Biochem Flashcards
Which amino acid has an R absolute configuration and why?
Cysteine, because the -CH2SH group has priority over -COOH group
Still is an L amino acid
Which amino acids have alkyl side chains?
Alanine, valine, leucine, isoleucine
Which amino acids have amide side chains?
Asparagine and Glutamine (polar)
What is the effect of a point mutation changing E -> Y?
E = glutamate Y = tyrosine
Acidic side chain to aromatic side chain
What is the effect of a point mutation changing D -> K?
D = aspartate K = lysine
Acidic to basic side chain
At pH 7, what will be the protonation status of amino acids?
Carboxylate group unprotonated
(-COO-)
Amino group protonated (-NH3+)
What is the approximate pI of aspartate if pKa1=1.88, pKa2=3.65, and pKa3=9.60?
Aspartate is acidic so
pI = (pKa, R + pKa, COOH) / 2
Because acidic amino acids have 2 COOH groups that are deprotonated before NH3+
(1.88+3.65)/2 ~ (2+4)/2 ~ 3 (2.77)
Acidic side chains have low pI
What is the pI of arginine if pKa1=2.17, pKa2=9.04, pKa3=12.48?
Arginine is basic, extra amino group (+2 when fully protonated)
pI = (pKa, NH3+ + pKa, R) / 2
(9.04 + 12.48) / 2 ~ (9 + 13) / 2 ~ 11 (10.76)
Basic side chains have high pI
Explain the reason for the partial double bond character of the C-N amide bond in the peptide bond
Amide groups have delocalized pi electrons in carbonyl
Amino nitrogen has lone pair
Thus, resonance
At pH 7, the charge on glutamate is
-1
Both carboxyl groups are deprotonated
Which amino acid is most likely to be found in the transmembrane portion of an alpha helix?
- Lysine
- glutamate
- aspartate
- phenylalanine
Phenylalanine- has hydrophobic side chain (benzene ring)
True or false: bases can catalyze peptide bond hydrolysis
TRUE
In an oxidation reduction reaction, what is the role of the reductant?
Reductants donate electrons
Oxidants accept electrons
What class of enzyme are kinases, and what is the major function of this class?
Kinases are transferases, which catalyze functional group transfer
What reaction does aminotransferase catalyze?
Transfer of amino group from aspartate to alpha-ketoglutarate
Aspartate becomes glutamate, alpha-ketoglutarate becomes oxaloacetate
What class of enzyme are phosphatases and nucleases?
Hydrolases
What class of enzyme catalyzes conversion of ATP to cyclic AMP and Pi?
Lyase- cleavage of single molecule into 2, does not require water
Synthases are a more specific term for what class of enzyme?
Lyases- catalyze cleave of single molecule into two products, but also small synthesis reactions (then called synthases)
Can isomerases catalyze reactions between stereoisomers or constitutional isomers or both?
Both: isomerases catalyze bond rearrangement
What class of enzymes catalyze large synthesis reactions, often requiring ATP?
Ligases
What are the x and y axes of the Mechaelis-Menten plot?
Y axis: v, reaction velocity
X axis: [S], substrate concentration
Where is the Km of an enzyme found on the Michaelis-Menten plot?
Find the 1/2Vmax, then find the value on the x-axis directly below ([S])
What is the Michaelis- Menten equation?
v = Vmax [S]
————
Km + [S]
Finish this sentence: at 1/2Vmax in MM kinematics, Km =
At 1/2Vmax, Km=[S]
What effect does lowering the Km of an enzyme have on substrate binding?
lower Km = higher affinity for substrate
Increased enzyme activity
What does Kcat measure in MM kinematics?
Kcat = rate of substrate turnover
How is catalytic efficiency calculated?
Catalytic efficiency = Kcat/Km
What are the axes of the Lineweaver-Burk plot?
LB plot is double reciprocal of MM plot:
Y axis: 1/V
X axis: 1/[S], extrapolated to negative
What does a Hill coefficient <1 imply?
