Module 11 - Biosynthesis of Cell Components

the two sets of reactions of photosynthesis

light reactions and dark reactions

both occur in chloroplast

photosynthesis

the conversion of sunlight energy into chemical energy by living organisms

end product: generation of organic molecules from atmospheric CO2

two stages: light and dark reactions

occurs in chloroplasts

chloroplasts

organelles that conduct photosynthesis

found in plants and eukaryotic algae

consist of thylakoids (with thylakoid space), chlorophyll, stroma

thylakoids

one component of a chloroplast

two membranes plus a third membrane system

has thylakoid space inside

within the chloroplast, they stack like coins

contain chlorophyll pigment

contains an electron transport, where a H⁺ gradient forms across it, to synthesize ATP

chlorophyll

one component of a chloroplast

green photosynthetic pigment in plants

found in photosystems of thylakoid membranes

yields a green color because it reflects green (absorbs other visible light wavelengths)

energy is absorbed from sunlight by electrons in a decentralized electron cloud → light energy is converted into chemical energy

chemical energy then jumps from chlorophyll to chlorophyll within the system

stroma

one component of a chloroplast

the space inside the chloroplast

thylakoid space

one component of a chloroplast

the space inside thylakoids

the light reactions of photosynthesis

H₂O is split → ½O₂ and 2H⁺ by a water-splitting enzymes

electrons are released from the splitting of H₂O → get energized by sunlight

energized electrons move through an electron transport in the thylakoid membrane → a H⁺ gradient forms across the thylkaoid membrane

energy in the H⁺ gradient is used to synthesize ATP (similar to oxidative phosphorylation in mitochondria)

final electron is NADP⁺ → gets reduced to NADPH

photosystem

a system within thylakoid membranes; part of the light reactions

has a central photosynthetic reactions center with a special pair of central chlorophylls that accept and donate electrons, and 100s of antenna chlorophylls that harvest sunlight energy

sunlight excites electrons in antenna chlorophylls into an unstable high-energy state

energy jumps from chlorophyll → chlorophyll until it reaches the two central chlorophylls

the central chlorophylls trap and donate the energy as energized electrons to an electron transport chain

difference between photosystems I and II (accepting electrons)

PI accepts electrons from plastocyanin

PII accepts electrons from water

electron transport in the thylakoid membrane

photosystem II: energy is transferred through antenna chlorophylls to central chlorophylls and donated to an ETC

ETC: plastoquinone (Q), then cytochrome bf complex

a water-splitting enzyme extracts electrons from H₂O to replace electrons donated by PSII (generates O₂ and H⁺)

cytochrome bf complex: an H⁺ pump that uses energy of electrons to pump H⁺ into thylakoid space

electrons are carried to photosystem I by plastocyanin

dark reactions of photosynthesis

aka the Calvin cycle

ATP and NADPH generated during light reactions are used to synthesize glucose

occurs in the stroma

carbon fixation: a CO₂ is added to each of three molecules of ribulose 1,5-bisphosphate (RuBP)

yields 3 molecules of a 6-carbon unstable intermediate

^catalyzed by rubisco

intermediates split into 2 3-carbon molecules (each, so x2)

product: 6 molecules 3-phosphoglycerate, and incorporation of carbon into the living world

two cycles run: output is 2 molecules of glyceraldehyde 3-phosphate → synthesize 1 glucose

balanced equation of photosynthesis in plants

6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂

gluconeogenesis

the synthesis of glucose from pyruvate

anabolic

most reactions are the reverse of glycolysis, but some of the enzymes needed are different for the irreversible steps (steps 1, 3, and 10 of glycolysis → steps 1, 8, and 10 in gluconeogenesis)

e.g. reverse reaction of glycolysis step 3 is catalyzed by fructose bisphosphatase, instead of phosphofructokinase

importance of different enzyme requirements in gluconeogenesis vs glycolysis

differences in enzyme requirements allows the cell to regulate glycolysis and gluconeogenesis independently

e.g. if ATP levels are high, glycolysis is decreased and gluconeogenesis is increased

e.g. if ATP levels are low, glycolysis is increased and gluconeogenesis is decreased

