides to the 5’ end of growing (new) DNA chains (only to the 3’ end).
oSynthesis of strand: template strand runs 3’ (same as fork), so new strand is built leading →5’
continuously (5’ 3’, adding to the 3’ end) after primer strand is produced. →
6. Okazaki fragments overcomes the second limitation of DNA :
polymerase III (can only add to 3’) by building the lagging strand in a
discontinuous fashion.
oSynthesis of strandlagging : template strand runs in the 5’ 3’ →
direction (opposite the fork) so if built continuously, new strand
would be built in wrong direction (3’ 5’). DNA polymerase →BUT
can only synthesize 5’ 3’ direction.→
oSo, lagging strand built continuously in fragments (Okazaki
fragments) each built in 5’ 3’ direction, but OVERALL, in 3’ 5’ → →
direction (same as fork); “backwards leap frog”.
33
oAfter 1 Okazaki fragment is built, another primer then fragment is built.
st
oEach fragment is built in the 5’ 3’ direction, but are laid down in the overall →
3’→5’ direction (same as fork).
oEach fragment is laid down individually or discontinuously and then
connected to others.
7. DNA Polymerase I (both strands): follows replication fork, replacing the primer
strand with DNA and correcting errors when they are found.
8. DNA Ligase (only lagging strand): connects Okazaki fragments by closing last
gap between fragments.
-Telomeres: (specialized form of DNA replication) the ends of eukaryotic
chromosomes are called telomeres. They have special repeated sequences that
prevent the ends of chromosomes from attaching to one another.
•The replication of telomeres is problematic b/c replication of the lagging
strand does not start at the very end of the chromosome (b/c of DNA
polymerase III’s limitation).
•As a result, telomeres may shorten over many rounds of replication;
shortened telomeres are an implication of aging.
•Some cells, including cancer cells, have the enzyme
telomerase, which lengthens telomeres.
•Telomerase attaches to the 3’ end of a DNA strand.
•An internal RNA template is used to line up DNA
nucleotides and extend the 3’ end of the chromosome.
•After the 3’ end is lengthened, it can be long enough for DNA polymerase to attach and produce
another okazaki fragment (primase RNA primer 1→st).
•Okazaki fragment extends bottom strand in 5’ 3’ direction. Now the entire chromosome is longer. →
•RNA primer is eventually removed.
- Molecular structure of prokaryotic chromosomes:
•Are circular double strands of DNA with both ends connected.
•Proteins do not regularly and permanently attach to them.
•Typically 1 main chromosome in a cell, sometimes with extra small circular chromosomes called
plasmids.
- Molecular structure of eukaryotic chromosomes:
•In contrast, these consist of both DNA and proteins.
•Many of these proteins are histones which form nucleosomes, around which DNA is
wrapped around.
•2 copies of each of the 4 histones compose nucleosomes.
•They contain many + charged peptides to attract and bind DNA.
•A 5 histone H1 binds linker DNA which occurs between the DNA segments
th
wrapped around nucleosomes.
•DNA wrapped around nucleosomes resembles “beads on a string”.
•Adjacent nucleosomes are organized into thicker fiber, 30 nm in diameter.
•The 30 nm fiber of each chromosome is attached to a filamentous network of
proteins termed the nuclear matrix.
•The matrix consists of protein fibers which line the inner nuclear membrane (nuclear
lamina) and other fibers stretching throughout the nucleus.
•Other proteins connect regions of DNA to the nuclear matrix, and bend the DNA into
radial loop domains containing 25,000-200,000 nbp (nucleotide base pairs).
•DNA and the chromosomes that they make up are anchored to specific regions in
the nucleus.
•Chromosomes are not free to move within the nucleus, but are restricted to specific
regions by binding to the nuclear matrix.
•During cell division, chromosomes condense into thicker, shorter structures by a series
of loops and bends, so they can be moved without tangling and breaking the long
DNA fibers.
CHAPTER 12: Gene Expression at the Molecular Level
34
- Inborn errors of metabolism:
•Early 1900s—Gregor Mendel’s work on genetics was rediscovered and finally understood.
•In 1908—Archibald Garrod (British physician studying the inheritance of disease Alkaptonuria)
proposed a link between genes and the production of enzymes.
•Biochemists understood at this time that metabolic pathways consisted of a series of enzymes, each
one converting one chemical into another.
•Garrod applied Mendel’s theory on genes to the pathway for the breakdown of Phenylalanine and
the disease Alkaptonuria.
