Biochem Test 2

Front 1

3 Reasons Hydrolysis of ATP is highly exergonic

Back 1

1.) Charge Separation upon hydrolysis relieves bond strain

2.) Pi is stabilized by formation of a resonance hybrid

3.) ADP immediately ionizes, releasing a proton into solution

Front 2

Reasons Certain compounds contain high negative free energies of hydrolysis

Back 2

1.) Charge separation upon hydrolysis relieves bond strain

2.) Products stabilize by ionization

3.) Products stabilized by resonance stabilization

4.) Products are stabilized by isomerization or tautomerization

Front 3

Contain High Energy Bonds

Back 3

1.) 1,3-BPG -> Pi
2.) Creatine Phosphate (Pi)
3.) PEP -> Pi
4.) Acetyl CoA -> (S)
5.) ATP, GTP, UTP, CTP

Front 4

High Energy Bond

Back 4

Equal to or greater the free energy change than ATP (-7.3)

Front 5

Reversible Competitive Inhibitor

Back 5

Km - Increase
Vmax - Unchanged

Front 6

Reversible Uncompetitive Inhibitor

Back 6

Km - Decrease
Vmax - Decrease

Front 7

Reversible Noncompetitive Inhibitor

Back 7

Km - Unchanged
Vmax - Decreased

Front 8

Two classes of Mechanism based inhibitors

Back 8

1.) Covalent
2.) Suicide Substrates

Front 9

Mechanisms of Enzyme Regulation

Back 9

1.) Concentration of S or I
2.) Product concentration
3.)Allosteric Activators &/or Inhib
4.) Covalent Modification
5.) Binding of Modulator Proteins
6.) Proteolytic Cleavage
7.) Enzyme Level, ie. effects on transcription or translation

Front 10

Levels of a particular protein can be controlled by these factors

Back 10

1.) Regulation of gene transcription
2.) Stabilization of mRNA i.e. increased translation
3.) Regulated degradation - the proteosome

Front 11

Metabolic Pathways can be regulated at multiple points using a variety of mechanisms:

Back 11

1.) Regulation of rate-limiting step
2.) Feedback regulation
3.) Feed-forward regulation
4.) Tissue isozymes of regulatory proteins
5.) Counter Regulation of opposing pathways
6.) Substrate channeling through compartmentalization

Front 12

activation-transfer coenzymes

Back 12

Thiamine Pyrophosphate
Coenzyme A
Biotin
Pyridoxal Phosphate

Front 13

Oxidation-Reduction Coenzymes

Back 13

NAD+
FAD
Vit C
Vit E

Front 14

Ox-Phos Requires:

Back 14

1.) e- donor (NADH/FADH2)
2.) e- acceptor (O2)
3.) Intact Inner membrane, impermeable to H+
4.) Components of ETC
5.) ATP Synthase

Front 15

Complex 1
(NADH Dehydrogenase)

Back 15

Consists of:
1.) FMN binding protein
2.) at least 6 Fe-S proteins

- initially transfers a hydride (2 e-) to FMN

- transfer of 2 e- to Ubiquinone (forming ubiquinol) provides E for mvment of 4 e- into innermembrane space

Front 16

Complex II
(Succinate Dehydrogenase)

Back 16

- contains bound FAD & several Fe-S centers

- component of CAC --> catalyzes succinate to fumarate generating FADH2 which is immediately oxidized into ETC

- entry route for FADH2 only, NADH using complex I

Front 17

Other Flavoprotein e- donors for CoQ

Back 17

1.) Glycerol 3-Pi dehydrogenase, G3P-->DHAP
- Shuttles e- from cytosolic NADH to ETC

2.) ETF Q:oxidoreductase, transfers e- to ubiquinone
- gets e- from FA-oxidation

* Energy drop present in NADH to complex I therefore e- mvment, but no E drop in FADH2 to Q so no e- mvment

Front 18

Co-Q (Ubiquinone)

Back 18

- lipid soluble due to h-phobic side chain

- consists of a benzoquinone and isoprenoid chain

- Can trans 2 H+, & either 1 or 2 e- depending on radical or not (not usually though)

Front 19

Complex III
(Cytochrome C oxidoreductase)

Back 19

- pumps 4 H+, by sep. pathways through oxidation of QH2

- dimeric Complex, binds 4 Fe-S clusters & 4 cytochromes (b & c1)

- Moves 4 H+ by coupling with QH2 oxidation

Fxnal Core has 3 subunits
1.) Cytochrome b (2 hemes)
2.) Fe-S protein
3.) Cytchrome C1 (1 Heme)

