bch4024 exam 2

catabolism

energy-producing, break down molecules

reduced organic compounds (electron carriers)

NAD+ and FAD

entropy

a measure of the number of microstates or configurations of a system, and often related to increased disorder

2nd law of thermodynamics

heat flows from a hot body to a cold body (+ ΔS) (increase entropy)

ice melting

absorbs heat (+ Δ H), but offset by large +ΔS

enzyme/products vs enzyme/substrate

enzyme/products have greater entropy

protein folding entropy

negative entropy, but by removing waters in condensation rxns net positive bc water’s entropy is much greater

how do living systems maintain order

they extract usable energy from surroudnings, release useless energy (heat), and increase entropy in universe

free energy eq

ΔG = ΔH - TΔS

endergonic reaction

uphill, more positive ΔG, unfavorable

always spontaneous

-ΔH, +ΔS

spontaneous at high temps

+ΔH, +ΔS

spontaneous at low temps

-ΔH, -ΔS

never spontaneous

+ΔH, -ΔS

ΔG and direction of rxn

+: unfavorable, backward

-: spontaneous, forward

ΔG’

biochemical standard state (pH 7, H2O 55 M)

standard cond formula

ΔG = -RT ln(Keq)

hydrolysis rxns tend to be very

favorable

complete oxidation od reduced compounds is

strongly favorable; stepwise and controlled

best sources of energy

weak covalent bonds. strong bonds require lots of energy to be broken, while weak bonds are thermodynamically unstable and break easily

molecular oxygen spin state

triplet, 2 electrons unpaired

direct electron transfer to a triplet is

unfavorable (spontaneous combustion does not readily occur)

cofactors like metal ions and FAD can

catalyze consecutive single-electron transfers needed for utilization of o2

homolytic

rare, electrons split and generate radicals

heterolytic

electrons remain w/ one fragment, products are highly unstable and reactive. produces protons, nucleophiles, etc.

why do several phosphorlyated compounds have large ΔG for hydrolysis

-phosphoenolpyruvate, 1,3-bisphosphoglycerate, phosphocreatine

-electrostatic repulsion w/i reactant molecule is relieved

-products are stable via resonance

-product undergoes further tautomerization

why is ATP so favorable

AMP does not have a high energy bond, while ATP has 2 high energy, unstable phosphoanhydride bonds. ATP hydrolysis can be coupled to other reactions.

hydrolysis relieves electrostatic repulsion.

ATP group transfer

ATP’s high energy groups are exchanged:

-P to COO

-AMP to amino acid

-P to C-OH
forming polymers coupled to breakdown of ATP

thioesters

high energy substrates such as acetyl CoA, much less resonance so less stable (high energy)

acetyl-CoA

important donor of acyl groups in fatty acid biosynthesis. reacts w/ another molecule to raise its energy state or to hold onto its energy

difference in free energy between reactant & hydrolysis products (resonance stabilized)

greater for thioesters than oxygen esters

group activation using ATP

raises a molecule’s energy state

redox reactions

electron transfers (group transfer). often use dehydrogenases

CO2

most highly oxidated compound in living systems

redox reactions can occur via

-direct electron transfer

-as a H atom (H+, e-)

-as a hydride ion (H-)

-direct combination with oxygen

reduction potential

higher E: higher affinity for electrons

electrons are transferred from a lower E to a higher E

E acceptor > E donor for -ΔG

NAD

accepts/donates 2 e- at a time

can dissociate after rxn

catabolic rxns (NAD+ high, NADH low)

NADPH

activated carrier w/ high energy bonds

anabolic rxns (NADP+ low, NADPH high)

flavin

vitamin B2, precursor to FAD. tightly bind to proteins

FAD

accepts/donates 1 or 2 e- at a time

permits use of molecular oxygen as ultimate electron acceptor (bc 1 at a time)

can work with homolytic rxns

can shift its reduction potential

maintaining homeostasis

concentrations of metabolites at steady state, where rate of synthesis equals rate of breakdown

regulation of homeostasis

-feedback inhibition (T): products inhibit their own biosynthetic pathways

positive feedback: product activates its own synthesis

metabolic regulation

reaction rate is dependent on

-concentrations of reactants vs products

-temp, pH, cofactors, coenzymes

-activity of catalyst: instrinsic rate, signal transduction, etc.

at low substrate concentrations

rate is more sensitive, frequency of substrate meeting enzyme. most enzymes work best at Km

key enzymes operate

far from equilibrium (converts far more in one direction than the other)

isozymes

different enzymes that catalyze the same rxn with different kinetics and regulation

hexokinase I and IV

hexokinase I: expressed in all tissues at dif levels

hexokinase IV: only in liver, converts glucose into G6P for glycogen. has higher Km so it can fxn at higher glucose levels

phosphorylation

protein kinases add a phosphate to Ser, Thr, and Tyr

dephosphorylation

catalyzed by protein phosphatases

proteins have a finite lifespan

range of half-lives, ubiquitination is important degradative process, sends it to proteosome

ATP and AMP are

key cellular regulators

-slight decrease in ATP leads to large increase in AMP, which is a more potent allosteric regulator

-AMP kinase regulates homeostasis. activates energy producing pathways when low

when is hexokinase released to cytosol

when glucose concentrations are high (F6P)

G6P

allosterically inhibits hexokinase, activates glycogenesis

committed step in glycolysis

fructose 6-phosphate → fructose 1,6-bisphosphate, catalyzed by PFK-1. only activated when ATP is low bc its an allosteric inhibitor