Negative cooperation
Further binding decreases ligand affinity
How does temperature affect enzyme activity?
Enzyme activity doubles in reaction velocity for every 10 degree C increase until temp is too high and enzyme denatures
Explain the following for competitive inhibition:
- where does it bind
- how does it affect Vmax and Km
- what does its LB plot look like
Competitive inhibition binds active site - can be overcome by adding more substrate
Does not alter Vmax because adding more substrate can overcome it, so Vmax can still be reached eventually
Measured Km is increases because more substrate is needed to reach half Vmax
Lines cross on Y axis (1/V) on LB plot
Explain the following for no competitive inhibition:
- where does it bind
- how does it affect Vmax and Km
- what does its LB plot look like
Noncompetitive inhibition binds allosteric site (conformation change)
Binds equally well to E and ES
Decreases Vmax because less enzyme is available to react due to altered conformation
Lines cross on -x axis (-1/[S]) on LB plot
Explain the following for mixed inhibition:
- where does it bind
- how does it affect Vmax and Km
- what does its LB plot look like
Mixed inhibitors bind allosteric site, either E or ES with different affinity
Prefers E: increase Km
Prefers ES: decreases Km
Decreases Vmax
Intersect at point not on either axis on LB plot
Explain the following for uncompetitive inhibition:
- where does it bind
- how does it affect Vmax and Km
- what does its LB plot look like
Uncompetitive inhibitors bind allosteric site, only bind ES
Decreases Km (binds ES) Decreases Vmax
Parallel lines on LB plot
Compare alpha and beta anomers of glucose- what is different about their respective substituents?
Alpha anomer of glucose has the OH group on C1 axial and trans to the CH2OH group
Beta anomer of glucose has the OH group on C1 equatorial and cis to the CH2OH group
What physical property of water allows for sweating to reduce body temperature?
High heat capacity- absorbs a lot of heat that is then evaporated off
Explain why competitive inhibition causes an increased Km and constant Vmax
Ligand analogue binds active site, causing increase in apparent Km—> more ligand needed to get half enzymes full because active sites are being filled
Competitive inhibition can be overcome by high substrate concentration, so Vmax is the same
What is the expression of probability of having 4 children, 2 girls and 2 boys in any birth order?
6 combinations of 2girls/2boys
1/2 chance of having a boy or girl
So each of 6 combinations is (1/2)^4 (4 children)
Multiple events possible (combinations) means adding probabilities
6 (1/2)^4
What does a phosphodiester bond do?
Links 3’ and 5’ carbons of 2 sugars
Do point mutations always affected secondary structure?
No, point mutants do not necessarily affect secondary or tertiary structure
What’s an enol?
C=C and OH group present
How does SDS PAGE work?
SDS detergent equalizes charge, then separates by size
What is ELISA used for?
Immunological technique to identify presence of protein
Hormones are found in low concentrations but have strong effects. Which type(s) of receptors are hormones likely to act on:
- ligand gated ion channels
- enzyme linked
- GPCR
Enzyme linked and GPCR-
For low concentration to have strong effect, need to initiate second messenger cascade with amplification (both of these do this)
In Fischer projections, how do the hydroxides of the highest numbered chiral center differ in D and L sugars?
D sugars: hydroxide of highest numbered chiral center on the right
L sugar: hydroxide of highest numbered chiral center on the left
When converting a Fischer projection to a Hawthorn projection, any group on the right in the Fischer projection…
Groups on the right of a Fischer projection point down in a Hawthorn projection
Which type of glycerophospholipid has a single hydrogen atom as its head group?
- cerebroside
- ceramide
- gangliosides
Ceremides- single H atom as head group
Cerebroside- glycosphingolipid with a single sugar as head group (no net charge at physiological pH)
Ganglioside- sphingolipid with oligosaccharide head group and 1+ NANA (sialic acid), négative charge
What is the structure of steroids?
Three cyclohexane and one cyclopentane
What’s a shortcut to determine if a molecule is polar?
Each polar group “overrules” 5 carbons
True or false: phosphate is nonpolar
FALSE: Phosphate is POLAR
What does a Keq of 1 indicate?