- Contains 2 binding sites in core for Ubiquinone

Front 20

Complex IV
(Cytochrome C oxidase)

Back 20

- pumps 2 H+, by passing e- from cyto-c to O2 making H2)

- 3 Subunits
1.) two heme groups (a, a3) & one Cu ion (CuB)
2.) dinuclear Cu center (2 Cu ions)

- processes 1 e- at a time

- has a lower Km for Mg, pulls O2 from Mg

Front 21

Respiratory Chain Inhibitors

Back 21

Rotenone
- Inhibits Complex I

Antimycin
- Inhibits Complex II

CN- or CO
- Inhibits Complex IV

*everything before inhibitor is reduced after is still oxidized

Front 22

ATP Synthase

Back 22

2 components
1.) F1
- periph. prot. cat. ADP->ATP
2.) Fo
- Int. mem. prot.
- pore for H+ to travel in into matrix
- sens. to oligomycin

Front 23

F1

Back 23

- Knob
- contains a "turbine" of cat. subunits that condense Pi w/ADP
to form ATP
- Faces Matrix side
- 5 subunits a,b,y,d,e
- a3b3yde
- each b subunit has a ATP synth site
- y is shaft
- 3 b w/ 3 sep. conf.

Front 24

Fo

Back 24

- Stalk
- has a H+ channel spanning membrane that directs proton flow through the catalytic turbine
-3 subunits a,b,c
- ab2c10
- embedded in membrane

Front 25

ATP synth is catalyzed by ?

Back 25

ATP Synthase & rotational catalysis

- H+ mvment cause rotation c(Fo) & y(F1) subunits in same drxn

Front 26

Binding Change Mechanism

Back 26

1.) Open Site - ADP/P binds
2.) Loose - ADP/P constricted
3.) Tight - ATP synth

- counterclockwise rotation of sites with inflow of H+ driving this mechanism

Front 27

5 reasons why ADP controls rate of O2 consumption

Back 27

1.) ADP-->ATP by ATP synthase
2.) Release of ATP requires H+ flow through ATP synthase into matrix
3.) Use of H+ from IMS dec. H+ gradient
4.) As a result, ETC pumps more H+ and reduces more O2
5.) As NADH donates e- to ETC, NAD+ is regenerated and return to TCA cycle

Front 28

Causes of OX-Phos uncoupling

Back 28

1.) Chemical Uncouplers
- 2,4 DNP; ionophores
- lipid soluble weak acids
2.) Uncoupling proteins
- thermogenin(UCP1) in brown fat
- Prot. pore shorts ATP-synthase
3.) Basal Leakage

- Leakage of H+ across the IMM back into matrix dissipates gradient causing cessation of ATP synthesis, but ETC continues

Front 29

PMF is responsible for:

Back 29

1.) Providing E for ATP synth
2.) Transporting substrates (ADP & Pi) into & product (ATP) out of mito matrix

Front 30

Stiochiometry of ATP Synthesis

Back 30

(4 H+ per ATP)

NADH --> 10 H+, 2.5 ATP
- 3 H+ for ATP synthase
- 1 for phosphate translocase

FADH2
- 6 H+, 1.5 ATP

Front 31

3 Tenets of Chemiosmotic Theory

Back 31

1.) unidirectionally pumping of e- by ETC complexes I, III, IV
2.) PMF formed due to H+ impermeable membrane
3.) Electrochemical potential drives ATP synthase

Front 32

2 components of PMF

Back 32

1.) Chemical Pot. E
2.) Electrical Pot. E due to sep. of charge that occurs when H+ is moved across membrane w/out counterion

Front 33

2 ways to make a + deltaG move forward

Back 33

1.) inc. substrate
2.) dec. product

*Le Chatlier's Principle

Front 34

Inc. fluidity of membrane

Back 34

inc. temp
inc. unsat. FA
dec. Chol

Front 35

Dec. fluidity of membrane

Back 35

dec. temp
inc. sat. FA
inc. chol.