PFK-2/FBPAse-2

activates glycolysis if AMP is high, gluconeogenesis (opposite) if AMP is low

pyruvate kinase

allosterically activated by fructose 1,6-bisphosphate to increase glycolysis

allosterically inhibited by high energy markers (ATP, acetyl-CoA…)

inactivated in response to glucose depletion in liver (sends glucose to brain)

carbohydrate formula

Cn(H2O)n

carbohydrate uses

-energy sources and storage

-structural components of cell walls and exoskeletons

-cell signaling

-glycoproteins and proteoglycans

D enantiomers

right, more common in living organisms. both forms of enantiomers have identical properties but different enzyme binding

epimers

differ at only one carbon

diastereomers

non-mirror images, different properties

pentoses and hexoses reaadily undergo

intramolecular cyclization (rings) in equilibrium with open chain

anomeric carbon: former carbonyl carbon becomes new chiral center

alpha and beta positions

alpha: trans, beta cis

standard glucose

dextrose

two sugar molecules can be joined by

a glycosidic bond between an anomeric carbon and a hydroxyl carbon

polysaccharides are synthesized and degraded from

their nonreducing ends

glycogen

main storage polysaccharide in animals. made up of branched glucose, soluble, mostly in liver & muscles

alpha1-4 linked chains; branch points alpha1-6 linkers every 8-12 residues

starch

main storage polysccharide in plants, made of branched glucose.

amylose

unbranched polymer of alpha1-4 linked residues in starch, broken down by amylases.

amylopectin

branched glycogen but the branch points with alpha1-6 linkers occur every 24-30 residues (farther apart). insoluble

cellulose

unbranched glucose found in plants

beta1-4 linked chains

structure is tough and insoluble

why is cellulose a difficult substrate to act on

its fibrous structure & water insolubility. most animals cannot use it as a fuel source bc they lack the enzyme to hydrolyze beta1-4 linkages (cellulase, found in fungi & bacteria)

chitin

hard, flexiible, insoluble; found in cell walls in mushrooms & exoskeletons

beta1-4, unbranched N-acetylglucosamine (broken down by chitinase)

agarose

complex mixture of galactose

serves as cell wall in some seaweeds, found in many foods and in the lab

glycosaminoglycans

linear polymers of repeating disaccharide units, made up of glucosamine (negative)

form extracellular matrix meshwork (connective tissue)

extracellular matrix meshwork

-hyaluronan: lubrication of joints & eye

-chondroitin: cartilage, tendons, ligaments, aortic walls

-keratan: cornea, cartilage, bone

-herapin: growth factor, inhibits antithrombin/coagulation. treats a lot of illnesses

branched sugars

glycogen and amylopectin

linear sugars

amylose, cellulose, chitin, heparin

glycoproteins

small sugars attached to anomeric carbon. sugar code: protein recognition. lotsc of important fxns

glycoprotein linkages

O-linked: sugars to Ser, Thr via glycosidic bond

N-linked: Asn via N-glycosyl bond

glycolipids

lipids with covalently bound sugars. cell membranes, blood types

proteoglycans

glycosaminoglycans attached to large rod-shaped protein in cell membrane to form connective tissue. help regulate growth & lubricate joints

extracellular matrix (ECM)

material outside of cells, attachments. strength, elasticity, physical barriers, etc. cells attach via integrins

ABO blood type antigens

glycolipids

sugar recognition plays key role in immune system

selectins

proteins that recognize sugars; what immune system uses to detect the health of cell. mediate inflammatory responses in arthritis

A1C

measures hemoglobin glycation, long term glucose test that estimates blood glucose over past 120 days

plants build organic compounds from CO2

they can make 3-C intermediates like glyceraldehyde 3-phosphate

what occurs in cloroplast

Calvin Cycle: converts CO2 to glyceraldehyde 3-phosphate (sugars), requires 24 photons

Calvin cycle

CO2 reacts with ribulose 1,5-bisphosphate to make glyceradldehyde 3-phosphate, converted into glucose

3 CO2 + 6 NADPH + 5 H2O + 9 ATP → G3P + 2 H+ + 6 NADP+ + 9 ADP + 8 Pi

where does energy for Calvin Cycle come from

ATP and NADPH, catalyzed by rubisco (most common enzyme)

rubisco’s active site

O2 competes with CO2 for active site. 25% of the time, O2 binds bc its more common in atmosphere, forming 2-phosphoglycolate. This is metabolically useless, and salvaging its carbon requires energy. sent to peroxisome which converts it to glycine, then sent to mitochondria to make serine, then back to chloroplast as glycerate.

C3

CO2 is fixed into 3-phosphoglycerate (most crops)

C4

CO2 is fixed into oxaloacetate (4C). avoid rxns w O2, low water loss. grow well in hot, sunny climates, evolved 30 mya due to declining CO2 levels

CAM

CO2 is fixed into malate, split rxns into day and night. avoid rxn w/ oxygen, open stomata at night to minimize water loss, compartmentalize rxns. evolved 20 mya

plant energy

starch provide bulk of energy storage, made in chloroplasts for short-term storage, or amyloplasts for long-term. store lipids and proteins in seeds for energy

sucrose is made in cytosol for transport; formed in gluconeogenesis & broken down in glycolysis

plants can convert acetyl-CoA into glucose & make sugar from fatty acids in glycoxylate cycle

cell walls

cellulose is made of glucose and very strong due to H-bonds

lignin crosslinks sugars, conducting water. (last to decay into CO2, carboniferous period, breaks down into vanillin)

bacterial peptidoglycan

cell walls made of peptidoglycan: made of N-acetylglucosamine and N-acetylmuramic acid

inhibited by penicillin, cleaved by lysozyme

gram-negative have thin wall, gram-pos a thick

glycolysis

the breakdown of glucose into pyruvate

glucose as source of fuel

-yields good amount of energy upon oxidation (ATP, NADH, NADPH, FADH)

-can be efficiently stored as glycogen, starch, and cellulose

-many organisms and tissues can meet their energy needs on glucose only