Advanced Biochemistry - Metabolism 45 questions assignment

The Amazing Plas/d!

(all plant cells have Plas/ds and the plas/ds are always metabolically ac/ve) {except “dead cells” such as xylem sieve

tube cells}

The Chloroplast/Plas/d

•  The Chloroplast/Plas/d is a unique organelle •  It is the Organelle of Assimila/on •  It contains a genome and protein synthesizing apparatus (ribosomes), a complete set of tRNAs

•  Plants Start with : CO2, SO4, NO3, H20 + metal ions (Mg, Mn, Ni, Fe, Mo, Na, Ca, K, Zn, Cu, Co)

•  And produce a mul/cellular organism consis/ng of CHO, R-NH2, R-SH.

•  Plants Assimilate H atoms (from water)

Chloroplast Corn (Zea Mays)

Plas/d (root /p)

E/oplast (plas/d before greening)

Chromoplast

Peroxisome, Glyoxysome

The Plant Cell – Diagram (Heldt)

All living plant cells have mitochondria too!

The Chloroplast Genome

•  About 155,000 base pairs (bp) {virus, 170K bp, E. coli 4600K bp, human 320,000K bp, plant up to 1,500,000K bp, human mito 16K bp, plant mito 200K bp} in circular (?) chromosome. Mul/ple copies per plas/d.

•  Chloroplast genome encodes about 100 genes rRNA, tRNA, 21 ribosome proteins, RNA polymerase subunits, 28 thylakoid proteins, Rubisco large subunit (but not the small subunit), AcCoA Carboxylase, NADH dehydrogenase subunits

•  Genes arranged in operons; introns are found

Chloroplast Proteome

•  Chloroplast contains approximately 3000 proteins (E. coli 4200; minimal organism 473).

•  > 90% are nuclear encoded •  5 compartments •  In leaf /ssue, 50% of chloroplast soluble protein is Rubisco! (slow enzyme)

Roles of Ferredoxin in Chloroplast

•  Reduc/on of NADP to NADPH •  Electron donor for nitrite reductase •  Electron donor for glutamate synthase •  Electron donor for sulfate reductase •  Electron donor for faiy acid synthase •  Electron donor for thioredoxin

Roles of the Plas/d Compartments •  Plastocyanin is a nuclear-encoded protein that is func/onal in the thylakoid lumenof the chloroplast. ... Its

transport route involves two steps, import into the chloroplasts and subsequent rou/ng over the thylakoid membrane into the lumen.

•  Thylakoid membranes contain integral membrane proteins which play an important role in light harves/ng and the light-dependent reac/ons of photosynthesis. There are four major protein complexes in the thylakoid membrane: Photosystems I and II. Cytochrome b6f complex.

•  The Stroma contains many enzymes of metabolism including the Calvin Cycle, N assimila/on, S assimila/on, faiy acid biosynthesis, starch metabolism, protein synthesis, DNA replica/on, RNA synthesis, amino acid synthesis, tetrapyrole synthesis and more.

•  The outer membrane of the chloroplast envelope, like that of mitochondria, contains porins and is therefore freely permeable to small molecules. In contrast, the inner membrane is impermeable to ions and metabolites, which are therefore able to enter chloroplasts only via specific membranetransporters.

•  The triose phosphate translocator is an integral membrane protein found in the inner membrane of chloroplasts. It exports triose phosphate (Dihydroxyacetone phosphate) in exchange for inorganic phosphate and is therefore classified as an an/porter. The imported phosphate is then used for ATP regenera/on via the light- dependent-reac/on; the ATP may then for example be used for further reac/ons in the Calvin-cycle.The Translocator protein is responsible for expor/ng all the carbohydrate produced in photosynthesis by plants and therefore most of the carbon in food that one eats has been transported by the triose phosphate translocator.. Many transporters, including protein transport are found in the inner membrane

•  Source: Heldt, Wikipedia

•  Cytoplasmic transla6on and N-terminal transit sequences •  For many (but not all) chloroplast proteins encoded by nuclear genes,

cleavable transit pep.des are added to the N-termini of the polypep/des, which are used to help direct the polypep/de to the chloroplast for import (N-terminal transit pep/des are also used to direct polypep/des to plant mitochondria).] N-terminal transit sequences are also called presequences[36]because they are located at the "front" end of a polypep/de— ribosomes synthesize polypep/des from the N-terminus to the C-terminus.

•  Chloroplast transit pep/des exhibit huge varia/on in length and amino acid sequence. They can be from 20–150 amino acids long—an unusually long length, sugges/ng that transit pep/des are actually collec/ons of domains with different func/ons. Transit pep/des tend to be posi/vely charged, rich in hydroxylated amino acids such as serine, threonine, and proline, and poor in acidic amino acids like aspar/c acid and glutamic acid. In an aqueous solu/on, the transit sequence forms a random coil.

•  Not all chloroplast proteins include a N-terminal cleavable transit pep/de though. Some include the transit sequence within the func/onal part of the protein itself. A few have their transit sequence appended to their C-terminus instead. Most of the polypep/des that lack N-terminal targe/ng sequences are the ones that are sent to the outer chloroplast membrane, plus at least one sent to the inner chloroplast membrane.

•  hips://en.wikipedia.org/wiki/Chloroplast_DNA#Proteins_encoded_by_the_chloroplast

Nitrogen Assimila/on In Bacteria

NH4+ à Glutamate (Glutamate Dehydrogenase) only under High Ammonium condi/ons NH4+ + Glutamate + ATP à Glutamine + ADP + Pi (GS) Gln + aKG à 2 Glu (Glutamate Synthase) most condi/ons NO3- à NO2- à NH4+ à Glutamine When Nitrate is N source N2 à NH4+ (only some bacteria when no other N source available

In Plants GS + Glutamate Synthase NO3- à NO2- à NH4+ (Nitrate Reductase, Nitrite Reductase) Urea à NH4+ à GS, Glutamate Synthase

GS, Glutamate Synthase in Plas/d Nitrate Reductase in cytoplasm; Nitrite Reductase in Plas/d Urease in Cytoplasm

Chromoplast