Keq of 1 means free energy change is 0 (delta G = 0)
Why would raising the temperature of a reaction in vivo not help increase reaction rate?
Increasing reaction temperature IN VIVO is not ideal… body needs ideal temp (you’ll kill everything!)
What type of linkage is created in formation of peptide bond?
Amide linkage
Double stranded RNA is marked for degradation. Which of the following strands of RNA would prevent mature mRNA in cytoplasm from being translated?
- identical to mRNA being produced
- antisense mRNA to one produced
- sense mRNA to one produced
Antisense mRNA to one produced- needs to bind mRNA to make it double stranded RNA which will be degraded
Which of the following will be low after an overnight fast? Malate dehydrogenase Glucokinase Alpha-ketoglutarate dehydrogenase Phosphofructokinase-1
Glucokinase
PFK-1 will still be used with other sources of glucose (glycogen, gluconeogenesis)
When fatty acid beta oxidation is active in liver, mitochondrial pyruvate will be:
- carboxylated to phosphoenolpyruvate for entry into gluconeogenesis
- carboxylated to oxaloacetate for entry into gluconeogenesis
carboxylated to oxaloacetate for entry into gluconeogenesis
Patient presents with lysing RBC and Heinz bodies (oxidized hemoglobin). Which enzyme is defective:
- fructose-1,6-biphosphate
- glucose-6-phosphate dehydrogenase
- pyruvate kinase
-glucose-6-phosphate dehydrogenase
Need NADPH from PPP
Name 3 uses for NADPH
Lipid biosynthesis
Bleach formation
Glutathione (ROS protection)
Match structure to link:
Linear, branched
alpha-1,6 and alpha-1,4
Linear- alpha-1,4 glycosidic link
Branched- alpha-1,6 glycosidic link
Match transporter to location and kinetics
GLUT2 and GLUT4
Liver, adipose-muscle
First order, zero order
GLUT2- liver (glucose sensor), first order kinetics (high Km)- not responsive to insulin
GLUT4- muscle/adipose, zero order kinetics (low Km)
What is the rate limiting step of glycolysis
PFK-1
What happens to UDP-glucose in glycogenesis?
Glycogen synthase + branching enzyme create glycogen
What 2 processes maintains blood glucose during fasting
Gluconeogenesis and glycogenesis
What is the net charge on lysine at pH 7.4 if pKa1=2.6, pKa2=9.06, pKaR=10.54?
+1
At this pH, carboxyl group has -1 charge, both amino and R group have +1 charge—> +1 net charge
In an aromatic ring system, each carbon atom must be what hybridization?
Sp2
Needed to be planar, so that each atom will have p orbital available for overlap
Also sp2 has 120* bond angles which reduce ring strain
Given a genome with 50% AT content, the probability of AUUUA sequence is one in every how many nucleotides?
50% AT means 50% GC. 25% (1/4) of having the necessary base at each position. There are 5 nucleotides in this sequence, so it’s (1/4)^5 or 1/1024, or 1 in every 4^5 bases
What are loading controls for in western blots?
Ensure the same quantity of protein was loaded for all samples
Where X represents the conjugate base, which of these acids will have the smallest H-X bond dissociation energy:
Acid A, pKa of 4.10
Acid B, pKb of 10.90
Stronger acids will have smaller dissociation energy
14 = pKa + pKb
So Acid B is stronger because 14-10.90 = 3.10 pKa
If 2 solutions are separated by biological membrane with 100mM Na3PO4 on one side and 200mM NaCl on the other side (with equal amounts of water)- where will water go?
No net movement of water because Na3PO4 has van’t Hoff factor of 1 while NaCl has van’t Hoff factor of 2 (2 ions produced when dissociated)
(Osmotic pressure P=iMRT)
If germ cells of an organism divide without DNA replication that normally occurs before meiosis, what type of chromosome will be found at the metaphase plate during Meiosis I?
DNA replication produces dyads
So this organism will have no sister chromatids- it will have monads on the metaphase plate
How does impurity affect the melting point range?
