biochem processes fixed

Translation

Translation is the process of synthesizing proteins from mRNA. Steps: 1. Initiation 2. Elongation 3. Translocation 4. Termination

Folding

Folding is how a polypeptide adopts its 3D functional form. Steps: 1. Co-translational Folding 2. Hsp70 Binding 3. GroEL/GroES Assistance 4. Quality Control

Degradation with steps

Degradation removes misfolded or unwanted proteins. Steps: 1. Ubiquitination 2. Proteasome Recognition 3. Unfolding and Degradation 4. Autophagy

Translocation

Translocation delivers proteins across membranes. Steps: 1. SRP Binding 2. Targeting to ER 3. Sec61 Translocation 4. Membrane Insertion

Membrane Protein Biogenesis at the ER

Membrane protein biogenesis positions proteins in the ER membrane. Steps: 1. TMD Synthesis 2. ER Targeting 3. Lateral Insertion 4. Accessory Help

Photosynthesis (Light Reactions)

Photosynthesis light reactions generate ATP and NADPH. Steps: 1. PSII Activation 2. Electron Transport to b6f 3. PSI Activation 4. NADPH Production

Carbon Assimilation Reactions (Calvin Cycle)

Carbon assimilation fixes CO₂ into sugar in the Calvin cycle. Steps: 1. Carbon Fixation 2. Reduction 3. Regeneration 4. Synthesis

ATP Synthesis

ATP synthesis uses proton motive force to make ATP. Steps: 1. Proton Pumping 2. c-Ring Rotation 3. Gamma Rotation 4. ATP Formation

Initiation

Ribosome assembles on start codon with initiator tRNA.

Bacteria: mRNA and initiation factors (like fMet) bind to 30S subunit. rbs in mRNA pairs with rRNA in 30S. 50S comes in after an initiation factor hydrolyzes GTP

Eukaryotes: 40S subunit binds to both ends of mRNA (5’ cap and 3’ poly-A tail. Also requires more initiation factors

Elongation

Aminoacyl-tRNAs enter A site

3-way interaction between mRNA, tRNA anticodon, and rRNA (rRNA checks backbones of other two) that will accelerate GTPase activity of EF-Tu through conformational changes, allowing release of the amino acid.

Then peptide bond is formed through entropy trap and proton shuttle

Translocation in Translation

"Ribosome shifts along mRNA, moving tRNAs to new sites."

Termination

Stop codon is recognized by release factor; polypeptide is released; peptidyl transferase binds to a water molecule due to changes induced in active site by release factor

Co-translational Folding

Folding begins as chain emerges from ribosome tunnel.

Hsp70 Binding

Hsp70 binds exposed hydrophobic regions to prevent misfolding.

GroEL/GroES Assistance

GroEL/GroES encapsulates proteins to assist folding.

GroEL stores and refolds and GroES is the cap that binds to GroEL

Quality Control

Misfolded proteins are refolded or targeted for degradation.

Ubiquitination

E3 ligases attach ubiquitin chains to target proteins.

Proteasome Recognition

Proteasome recognizes ubiquitinated substrates.

Unfolding and Degradation

Proteins are unfolded and degraded into peptides in the proteasome.

Autophagy

Large aggregates are degraded via autophagy.

SRP Binding

SRP binds to signal sequence on nascent chain.

Targeting to ER

SRP directs ribosome to SRP receptor on ER.

Sec61 Translocation

Ribosome docks at Sec61; translation resumes into channel.

Membrane Insertion

Hydrophobic sequences insert into membrane of ER via Sec61 based on interactions w/ nascent chain, ribosome, and other proteins.

TMD Synthesis

Hydrophobic TMDs are translated by ribosome.

ER Targeting

SRP targets ribosome to the ER membrane and binds to SRP receptor

Lateral Insertion

Sec61 opens laterally to insert TMDs into bilayer.

Accessory Help

EMC or other factors help insert weakly hydrophobic TMDs.

Get1/2 insert tail-anchored proteins.

Oxa1 family helps insert short domains

PAT/GEL/BOS help insert hydrophilic multipass proteins

PSII Activation

P680 in PSII is excited by light; splits water after photochemical reaction

Electron Transport to b6f

Electrons move from excited P680* through plastoquinone to cytochrome b6f.

PSI Activation

P700 in PSI is excited and electrons pass to ferredoxin.

NADPH Production

ferredoxin transfers electrons to ferredoxin:NADP⁺ and oxidoreductase which reduces NADP+ to NADPH. The electrons are replaced by plastocyanin from b6f complex

Carbon Fixation

RuBisCO adds CO₂ to RuBP.

Mg2+ in active site, carbamoyl Lys abstracts proton from RuBP (rds) allowing it to attack CO2. Then there is hydroxylation at C3, allowing it to be cleaved as an aldol, yielding 1 3PG and another that is formed after abstracting proton from carbamoyl Lys. Carbamoylation of lysine activates Rubisco

Reduction (Calvin Cycle)

3-PGA is reduced to G3P using ATP and NADPH.

Regeneration (Calvin Cycle)

5 G3P is recycled to regenerate 3 RuBP using ATP.

What does G3P do after leaving Calvin cycle?

Some G3P exits cycle and contributes to glucose synthesis, energy storage as starch, or energy transport as sucrose

Proton Pumping

Electron transport chain pumps protons across membrane.

c-Ring Rotation

"Protons move through c-ring of F₀; measured in PMF

Gamma Rotation

"γ subunit rotates within F₁

ATP Formation

β subunits catalyze ATP formation from ADP and Pi.