•Garrod knew Alkaptonuria was inherited and proposed that it was caused when one inherited
recessive, defective genes from both parents.
•Garrod = first to link genes with enzyme production.
•Garrod termed the defective genes “inborn errors of metabolism” and began the field of genetics.
•Beadle and Tatum saw Garrod’s work
while working on the nutritional needs of
a mold called Neurospora.
•They exposed the mold spores to X-rays
→ mutations, and isolated mutant strains that couldn’t produce certain nutrients (working on the
inheritance/genetics of these mutant strains).
•The metabolic pathway of Arginine production was known to be controlled by 3 enzymes.
•Had several strains of which could not produce Arginine. Neurospora
•Found that different strains had different mutations (in genes) which all prevented Arginine synthesis,
but at different steps in the pathway.
•They first proposed that each gene controlled a separate enzyme: the “one gene, one enzyme”
theory.
- The one gene, one enzyme theory has been modified over time:
1. Genes control the production of enzymes, but not all genes do
code for enzymes.
2. Not all enzymes consist of a single polypeptide. Some multimeric
enzymes are formed by the product of multiple genes, each
producing a separate polypeptide which combine to form the
mature/complete enzyme one gene, one polypeptide→.
3. Some genes are alternatively spliced to produce multiple proteins,
or versions of a protein. So some genes produce multiple proteins.
oe.g. 20,000 human genes → ~500,000 proteins.
- The central dogma of biology: traces the path of information flow
within cells (created by Crick).
•DNA transcribed mPRA translated polypeptide
→
→
→
→→ →
→
→
→→
- Transcription: DNA-directed RNA synthesis
•RNA polymerase: the one molecule/enzyme concerned with transcription.
•Promoter: region of gene where RNA polymerase attaches to transcribe the gene.
•Occurs on template strand only.
•Occurs on one gene at a time only.
•RNA polymerase attaches to DNA at promoter and denatures (unwinds) DNA.
•In eukaryotes, a variety of proteins are involved in this ^ attachment.
•They are called initiation and transcription factors
•Ribonucleoside triphosphates line up opposite to the
DNA template strand and RNA polymerase connects
them together in the 5’ 3’ direction. Adds nucleotides →
to the 3’ end of the growing strand (like DNA poly 3).
oPrecursors for transcription.
oMechanism: removal of pyrophosphate and
polymerization of nucleotide to 3’ end of growing
RNA chain.
•Termination occurs in a variety of ways in different RNAs.
•The final product (primary transcript or pre-RNA),
however, is not the finished product.
- 3 types of RNA:
35
1. mRNA: carries the info from DNA to the ribosome.
2. rRNA: a component of ribosomes.
3. tRNA: escorts amino acids to the ribosome.
•ALL 3 ARE TRANSCRIBED IN THE SAME WAY!
- Within a single chromosome, different strands of the double stranded DNA form the template strand.
Post-transcriptional modification of RNA:
- RNAs are all post-transcriptionally modified in a variety of ways (8):
1. Addition of a 5’ 7-mathyl guanosine “cap” occurs in mRNA only (attached to 5’ end).
•Allows mRNA to exit nucleus & bind to ribosome.
2. Addition of a poly-A “tail” also occurs in mRNA only.
•Allows mRNA to be exported from nucleus & to persist in
cytosol.
3. Splicing:
a. the removal of (intervening regions) can occur introns
to any type of RNA, from the action of spliceosomes: a
complex of RNA and proteins.
oThe removal of introns → RNA transcript much
shorter than the corresponding gene (DNA).
b. (Alternative splicing): not all exons are always included in
the final mRNA either.
oIf different combos of exons are used to
produce different mRNAs, different proteins may
be produced in different cells or tissues from the
same gene.
oREMEMBER: ~20,000 human genes ~500,000 →
proteins.
4. Primary/pre transcript may be cut into more than one RNA (all
RNAs exhibit this modification, but it always occurs in rRNA.)
5. The removal of nucleotides form the 5’ and/or 3’ end (occurs
in all RNAs).
6. The addition of CCA to 3’ end (if it doesn’t already end with CCA); occurs in tRNA only.
7. The chemical modification of bases occurs in tRNA only.
8. RNA editing: a process by which 1 or more nucleotides in an RNA can be changed, added, or removed.
•In substitution editing, 1 nucleotide is substituted for another.
oEnzymes modify or change one base into another.
oCytidine deaminase converts a C in the RNA to uracil (U).
oAdenosine deaminase converts an A to inosine (I), which the ribosome translates as a G
(similar to modification #7).