Lowers and widens the melting point range
Why are glycogen stores in skeletal muscle critical during prolonged exercise?
- myosin hydrolyzes ATP during muscle contraction
- actin requires ATP for polymerization
- exposure of myosin binding site requires ATP
myosin hydrolyzes ATP during muscle contraction
ATP is required for sliding filament model- ATP hydrolysis needed to cock the myosin head, binding of ATP to myosin head necessary to release myosin head from actin filament for next contraction
(Calcium binds troponin to move tropomyosin and expose actin filament binding site)
Following ingestion of meal high in simple carbs, primary metabolic process is:
- glycolysis
- gluconeogenesis
- glycogenesis
Glycogenesis: building glycogen stores
Glycolysis only partially contributes because it shuts down after cell has enough energy
Glycogen built can grow to any size
A women who is a heterogenous carrier for Duchenne MD has a son with a normal man- what is probability son will have MD?
50%
Which of these is true:
- prions can be inherited
- prions can cause pathology outside of the CNS
Prions are usually acquired through food but can be inherited
Only cause pathology within the CNS
After pyruvate enters the mitochondrion via active transport, it is?
Decarboxylated
Oxidized
Both
Via PDH complex in mito matrix
What is pyruvate cleaved into? Is this reversible?
2-carbon acetyl group and CO2
Not reversible (can’t make glucose from acetyl co-A)
Which of these is (are) required for PDH complex?
Vitamin B1
Mg2+
NAD+
All of them
In the formation of acetyl-coA, lipoic acid’s disulfide group acts as a ___ agent, then FAD acts as a ____ agent of lepoic acid
Disulfide groups in lipoic acid act as oxidizing agent to create acetyl group (bonded to lipoic acid via thioester linkage)
FAD reoxidizes lipoic acid for figure acetyl-CoA formation
Because fatty acyl-CoA Cabot cross inter mito membrane, the fatty acyl group is transferred to _____? What kind of reaction is this?
Fatty acyl group transferred to carnitine via transestérification reaction
Alcohol dehydrogenase can convert alcohol to acetyl-CoA, but also causes NADH buildup. How does this effect metabolism?
TCA is inhibited
Acetyl-CoA used for fatty acid synthesis
Why can’t the TCA be run under anaerobic conditions, even if it doesn’t require oxygen?
If ETC isn’t running, NADH and FADH2 build up, inhibit cycle
What’s the rate limiting enzyme in TCA?
Isocitrate dehydrogenase
What’s the difference between a synthase and a synthetase?
Synthetases require significant energy input
Dehydrogenases are a subunit of what type of enzyme?
Oxidoreductases
Transfer hydride ion to electron acceptor
Which provides more ATP?
NADH
FADH2
NADH (2.5 ATP vs 1.5)
In Complex I of the ETC, what does electron transfer occur between?
NADH —> coenzyme Q (ubiquinone)
Which ETC complex is a part of 2 distinct pathways simultaneously?
Complex II, succinate-CoQ oxidoreductase
Part of TCA and ETC
Which ETC complex uses cytochrome c?
Complex III
What is a cytochrome?
Protein with heme group in which iron is reduced to Fe2+ (and reoxidized to Fe3+)
What are the 2 NADH shuttles and which one is more efficient?
Glycerol 3-phosphate shuttle (produces FADH2)
Malate-aspartate shuttle (produces NADH, more efficient)
How does DHAP link glycolysis and fat metabolism?
DHAP is intermediate in glycolysis
Glycerol of triglycerides can be shunted into glycolysis for energy
What happens to long chain fatty acids in micelles?
- diffusion across intestine to lymphatic system
- transport into chylomicrons releases into lymph system
transport into chylomicrons releases into lymph system
True or false: adipocytes cannot undergo gluconeogenesis
TRUE. they cannot
Statin drugs inhibit HMG-CoA reductase. What are they used for?
Hypercholesterolemia
Which is the correct order of fatty acid synthesis?