Front 36

Prop. of lipid membranes

Back 36

1.) Self-seal
2.) Self-assemble
3.) Rotational diffusion
4.) Lateral diffusion
5.) slow transveres exchange of lipid components
6.) Impermeable to most polar solutes
7.) approx. 3 nm thick

Front 37

Types of membrane transport

Back 37

1.) Channels - Not Saturable
- Pores
- Gated Channels
2.) Carriers
- Facilitated diffusion
- Primary active transporters
- secondary active transporters

Front 38

Stimuli for gated channels

Back 38

-voltage
-ligand
-pressure
-phosphorylation

Front 39

Hallmarks of facilitated diffusion

Back 39

- high rates of diffusion down a concentration gradient
- saturability
- specificity

Front 40

GLUT transporters

Back 40

GLUT 1- RBC
GLUT 2 - Liver
GLUT 4 - Skeletal muscles, under control of insulin

Front 41

specificity constant

Back 41

Kcat/Km

Front 42

Kcat(Turnover number)

Back 42

Vmax/Et

- # of substrate molecules turned over to product in a given unit of time by a single enzyme molecule at saturating conditions

Front 43

slope of lineweaver burke

Back 43

Km/Vmax

x-intercept=1/Km
Y-intercept=1/Vmax

Front 44

2 types of multisubstrate rxns

Back 44

1.) Sequential
- Both Sub bind simultaneously
- Km decreases as second substrate increases
- can be regulated by just varying one substrate

2.) Ping-Pong
- substrates bind alternating
- Km inc w/ increasing substrate
- transfer of a functional group between substrates
- same graph as uncomp. rev. inhibition

Front 45

An activation coenzymes does all the following

Back 45

1. Forms a covalent bond with a substrate molecule
2. Forms a bond that contains a lot of energy
3. Does interact with the enzyme
4. Binds to the substrate
5. Activates the substrate for transfer

Front 46

Thiamine Pyrophosphate

Back 46

Activation Coenzyme
- Binds to the carboxyl group of pyruvate
- PP + Thiamine in humans
- Fxnal group TPP
- Forms Carbanion & covalent bd

Front 47

Coenzyme A

Back 47

Activation Coenzyme
- Reacts to form a thioester with acyl groups.
- Binds reversibly
- Possesses sulfydryl
- donates 2 carbons in CAC that are oxidized to CO2

Front 48

Biotin

Back 48

2. It activates and transfers CO2 to compounds in carboxylation reactions
3. It is a coenzmyme for carboxylase enzymes
4. It is a prosthetic group
5. It forms a covalent bond with CO2

Front 49

Pyroxidal Phosphate

Back 49

Activation Coenzyme

1. Is an activation-transfer coenzyme
2. Is also called vitamin B6
3. is involved in transferring amino groups
4. can be covalently bound to the enzyme
5. can form a covalent bond with the substrate

Front 50

NAD+

Back 50

1. Is synthesized from the vitamin niacin
2. Is a coenzyme for many dehydrogenase enzymes
3. Accepts hydride ions and becomes NADH when oxidizing substrates
4. Contains an ADP group that binds to the enzyme

Front 51

Mechanism based Inhibitors
(Covalent)

Back 51

Diisopropylphosphoflouridate
Sarin
Malathion

Covalently binds to enzyme inactivating it

Front 52

Mechanism Based Inhibitors
(Suicide Substrates)

Back 52

Allopurinol

- binds to active site of enzyme inhibiting it

Front 53

Effectors + & - of PKA

Back 53

+ NADH, Acetyl-Coa
- ADP, Pyruvate

Front 54

Intermediates of CAC, ways to exit

Back 54

Citrate -FA synth
alpha-keto - Glutamate
Succinyl-Coa - heme synth
Malate -gluconeogenesis
OAA - aspartate

*replenished by anaplerotic rxns

Front 55

Total Energy of CAC

Back 55

207
228 in acetyl group
There 90% eff.

Front 56

reasons why some CAC rxns are irreversible

Back 56

1.) product concentrations are low
2.) the enzymes are poor catalyts for the reversible rxn

Front 57

Fates of Glucose after meal

Back 57

1.) Liver
- Ox/Phos & VLDL
2.) Brain
3.) RBCs
- glycolysis
4.) Muscle
5.) Adipose

Front 58

Products of lipolysis during fasting

Back 58

1.) Glycerol for gluconeogenesis
2.) FA for Ox/Phos
3.) Ketone Bodies (Liver converts FA-->Ketone Bodies and release into Blood)

Front 59

Fates of Lipoproteins in fed state

Back 59

1.) Chylomicrons
2.) VLDL

Front 60

Fates of AA in Fed State

Back 60

1.) Protein Synth
2.) Synth of other N-containing metabolites
3.) oxidized to energy

Front 61

Sources of fuel for gluconeogenesis

Back 61

1.) lactate
- from RBCs glycolysis
2.) Glycerol
- from triglyceride breakdown
3.) AA
- from breakdown of muscle protein

Front 62

lipids that proteins attach to

Back 62

1.)Long Chain Fatty Acids
- inner membrane
2.) Isoprenoid
- inner membrane
3.) GPI
- extracellular face