•In insertion/deletion editing, nucleotides are added or removed.
oUses guide RANs produced by separate genes, to bind and identify the RNA molecules
where a nucleotide will be added or removed.
oRNA editing has been found in all 3 major types of RNA.
oErrors in RNA editing can cause mental disorders such as schizophrenia.
36
- Translation:
1. All 3 RNAs are used for translation:
•mRNA carries the info
•tRNA brings the amino acids
•rRNA is a component of ribosomes
2. aminoacyl-tRNA synthetase enzymes are also used to “load”
amino acids onto corresponding tRNA molecules.
- mRNA—the genetic code:
•triplet code: 3 bases make up a codon.
•Codon: a sequence of 3 bases in mRNA which code for an
amino acid.
•The codon AUG is the initiation/start codon; marks the point
where translation begins.
•There are 3 codons (terminators) which stop translation rather
than insert an amino acid UAG, and UGA: UAA, .
•Genetic code is degenerate (redundant) since most amino
acids are represented by more than one codon.
- Transfer RNA:
•2D shape: 3-leaf clover
•Acceptor stem: amino acid is attached to the 3’ end of tRNA.
•3D shape of tRNA is L-shaped.
•The anticodon loop is across from the acceptor stem, it pairs
with the codon on mRNA.
- Aminoacyl-tRNA Synthetase:
•“load” proper amino acid onto tRNA using energy from ATP.
•First, it binds ATP and the specific amino acid recognized by the activating enzyme. The energy from
ATP is transferred to the amino acid as AMP.
37
•Then, the specific tRNA
recognized by the
synthetase is bound and the
amino acid transferred from
the AMP to the tRNA.
•Finally, the tRNA, charged
with the appropriate amino
acid is release, as is the
enzyme (in an unaltered
state) and the AMP.
- Ribosomes:
•Structure: large and small subunits
each constructed of one or more
rRNA and -50 proteins20 .
•S = Svedberg units: sedimentation
rates based on mass, density &
shape; can’t be added simply (50 +
30 = 70 here).
•Self-assembly: the parts
automatically come together to
form ribosomes.
•Ribosome has 3 positions to hold tRNAs:
1. A site: holds new tRNA (except for the very 1
st
tRNA).
2. P site: holds tRNA with polypeptide chain.
3. E site: holds empty tRNA to exit the ribosome.
- Function of translation:
•RNA-directed polypeptide synthesis
1. Small ribosomal subunit attaches to 5’ end of
mRNA.
2. First tRNA attaches to small subunit P site and binds with AUG.
3. Large ribosomal subunit attaches to form the complete ribosome.
4. Once 1 aminoacyl-tRNA has attached to the P-site, the 2 aminoacyl-tRNA attaches at the A-
st nd
site of the ribosome, matching the 2 codon of the mRNA.
nd
▪mRNA-ribosome-tRNA complex positions the amino acids so they are
adjacent to one another.
5. Peptidyl transferase catalyzes a peptide bond between the first 2 amino acids by transferring
(backwards) the 1 amino acid from the 1 tRNA to the 2 amino acid on the 2 tRNA.
st st nd nd
6. Translocation moves the ribosome (3’ direction) to the next codon, with release of the 1 tRNA
st
from the exit (E site).
▪The 1 amino acid is already attached to the 2 and both are attached
st nd
to the second tRNA (in the P site).
7. The 3 aminoacyl-tRNA anticodon attaches to the A site of the ribosome according to the 3
rd rd
mRNA codon.
38
8. Peptidyl transferase catalyzes the next peptide bond. The ribosome translocates in the 3’
direction once more.
9. Repeat of steps 6-8.
10. Upon reaching a termination (stop) codon, a releasing protein attaches to the A site instead of
an aminoacyl tRNA.
▪The releasing factor binds to the A site and causes the release of the last
tRNA and the polypeptide.
▪The 2 ribosomal subunits are released from the mRNA and are recycled to
find the same or another mRNA to translate.
- Each mRNA is translated by numerous ribosomes at the same time. Once the 1st ribosome clears the 5’ end,
the next attaches.
- A polysome is one mRNA and all the multiple ribosomes translating it at the same time.
- Once synthesized (or during synthesis), proteins with transit sequences may be exported to various organelles.