- activation followed by bond formation, reduction, dehydration, reduction
- two reductions followed by dehydration and bond formation
activation followed by bond formation, reduction, dehydration, reduction
Majority of triacylglycerols stored in adipose originate from
Synthesis in liver
What is hormone sensitive lipase (HSL) used for?
HSL hydrolyzes triacylglycerols
Adipose does not respond directly to glucagon, so HSL is activated by fall in insulin
Lipoprotein lipase (LPL) does what?
Releases free fatty acids from triacylglycerols in lipoproteins
Which lipoproteins have the highest protein to fat ratio?
HDL
“Good”- cleans up excess cholesterol
Which chylomicron delivers cholesterol to tissues for biosynthesis?
LDL
Which shuttle is crucial for cholesterol synthesis?
Citrate shuttle- carries mito acetyl-CoA to cytoplasm (where synthesis occurs)
Fatty acids are long chain ____
Carboxylic acids
Double bonds in natural fatty acids are generally in what configuration?
Cis
What are the 2 major enzymes of fatty acid biosynthesis?
Acetyl-CoA carboxylase (rate limiting)
Fatty acid synthase
What is the rate limiting enzyme in beta oxidation?
Carnitine acetyltransferase I
What are the 4 repetitive steps of beta oxidation?
Oxidation (forms double bond)
Hydration (forms hydroxyl)
Oxidation (of hydroxyl to form carbonyl)
Split (into shorter acyl-CoA and acetyl-CoA)
All amino acids are glucogenic except for:
Leucine and lysine
Why are cells considered closed systems?
Constant pressure and volume —> no work can be done
DeltaU (internal energy) = Q (heat)
Can a reaction with negative deltaS and negative deltaH be spontaneous?
At low temp
deltaG = deltaH - TdeltaS
A spontaneous redox reaction will have a negative deltaG and a (negative/positive) value of E (electromotive force)
Positive value
After a meal, most of the energy needs of the liver are met by…
Oxidation of excess amino acids
Which happens first, gluconeogenesis or glycogenolysis?
Glycogenolysis (almost immediately at beginning of postabsorptive state)
What tissue is least able to change its fuel source in periods of starvation?
RBC- can only use glucose anaerobically
Which work faster, peptide hormones or steroid hormones?
Peptide hormones are fast, rapidly adjust metabolism
Steroid hormones have longer effects by modifying transcription
Which tissues require insulin for glucose uptake?
Adipose, resting skeletal muscle
Muscle cannot release glucose into the blood because it lacks this enzyme:
Glucose-6-phosphate
What effect do catecholamines have on metabolism?
Muscle/ liver glycogenolysis
Adipose lipolysis
After a meal, the liver extracts excess glucose to replenish its glycogen stores. What happens to any remaining glucose in the liver?
Converted to acetyl-CoA for fatty acid synthesis
Which tissue does not prefer glucose?
Cardiac- prefers fatty acids (think prolonged muscle use)
How is respiratory quotient depicted to change when you start exercising?
Approaches 1–> increased use of glucose for energy
RQ = (CO2 produced)/(O2 consumed)
What characteristic makes antioxidants effective?
Low reduction potential, so they can reduce other molecules and become oxidized themselves
Which of these is unique to or shared between fatty acids and triglycerides?
Carboxylic acids
Esters
Carbonyl
Fatty acids- long chain carboxylic acids
Triglycerides- esters
Both- carbonyls
Which amino acid is not chiral?
Glycine- does not have 4 unique substituents (R group is just H atom)
Most L-amino acids are S, but one L-amino acid is R- which one
cysteine (S has higher priority)
What do the amino And carboxylic acid groups look like for isoleucine in its zwitterion form?
NH3+, COO-
In peptide bond formation, the amine group nitrogen acts as ___ while the carbonyl carbon acts as ___
Nitrogen- nucleophile
Carbon- electrophile (on c terminus)
Trypsin and chymotrypsin cleave proteins on what side?
Carboxyl
What is Strecker synthesis?
