Biochem Final Review (All terms)

Components in TCS (two component regulatory systems)

Histidine Kinase and response regulator

Response Regulator Structure

N Term receiver domain

C term DNA binding domain

PhoP-PhoQ TCS activation conditions

Found in Salmonella

Activated in host cell conditions (Low Mg2+, low pH, antimicrobial peptide presence)

Action of TCS

Ligand induced binding triggers autophosphorylation

Phosphorylation of response regulator which binds directly to DNA for gene expression

Mechanisms the PhoP-PhoQ activates

mgtA expression-Blocked by high concs of Mg2+

rstA-increases Fe2+ uptake

Chromophore/Pigment

Light Absorbing Molecule

Light Reactions location

thylakoid membrane (chloroplast)

Carbon assimilation location

stroma (chloroplast)

Phycobilins

pigments used by cyanobacteria and red algae to absorb light

Chl a and Chl b

Pigments to absorb light. a found in all plants b only in green algae and land plants

Carotenoids

Accessory pigments absorb light at other wavelengths and protect from ROs

Photochemical reaction center

special pair of chlorophyll molecules (Chl)2 that convert light energy to chemical

Antenna molecules

pigments around the photochemical reaction center

ETC and charge separation

Flow of electrons through ETC causes proton to be pumped across thylakoid membrane used to produce ATP 

Cyclical electron flow

produces only ATP

Noncyclical electron flow

ATP+NADPH

PS1 vs PS2 Abs range

PS1-Far red (700nm)

PS2-Red (680nm)

Z scheme Explained

PS2 light gives initial boost to higher energy state

Descend through cytochrome b6f producing ATP

PS1 photon boosts up again reach summit giving energy to NADP+ forming NADPH 

PSII function

Splits water, release O2, supplies electrons and adds protons to lumen

PSI function

Excites electrons again reduces NADP+ to NADPH 

stoichiometry of light dependent reactions

2 photons-transfers one electron from H2O to NADP+

8 photons-release one O2

Calvin Cycle 3 Stages

Fixation of CO2

Reduction of 3-phosphoglycerate to a triose

Regeneration of ribulose 1,5 biphosphate (RuBP) (5/6 of triose molecules used to do this)

Location of the 13 enzymes in Calvin cycle

stroma

Rubisco Function

Fixes CO2 to RuBP to create two 3-phosphoglycertae (first stable product for c3 plants)

Rubisco form 1

Found in most plants

Rubisco form 2 

Found only in certain photosynthetic bacteria 

Rubisco Structure

8 large subunits (encoded in chloroplast genome)

8 small subunits (encoded in nuclear genome)

Rubisco Cofactors

Carbomoylated Lys and Mg2+

Carbon Assimilation summary

Rubisco fixes CO2 to RuBP to create two 3-phosphoglycertae

ATP and NADPH reduce 3-PGA to G3P (glyceradahyde 3 phosphate) 

Some G3P recycled to created more RuBP

Carbon Assimilation Stoichiometry

6 NADPH and 9 ATP Per G3P

Pi-Triose antiporter

imports Pi for photophosporylation and exports G3P for sucrose construction 

Photorespiration

Occurs because of high O2 presence rubisco can also accept O2 instead of CO2

Creates only one G3P and one wasteful G2P

Oxidative photosynthetic carbon cycle

Chloroplast, peroxisome and mitochondria

converts G2P into serine and eventually G3P

C4 Pathway

Concentrates CO2 around rubisco limiting photorespiration

PEP carboxylase and Rubisco Locations in C4 plants

Pep Carboxylase-mesophyll

Rubisco-Bundle sheath

C4 plant first stable intermediate 

Oxaloacetate

C4 Plants stoichiometry

5 ATP to assimilate one CO2

3 ATP- C3 Plants

Nitrification 

Oxidation of NH4+ to (NO2-) and then to NO3-

Denitrification

Reduction of NO3- and NO2- to N2 (Only anaerobic bacteria)

annamox bacteria

Anaerobic conversion of NH4+ and NO2- to N2

NH4+ harm

can dissipate pH gradients

Steps of NO3- assimilation

Nitrate Reductase reduces NO3-(nitrate) to NO2- (Nirtrite)

Nitrite reductase reduces NO2- to NH4+ (ammonium)

Nitrogen Fixation

N2 to usable forms of nitrogen like NH4+ or NO3-

Catalyzed by nitrogenase

Anaerobic N-fixing bacteria location

Within plant cells called heterocysts (No PSII=no oxygen production)

Glutamine synthase

Catalyzes the conversion of ammonium into amino acids (1st step)

End product is glutamine

GOGAT (aka glutamate synthase)

NADH GOGAT-non photosynthetic tissue

Fd GOGAT-cholorplasts

end product is 2 glutamates

Aminotransferase

Form other amino acids from taking amino group from Glu and putting on a-keto acid

Sulfur Assimilation in plants

Taken up as sulfate (SO4 2-) by H+-SO42- symporter

Needs to be activated first to form APS and PPi 

ATP Sulfurylase

Catalyzes the activation of sulfate

Sulfur assimilation Stoichiometry

Requires 10 e- to be converted to Cys

PTM Function

Post Translational Modifications turn proteins on/off

Phosphorylation

PO4 group added to serine threonine tyrosine (Papa always brings alcohol on his trips)

Oxidation (non-enzymatic)