Post-translational modifications (of proteins):
- Once synthesized, proteins may be modified in a variety of ways:
1. Proteolysis: cleaving polypeptide fragments fold into different shapes. →
2. Glycosylation: adding sugars important for targeting and recognition.
3. Phosphorylation: added phosphate groups alter shape of protein.
Role of endoplasmic reticulum in glycoprotein synthesis:
-Signal sequence: causes ribosome to be transported to the ER (co-translational sorting).
- When completed, eventual glycoprotein is release in the lumen of the ER and ribosomal subunits are released
to the cytoplasm.
CHAPTER 13/15: Mutation, DNA Repair, and Cancer:
DNA molecule chromosome—found in the nucleus of the cell (in order of biggest smallest) ; gene; →
Mutations are permanent, heritable changes to the DNA (nucleotide sequence).
- Point mutations: changes to nucleotide sequence of individual genes. 3 MAJOR TYPES:
1. Substitution: Replace one nucleotide with another.
•When one DNA nucleotide is substituted for another, one codon in the resulting
RNA will be altered always.
•Typically, this will alter one amino acid in the resulting protein → missense. This
change of one amino acid could -0-> little/no effect, or a lethal one.
oSickle cell anemia: GAG→ →glu in the DNA, becomes GUG val in the
RNA. This causes sickle shape of the red blood cells.
•Also possible the codon be changed to a stop codon and end the protein
prematurely. Will most likely destroy protein’s function → nonsense.
•Also possible b/c of redundancy of genetic code that the new codon would
code for the same amino acid. Protein would not be changed and function
normally. → silent.
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2. Addition: add one or more nucleotides to a gene.
3. Deletion: delete one or more nucleotides from a gene.
^^ both (addition & deletion) result in : shifts the triplet reading frameshift mutations
frame of the codons.
- Chromosomal mutations: changes to the entire gene order on
chromosomes. (to be covered in a later chapter, don’t worry ab this rn).
Mutations outside coding regions for the nucleotides of the RNA can also have :
effects.
Somatic vs. germ cell mutations:
- Only mutation in the germ line cells will be passed on to individuals of the next generation.
- Mutations in somatic (or body) cells are NOT.
- Somatic mutations, like cancers, can have serious health effects for the individual but one the individual, not
their children.
- Mutations may be result of natural causes (spontaneous) or outside factors (induced).
Causes of mutations:
-Mutagens are chemical/physical factors that alter the structure of the DNA.
- Nucleic acids are chemicals and can enter into reactions which convert them to something other than the four
normal bases of DNA.
-Nitrous oxide (found in smoked meats) can remove the amino group from cytosine or adenine, replacing it with
carbonyl group to produce uracil and hypoxanthine→.
•Cytosine normally pairs w/ guanine, but when converted to uracil, pairs w/ adenine.
•So a C-G pair is converted to a U-A (T-A) pair, a substitution mutation.
•Adenine normally pairs with thymine, but when converted to hypoxanthine, pairs with cytosine.
•So an A-T pair is converted to a H-C (G-C) pair, another substitution mutation.
- Base analogues are similar enough to the “real” DNA bases to be incorporated into DNA, but they don’t have
the same faithfulness in pairing. substitution mutations. →
- X-rays: ionizing radiation; physically cut DNA which may not be repaired correctly. Bases could be removed,
strands could be cut.
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- UV light: high enough energy to promote covalent linkages between adjacent
pyrimidine bases of backbone (T-T dimers).
•DNA polymerase does not recognize the dimer as a normal base and will
randomly insert a difference one on new strand.
•Substitution mutations are, therefore, promoted during replication.
DNA repair—solution to mutations:
- Nucleotide excision repair is one of the more widespread and better understood
mechanisms.
- UvrABA (ultra violet repair) complex scans DNA looking for errors, such as thymine dimers.
- When found, UvrABA releases the UvrA’s and recruits UvrC.
- UvrC cuts the sugar-phosphate backbone on both sides of the mutation.
- Then, UvrD (a helicase) is recruited to remove the damaged section from one cut to the
other.
CHAPTER 16 the eukaryotic cell cycle, mitosis and meiosis: :
Eukaryotic chromosomes:
-Chromatin: consists of DNA and proteins.
-DNA: one complete, double stranded DNA molecule (in an unduplicated chromosome).
-Proteins: there are both histones and nonhistone proteins.
•Nucleosome cores: consist of 2 copies each of 4 difference histone proteins.
•Histone H1: connects DNA to the nucleosome core and connects adjacent cores together.