Form amino acids from aldehydes and ketones (via imine, C=N)
Use KCN or NH4Cl
What reagents can effectively form amino acids from aldehydes and ketones (Strecker synthesis)?
KCN
NH4Cl
What is Gabriel synthesis good for?
Making primary amines using protected amine (phthalimide) in SN2 rxn
Does not undergo over-alkylation
Only works well for primary alkyl halides
How many residues apart are hydrogen bonds in alpha hélices?
4
A-B-B-A where A and A share hydrogen bond
Can you more easily overdose Vitamin D or Vitamin C?
Vitamin D- fat soluble vitamins can be stored and accumulate
Water soluble vitamins are easily excreted
What is the MM equation?
V0 = (Vmax)([S])
——————
Km + [S]
Why are uncompetitive inhibitors uncommon?
Bind only to enzyme- substrate complex
Limited time window
(Decrease Vmax and Km)
When a mixed inhibitor has high affinity for ES over E, it’s acting like what other inhibitor?
Uncompetitive
Decreases Km
When a mixed inhibitor has high affinity for E over ES, it’s acting like what other inhibitor?
Competitive
Increases Km
Prothrombin is an example of what?
Zymogen- inactive enzyme precursor
In a Fischer projection, the hydroxyl group attached to the highest numbered chiral carbon is on the right. What kind is it?
D
Left = L
When differentiating between a reducing and non-reducing sugar, what functional group should you look for?
Aldehyde = reducing sugar (can do redox)
Fatty acids are the only lipids that have what functional group?
Carboxylic acid, -COOH
What’s an easy way to recognize an alpha-1,4 linkage (which glycogen phosphorylase cleaves)?
Remember that glycogen is used for glucose storage- it’s a homopolymer
All monomers will be identical
pKa + pKb =
14
How many protons do NADH and FADH2 pump?
NADH- 10. 4 from complex I, 4 from complex III, 2 from complex IV
FADH2- 6. 4 from complex III, 2 from complex IV
Is anomeric carbon fixed stereocenter or invertible epimer
Anomeric carbon of sugar is invertible epimer
Epimers are beta vs alpha sugar, which anomeric carbon can convert between
Anhydrase =
Removal of water
Enzymes catalyze reactions in both directions (T/F)
TRUE
Kinetic factors determine __
Thermodynamics determine ___
Kinetics- rate of reaction
Thermodynamics- rxn equilibrium
Give graph units for first and second order reaction
First- ln[A]
Second- 1/[A]
What is produced each round of beta oxidation
An acetyl CoA generated each round, fatty acid chain shortened by 2 C
Final round generates 2 acetyl CoA
Odd numbered fatty acid chains cleave 5C chain in final step into acetyl CoA (2C) and succinyl CoA (3C)
Difference between prosthetic and coenzyme groups
Prosthetic tightly/ covalently bound
Coenzymes loosely bound
Name 3 major mechanisms of controlling blood pH (increasing blood pH)
- Exhale CO2
- Conversion of CO2 into HCO3- (bicarbonate, buffer system)
- Exertion of blood through kidneys
What effect will releasing H3PO4 (phosphoric acid) in blood have
Decrease blood pH
Dissociâtes into H2PO4- and H+, further dissociates into HPO4^2- and H+
T/F calcium is necessary for blood clotting
TRUE
What’s used as template during DSB repair
Sister chromatid
Can’t use template strand because in DSB both strands are damaged
Is amino or carboxyl terminus translates first
Amino
Translation is 5’-3’ and amino terminus is at 5’ end
Which will never affect reaction rate?
- putting reactants into aqueous solution
- increasing pressure in closed container
- removing product of irreversible reaction
removing product of irreversible reaction
Rate law doesn’t depend on concentration of reactants
What chemical mechanism allows biochemical reactions to proceed despite positive deltaG*’ values?