Redox reactions involving Cys Sulfur oxidation

Ubiquitination

Adds protein marker for degradation in proteosome

Role of Cys Redox PTMS

Redox signaling

Protection from irreversible oxidation

Activate certain proteins

Proteins that remove ROS

Superoxide Dismutase (SOD)

Catalase (Kat)

Peroxiredoxins(Prx)

Glutathione (GSH)

Protein that reduces H2O2

Kinases

Adds phosphate

Phosphatases

Removes phosphate

G Proteins summary

Heterotrimeric

Bind GTP (guanosine nucleotides)

Active-GTP

Inactive GDP

Adrenergic signaling

Epinephrine binds to GPCRs

G protein binds to adenyl cyclase (effector enzyme)

Adenyl cyclase produces secondary messenger cAMP

cAMP activates PKA (protein kinase A)

PKA phosphorylates other (target) proteins that trigger adrenergic response ie. activation of glycogen phosphorylase-break down of stored glucose

GPCR Signaling Summary

Ligand Binds to GPCR

G Protein becomes activated

Binds to an effector enzyme that produces second messenger

Second messenger continues activation cycle

PKA Gene Transcription

PKA Activates CREB that supports transcription of certain genes

cAMP phosphodiesterase 

Removes cAMP to AMP (involved in turning off signal of G protein)

Gi

Inhibitory G protein that binds to adenyl cyclase stopping cAMP production

Self inactivation of GTPase activity 

Alpha sub unit of G protein is activated with GTP but can self hydrolyze GTP to GDP to turn itself off 

Cholera and Pertussis toxins

Lead to constant activation of adenyl cyclase

cAMP is produced which triggers sodium ions to be pumped into intestinal lumen

Additon of water and other electrolytes are also excreted to reduce sodium conc

BARK

Used to desensitize proteins in b-adrenergic signaling

B-arrestin

Removes GPCR from the cell surface to prevent over activation

RTKs function and mechanism

Similar cell signaling to GPCRs

After 2 ligand binding occurs on 2 RTK extracellular domains self-phosphorylation of kinase domain occurs

Triggers additional phosphorylation of cytosolic tyrosines

Insulin signaling pathway

Insulin receptor (RTK) binds insulin and undergoes autophosphorylation

IRS-1 is phosphorylated on Tyr residues

Phosphorylation cascade continues until Ras is activated by GTP

Ras activates Raf(activates Raf-1)

Raf-1 phosphorylates MEK

MEK activates ERK 

ERK enters nucleus and phosphorylates transcription factors like ELk1 to alter cell function 

FOXO

“Fasting Nuclear Transcription factor” looks to promote things like stored glucose breakdown and lipid utilization needs to be deactivated with presence of insulin

Insulin Signaling termination

Triggered by activation of protein tyrosine phosphatases that remove phosphorylation of INSR and IRS

Antagonists that block IRS binding

What glucose transporters function at Vmax(blood glucose levels are above Km)

GLUT 1 3 4 

GLUT 2 function

glucose export(liver) sensing of blood glucose (pancreas)

GLUT 4 function

Insulin response transporter

GLUT 1 conformations

T1 glucose import T2 glucose export

Glucose Symporter

Uses Na+ with gradient to transport glucose against gradient in intestinal cells

Bicarbonate transporter function (capnophorin)

Antiporter that moves Cl- in and HCO3-(bicarbonate) into blood plasma (maintains electrochemical potential)

Aquaporin facts

Proton hopping discovered by Peter Agre

P Type ATP Pump

Phosphorylated and dephosphorylated during transport of Na+, K+ and other ions

F Type (and V) Type proton Pump

Transports protons using ATP Hydrolysis (makes ATP in reverse)

V type proton pump function

Acidifies lysosomes and other organelles

Na+/K+ ATPase Function

Maintains high Na+ conc outside cell and high K+ inside. Does this by pumping 3 Na+ outside cell while pumping 2k+ in

ABC Transporter Function

Pumps out drugs, peptides and nutrients (eukaryotes) but function both directions in bacteria

Potassium Channel Pore Helix

Has neg charged on c term of helix (inside cytosol) to attract K+

Potassium Channel Selectivity Filter

Has Carbonyl (C=O) to mimic water molecules bonded with K+ (reduces transport energy)

K+ channel voltage gating

s4 Helix has arg residues gets pushed outwards w/ depolarization 

causes S5 and S6 to open

Acetylcholine Receptor Architecture

Leu side chains of M2 Helices close channel (bulky and hydrophobic)

Binding of 2 ach cause twisting of M2 Helix

M2 helices now expose smaller polar residues to allow for ion transport (Na+ and K+)

Post Trans Modifications in Cis Golgi

M6P-phosphoryaltion of mannose

Removal of Mannose

Addition of other sugars (GlcNAc)

Post Trans Modifications in Trans Golgi

Additon of galactose (GAL)

Addition of other sugars like sialic acid (NANA)

Sulfation of tyrosines and carbs

Final sorting

COPI Coat protein Transport

Transports from Golgi to ER

COPI GTPASE Clathrin (on/off switch)

ARF

GDP Bound GTPase

Turned off

GTPase on switch

GEF converts GDP TO GTP

GTPase off switch

GAP converts GTP to GDP

COPII GTPase (on/off switch)

Sar1

COPII Transport

ER-Golgi

Clathrin Transport

Trans-Golgi to endosome

Rab function

Guides vesicle once uncoated to form SNAREs