•Nonhistone proteins: more varied but less numerous; control individual genes by binding or
dissociating from the DNA.
-Chromatids: duplicated vs. unduplicated:
•Chromosomes consist of 1 (unduplicated) or 2 (duplicated)
chromatids.
•Sister chromatids: genetically identical, one is used as template
to make the other.
•Centromere: visible as a constricted region, it represents the
area to which microtubules attach during cell divisions.
Chromosomes: homologous pairs:
- In diploid organisms, chromosomes are inherited in sets, one set from
each parent.
- There are 2 copies of each chromosome, one inherited from each
parent.
- The 2 copies of each chromosome are termed homologues, or
homologous chromosomes.
- Haploid organisms or cells, contain a single copy of each chromosome. (fungi)
- In diploid organisms, the only cells which are haploid (1 member of each pair)
would be the gametes, or sex cells.
The cell cycle:
- Cells go through regular cycle of growth then division.
- Cells to ~2x the size, replicate their DNA to 2 copies (interphase).grow →
- Then they divide:
•Splitting the cytoplasm (cytokinesis)
•And DNA (mitosis) equally between the 2 daughter cells.
-Interphase consist of 3 separate phases:
1. G1: protein synthesis and growth predominate, organelles replicate, and cell size doubles.
2. S: DNA replicates to build second (sister) chromatid using the original as a copy. (DNA replication).
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3. G2: protein synthesis again predominates, producing materials needed for division (e.g. Tubulin
for Microtubules, etc.)
Mitosis: distributes exact copies of genetic info to the daughter cells. This is the division of the nucleus (not
including cytokinesis). Consists of 4 phases:
1. Prophase:
a. Condensation of each individual chromosome (duplicated).
b. Disappearance of the nucleolus.
c. Centrosomes (pr. of centrioles) separate and move to opposite nuclear poles.
oReplicated during G1.
oEstablishes polarity of cell.
d. Disintegration of the nuclear membrane into vesicles.
e. Spindle fibers attach to chromosomes.
•Microtubule organizing regions (centrosome) controls growth of microtubules:
oPolar microtubules run from pole to pole.
oKinetochore microtubules run form centrosome to centromere.
2. Metaphase:
a. Spindle fibers moving chromosomes to metaphase plate (equator of cell).
3. Anaphase:
a. Separation of chromatids and movement to opposite poles.
b. Separase degrades proteins holding sister chromatids together.
c. Cytoplasmic dynein walks chromosomes along microtubules to the poles.
4. Telophase:
a. Cytokinesis (occurring simultaneously).
b. Reversal of prophase with decondensation of chromosomes reforming of nuclear membrane ,
and nucleolus breakdown of mitotic spindle, .
Cytokinesis: the division of the cytoplasm; accomplished using the
combined action of at least 20 different proteins. Mitosis + cytokinesis
divides entire cell into 2 daughter cells.
- in animal cells, accomplished by constriction of band of
microfilaments of actin and myosin ( ). cleavage
- In plant cells, vesicles are pulled down microtubule highways by
kinesin motors and they fuse to form the new plasma
membrane/cell wall ( ). cell plate formation
-The result of mitosis:
•Ploidy of cells formed: same as “mother cell”.
•Number of cells formed: 2.
•Genetic makeup of cells formed: genetic clones.
-Control of the mitotic cycle: 2 groups of proteins that do this:
•Cyclin-dependent kinases ( ) are proteins which are activated by binding to Cdk Cyclin.
oCdks are present throughout the cycle.
oCyclins are produced (as needed) then destroyed during particular stages in the
cycle.
oSo, the cell cycle is regulated by a cascade of protein kinase activities.
oSignal is amplified in strength by this cascade activity in cell signaling.
•Initially, only CDK is present in . No G1 Cyclins have been produced. G1
•Passage through G1 (general): if growth conditions are favorable, G1 cyclins are produced
that bind to and activated Cdks.
•General: active CDK phosphorylates the protein , thereby inactivating it. RB
oInitially, active RB blocks entry through the restriction point.
•During G1 (specific): Cdk4 activated by cyclin D. Cdk2 activated by Cyclin E (D & E = G1 cyclins).
oAnd, once again, active Cdks phosphorylate and inactivate RB which allows cell to pass
restriction point and enter S phase.
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•Specific: active/”blocking” RB normally binds E2F, a regulatory transcription factor.
oWhen RB is phosphorylated. It releases E2F, which then binds genes, promoting the transcription of
proteins that promote cell division (and passage through RP).