(ADP and ATP can be allosteric inhibitors or allosteric activators)

synthesis of nucleoside monophosphates

synthesis of subunits of nucleic acids

can be de novo or salvage

de novo nucleoside monophosphate synthesis

“from scratch”

long pathways that assemble nucleic acid subunits from smaller components

salvage nucleoside monophosphate synthesis

“recycling” of nitrogenous bases

short pathways to assemble nucleic acid subunits

purine nucleoside monophosphate synthesis via salvage pathways (summarized from extra information)

a pyrophosphate is converted into many intermediates, to inosate

or hypoxanthine → inosate (with HGPRT as enzyme)

inosate: an intermediate nucleotide

if either guanine or adenine added to inosate, either G monophosphate or A monophosphate will be made

HGPRT deficiency

a problem in purine salvage pathways

if deficient, hypoxanthine converts to uric acid instead of inosine

uric acid precipitates as crystals in joints → triggers gout

if severe, results in Lesch-Nyhan syndrome

assimilation of nitrogen

N₂ (atmospheric) gets reduced to NH₃ (ammonia) via N-fixing bacteria, and ATP is hydrolyzed

NO₃^- (nitrate in soil) is incorporated (reduced) to NH₃ by bacteria, fungi, and plants (NADH or NADPH is oxidized)

NH₃ is used in biosynthesis of amino acids to make organic compounds in all organisms

biosynthesis of amino acids

amino acids are derived from intermediates of aerobic cellular respiration (glycolysis and CAC)

there are twenty main amino acids

not all organisms have the enzymes necessary for synthesis of all twenty AAs

essential AAs must be obtained through diet

nonessential AAs can be synthesized (by humans)

the essential amino acids

histidine

isoleucine

leucine

lysine

methionine

phenylalanine

threonine

tryptophan

valine

must be obtained from dietary sources

the nonessential amino acids

alanine

arginine

asparagine

aspartate

cysteine

glutamate (glutamic acid)

glutamine

glycine

proline

serine

tyrosine

in humans, can be synthesized in the body

phenylketonuria

a deficiency of phenylalanine hydroxylase (enzyme that converts phenylalanine → tyrosine)

phenylalanine accumulates, gets deaminated to phenylpyruvate

children develop intellectual disability within the first year of life

can be prevented with newborn screening for elevated phenylalanine levels, and low phenylalanine diet (for mother while pregnant, and for child)

macromolecule synthesis

arrangement of free subunits into larger chains or complexes or macromolecules

nucleotides → nucleic acids

simple sugars → polysaccharides

amino acids → polypeptides

fatty acids and simple lipids → fats, lipids

require bond formation between subunits by dehydration synthesis

processes require synthesis of an activated (high-energy) intermediate before formation of the inter-subunit bond

nucleoside triphosphates are example of activated intermediates (energy from hydrolysis of these intermediates allows bond formation)

glucose storage

polysaccharides store glucose in larger units

glycogen in animals, starches and cellulose in plants

synthesis of polysaccharides involves glycosidic bond formation between simple sugars (requires energy)

synthesis is coupled with formation of a nucleotide sugar intermediate (activated, energy-yielding)

steps of polysaccharide synthesis

1) phosphorylation: glucose → glucose 6-P

2) isomerization: glucose 6-P → glucose 1-P

3) condensation: glucose 1-P → UDP-glucose (reaction with UTP and release of P-P)

(note: UDP-glucose is the activated intermediate)

4) formation of glycosidic bond: glucose is transferred from UDP to growing polysaccharide chain

peptide bond formation

forms between amino acids and a growing protein (polypeptide) chain

dehydration synthesis

requires energy from nucleoside triphosphate hydrolysis

involve aminoacyl-tRNAs as an activated intermediate

aminoacyl-tRNAs

activated intermediates in the formation of a peptide bond

elongation of a polypeptide chain

3 sites: E, P, and A (eject/exit, present, and aminoacyl; a way to remember?)

a tRNA is ejected from the E site

P site has a growing polypeptide chain on it

A site has a newly-bound tRNA

bond forms between growing chain and amino acid on A site

tRNA on P shifts to E site, tRNA on A shifts to P site, a new aminoacyl-tRNA comes to A site

cycle repeats