•Finally, once RB (the inhibitor) is inhibited, the cell can pass through G1 and proceed into S.
oG1 cyclins are then degraded.
•G1 cyclins not active from the phase of the remaining cycle onward. S
oDo not become active until G1 phase of next cycle.
•During the S phase, cyclin A is produced. It activated CDK2 which stimulates DNA replication.
•Passage through : after DNA is fully replicated, cyclin B is produced to activate Cdk1 for entry into G2
mitosis.
•So, different cyclins are produced at different stages of the cell cycle.
oThey activate different CDDKs which begin an enzyme cascade to activate passage through
different portions of interphase.
oCDKs, therefore, control the passage of cells through the cell cycle.
•Cells don’t want to prematurely advance through the cell cycle.
oRadiation damage stimulates production of p21.
oP21 binds G1-CDKs, preventing cyclin from binding and activating them before the DNA damage
can be repaired and the cell progresses to S phase.
Meiosis: a pair of nuclear divisions:
- The is a pictorial representation of all the chromosomes of an organism or a cell. karyotype
-Diploid cells have 2 copies of each chromosome; one inherited from each parent (duplicated).
-Homologous chromosomes are the 2 copies of each chromosome.
-Haploid cells have 1 copy of each chromosome, resulting from meiosis.
- The 1st meiotic division reduces the chromosome number from the diploid to the haploid number:
-Prophase I:
•Nuclear membrane disappears into vesicles.
•Nucleolus disappears.
•Centrosomes move to opposite nuclear poles.
•Spindle fibers form.
•As chromosomes begin to condense, synapsis
occurs.
oSynapsis: homologous chromosomes
pair and form bivalents.
oChiasmata form: exchange between nonsister chromatids. (arms are crossing)
•Genetic recombination occurs:
oSynaptonemal complex includes enzymes which cut non-sister chromatids and connect the
“wrong” ends to recombine the homologous chromosomes.
oThe added genetic variation produced by “shuffling” the genes (allows microevolution).
oIndependent assortment of chromosomes also increases genetic recombination.
-Metaphase I: Bivalents are moved to metaphase plate.
-Anaphase I: Homologous chromosomes are separated.
-Telophase I (concurrent with cytokinesis):
•Cytokinesis: forms 2 haploid cells.
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- The 2nd meiotic division is similar to mitosis, yet different. “sister” chromatids are separated.
-Interkinesis (between M1 and M2): DNA replication does NOT occur.
-Prophase II: mitotic spindle forms, connecting to “sister” chromatids.
-Metaphase II: individual duplicated chromosomes are lined up at the metaphase plate.
-Anaphase II: “sister” chromatids are separated to opposite poles.
-Telophase II: cytokinesis occurs concurrent with telophase, forming 4 haploid cells (w/
unduplicated chromosomes).
-Result of meiosis:
•Ploidy of cells formed: haploid
•Number of cells formed: 4
•Genetic makeup of cells formed: all different from each other and the original
“mother” cell.
Mitosis vs. meiosis:
Life cycles:
1. Kingdom animalia: multicellular, adult diploids (2n).
•Sexual reproduction: gametes (n) formed by meiosis.
2. Kingdom fungi: multicellular, adult haploids (n). already haploid so no need for meiosis.
•Sexual reproduction: gametes
formed by mitosis.
3. Kingdom planate: alternation of
generations.
•Sexual reproduction: gametes
(haploid spores; n) formed by
mitosis.
Meiotic errors during synapses or DNA replication :
(interphase), errors can occur.
•Duplications occur when a
portion of a chromosome is
duplicated and inserted into a
chromosome with the normal
copies. Usually fatal.
•Deletions: loss of a portion of a chromosome. Like duplications, this is usually fatal.
•Inversions: invert a chromosomal section 180 degrees. While not fatal, can reduce fertility.
•Translocations: move a section to another (non-homologous) chromosome. While not fatal, reduces
fertility.
•Errors in meiosis can also result in several other types of chromosomal mutations.
•Nondisjunction occurs when chromosomes do not separate during meiosis I or II.
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oA cell that receives both copies has 2 copies of that chromosome instead of 1.
oThe cell that receives no copy is lacking that particular chromosome altogether.
•Aneuploidy occurs when there is something greater or less than 2
copies in a diploid cell for one (or a few) chromosomes.
oCan be cause by nondisjunction during mitosis or meiosis.
oSo, 1 chromosomes is present only once or more than twice.
oAlmost always fatal.
oAn exception is for sex chromosomes and trisomy 21 (down
syndrome).
•Polyploidy occurs when all the chromosomes are present more than
twice.
oWhile fatal in humans, numerous examples are available for plants and animals (>2n).
oMakes new species.
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EXAM 5
CHAPTER 17/15 Simple Patterns of Inheritance: :
Laws of inheritance first described by Gregor Mendel, a monk.
Mendel’s experiments:
- Learned a quantitative approach; used the ratio of the different types of offspring to predict how genes were
inherited (before good understanding of mitosis/meiosis was achieved).
Modern definitions:
-Gene: section of DNA that codes for a particular trait.
-Allele: a variable of a gene.
-Homozygous: 2 copies of a gene (alleles) in a diploid
organism are the same.
-Heterozygous: 2 copies of a gene (alleles) in a diploid
organism are different.
-Genotype: genetic makeup of an individual.
-Phenotype: the physical expression of that genotype.
-Dominant: the one allele expressed in a heterozygote.
-Recessive: the allele not expressed in a heterozygous.
Mendel’s monohybrid cross:
- Tall plants (TT) x dwarf plants (tt):
•Parental genotypes: TT x tt
•Gamete types for each parent: T t
•Punnett square: →
•Genotypic ratio: all heterozygous (Tt)
•Phenotypic ratio: all tall plants.
- Cross of the 2 heterozygotes (still monohybrid cross):
•Parental genotypes: Tt x Tt
•Gamete types: T,t T,t
- Punnett square first put down gamete types, then fill in Punnett :
square.
•Genotypic ratio: 1:2:1 (1TT, 2Tt, 1tt)
•Phenotypic ratio: 3:1 (3 would be tall, 1 would
be short).
Mendel’s first Law (of segregation):
1. Adults are diploid (2 copies of each gene)
2. The 2 copies of each gene segregate one to each
gamete.
3. Fertilization restores the diploid number.
The test cross: individuals with the dominant phenotype can have
either 2 genotypes:
1. TT (homozygous dominant) or Tt (heterozygous).
2. To determine the genotype of an individual with the
dominant phenotype, cross them with a homozygous
recessive.
•If the test individual is homozygous dominant (TT)→ phenotypic ratio: all offspring are dominant
(Tt 4x).
•If the test individual is phenotypic ratio: 1 dominant : 1 recessive ( 2x, 2x). heterozygous (Tt)→Tt tt
Mendel’s Dihybrid cross: inheritance of 2 genes can be tracked.
-Parental genotypes: YYRR x yyrr
-Gamete types: YR, yr
•All offspring are heterozygous yellow and heterozygous round seed.
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•If 2 of these double heterozygotes are crossed (dihybrid cross):
oParental genotypes (F1): YyRr x YyRr
oGamete types: YR, Yr, yR, yr
oPunnett square: →
oPhenotypic ratio:
▪9 Yellow,Round
▪3 Yellow,wrinkled
▪3 green,Round
▪1 green,wrinkled
Mendel’s second Law (independent assortment: alleles of different genes will assort into gametes
independently of one another.
Complete/simple dominance: why do homozygous dominant and heterozygous individuals have identical
phenotypes? What is the link between genes and phenotype?:
- Enzymes are involved in biochemical pathways phenotypes. (purple flower example). →
- A gene codes for an enzyme which will convert a chemical precursor into a purple pigment.
- Homozygous dominant has 2 alleles, both produce functional enzyme and pigment.
•Colorless precursor molecule PP (protein P) purple pigment
→
→
→
→→ →
→
→
→→
- Heterozygote has one copy of the gene producing functional enzyme, but that functional one is
enough to convert all of the precursor to purple pigment.
•Colorless precursor molecule Pp (protein P) purple pigment
→
→
→
→→ →
→
→
→→
- Homozygous recessive has both copies of the gene producing defective enzyme. Without
functional enzyme, precursor not converted to enzyme. Flower remains colorless.
•Colorless precursor molecule pp (protein P) white.
→
→
→
→→ →
→
→
→→
-Rr x rr?:
1. All round
2. All wrinkled
3. 1:1
4. 3:1
5. 1:2:1
-Ssyy x ssYy?:
1. 9:3:3:1
2. 1:1:1:1
3. 3:1
4. 1:1
5. 1:2:1
Incomplete dominance:
- Complete/simple dominance is only one allele is expressed in a
heterozygote.
-INCOMPELTE dominance: both alleles are expressed in a
heterozygote (b/c dominant allele does not completely mask
recessive), so an intermediate phenotype is produced.
- Four o’clock example:
•Parental genotypes: RR homozygous red x WW
homozygous white
•Gamete types: →
•Combine gametes→all offspring are heterozygous.
•Phenotypic ratio: all pink
•Monohybrid cross:
•Parental genotypes: RW x RW
•Gamete types: R,W x R,W
•Combine gametes: →
•Genotypic and phenotypic ratio: 1:2:1
oRatios are same because each genotype has its own phenotype.
-Pink flower crossed to a white one, what is phenotypic ratio?:
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1. 9:3:3:1
2. 1:1:1:1
3. 3:1
4. 1:2:1
5. 1:1
•Parental genotypes: RW x WW
•Gamete types: R,W x W
•Phenotypic ratio: half pink, half white (1:1 phenotypic ratio).
Sex determination:
-Human males: XY, XXY, XYY, XXYY
-Human females: XX, X, XXX, XXXX
-Human sex determination:
•presence of a Y-chromosome (function SRY gene: sex-determining region) determines maleness.
•DAX1 gene activation on x chromosome determines femaleness.
Sex linkage:
-Sex chromosomes: those that contain the gene(s) which determine the sex of an individual.
-Autosomes: non-sex chromosomes.
Eye-color in Drosophila:
- Morgan’s observations: found white-eyed male fly, crossed to red eyed female all offspring were red eyed →
(cross #1).
- Brother x sister cross (cross #2) of red-eyed flies and got 3 red:1 white, but all white eyed were males. →
- Morgan’s hypothesis: eye color is sex-linked (in fruit flies).
-Fly cross #1
•Parental genotypes: XrXr x XwY
•Gamete types: XR Xw,Y
•Punnett square:
•Hemizygous: (not hetero or homo); genotype of individual with only one copy of a
sex-linked gene. Can be either hemizygous dominant or hemizygous recessive.
•Phenotypic ratio: , all red-eyed females all red-eyed males
-When brother x sister cross #2 made:
•Parental genotypes: XrXw x XrY
•Gamete types: Xr,Xw Xr,Y
•Punnett square:
•Phenotypic ratio: 3 red:1 white, but all white-eyed flies were male.
- If a white eyed female is crossed to a red eyed male
(cross #3), what is the expected phenotypic ratio? → all
white male and all red female.
•Whatever is on the X chromosome is what will show up
in males because they do not have another X
chromosome to counteract the allele they receive. There is
no eye color gene on the Y chromosome.
Gene dosage compensation: a process that equalizes expression of X-linked genes in male and female mammals
(anything evening the playing field, multiple examples):
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-X-inactivation is 1 proposed mechanism
•1 X chromosome inactivated in each female cell
•Reduces # of expressed copies of X-linked genes from 2 1 in females. →
•So expression roughly = in male and female.
- Barr bodies: small dark-staining bodies in the interphase nuclei of female but not
male (inactivated X-chromosomes; heterochromatic and highly condensed).
- Lyon hypothesis Barr bodies are heterochromatic (highly condensed and :
inactivated)
•Must have 1 activated X per cell (and usually only one).
•Evidence supporting Lyon hypothesis: one X is always active, rest are inactive Barr bodies. →
oTypical females (XX): 1 Barr body
oTypical males (XY): 0 Barr bodies
oKlinefelter males (XXY): 1 Barr body
oTurner females (X0): 0 Barr bodies
oTriple X females: (XXX): 2 Barr bodies
oCalico cats are always females.
oThey are heterozygous for color (the orange and black parts).
•Heterozygous females still show dominant trait.
oBut for many X-linked traits in humans, heterozygous females
usually show dominant trait.
oExpression of dominant allele in 50% of cells sufficient to
produce dominant phenotype.
oRecessive X-linked form of hemophilia
▪Heterozygous females usually have healthy
phenotype.
▪Normal blood clotting protein produced in
approximately 50% of liver cells enough to prevent
hemophilia.
Pedigree analysis: symbols used:
-Generations: with Roman numerals
-Individuals: with Arabic numbers
Example #1: for an autosomal gene.
- Is the trait dominant or recessive?
- What is the genotype of each individual/shape? →
- Tell ale sign of recessively inherited trait?
- Affected child that has 2 unaffected parents.
- If the trait in question was dominant, the child would
have inherited one dominant allele from at least one of
his/her parents means that at least one of the parents would also show →
the dominant trait.