Reaction coupling
What does deltaG*’ represent
Free energy change of proceeding from standard state concentration to equilibrium
deltaG =
deltaG*’ =
deltaG = deltaG*’ + RTlnQ
deltaG*’ = -RTlnKeq
Because at equilibrium, Q=Keq and deltaG=0
If Keq=1, deltaG*=
0
deltaG*’ = -RTlnKeq
ln(1)=0
If Q=1, deltaG*=
DeltaG* = deltaG when Q=1
deltaG = deltaG*’ + RTlnQ deltaG*’ = -RTlnKeq
T/F: substrate level phosphorylation must be coupled to an exergonic reaction
TRUE
Irreversible enzymes of glycolysis
Which is committed step
- Hexokinase
- PFK1 (phosphofructokinase)
- Pyruvate kinase
PFK1 is committed step
How does DHAP become incorporated into glycolysis?
Dihydroxyacetone phosphate (DHAP) —> glyceraldehyde 3-phosphate
Via enzyme triose phosphate isomerase
How is glycogen funneled into glycolysis?
Glycogen phosphorylase produces glucose 1-phosphate
Phosphoglucomutase converts glucose 1-phosphate to glucose 6-phosphate, which is funneled into step 2
How is fructose funneled into glycolysis? Say how for both muscles/kidneys and liver
In muscles and kidneys, hexokinase converts fructose to fructose 6-phosphate, which is then funneled into 3rd step of glycolysis
(After glucose 6-phosphate converted via isomerase to fructose 6-phosphate)
In liver, fructokinase converts fructose to fructose 1-phosphate, then an aldolase converts it to glyceraldehyde 3-phosphate and DHAP (DHAP funneled in by triose phosphate isomerase)
What makes ethanol fermentation unique to lactic acid fermentation
Carbon skeleton changes
Pyruvate (3C) broken to ethanol (2C) and CO2
Irreversible steps of gluconeogenesis
Glucose 6-phosphatase
Fructose 1,6-biphosphatase (F-1,6-BP)
Phosphoenol pyruvate (PEP) carboxylase (+GTP)
Pyruvate carboxylase (+ATP) produces oxaloacetate
Major products of pentose phosphate pathway
NADPH
ribose 5 phosphate
What are the 3 destinations of pyruvate
PDH complex —> acetyl CoA
Lactate dehydrogenase —> lactate
Pyruvate carboxylase —> oxaloacetate (gluconeogenesis)
Where are 3 places you can get acetyl CoA
PDH complex
Beta oxidation
Amino acid metabolism
Where are the 3 places that produce NADH in TCA?
Isocitrate -> alpha ketoglutarate via isocitrate dehydrogenase (CO2 produced here too)
Alpha ketoglutarate -> succinyl CoA via alpha ketoglutarate dehydrogenase complex (CO2 produced)
Malate -> oxaloacetate via malate dehydrogenase
Where are GTP and FADH2 produced in TCA? (Hint: back to back)
Succinyl CoA -> succinate produces GTP
succinate -> fumarate produces FADH2
Each NADH produces how many ATP, what about FADH2
NADH- 3 ATP
FADH2- 2 ATP
What happens in malate aspartate shuttle
Why do we need it
What anti porter and other shuttle is involved in this cycle
NADH can’t pass through inner mito membrane
NADH donates 2 e- to oxaloacetate, converting it to malate. Malate enters matrix via
Malate alpha-ketoglutarate anti porter
Converted back to oxaloacetate in matrix and NADH generated
Oxaloacetate converted to aspartate and goes back to cytosol via glutamate-aspartate shuttle
Why is glycerol 3 phosphate shuttle less favorable than malate aspartate shuttle
What does it do
NADH donates 2 e- to DHAP to form glycerol 3-phosphate. In the mito matrix G3P turned back into DHAP and e- go to FAD to make FADH2
Less efficient because it makes FADH2 instead of NADH
What does carnitine shuttle transport
Carnitine acyltransferase attaches fatty acyl group from acyl-CoA to hydroxyl group of carnitine
To get fatty acids through inner mito matrix for beta oxidation
What does citrate acetyl CoA shuttle (tricarboxylate transport system) do?
Acetyl CoA in mitochondria are used for fatty acid synthesis in cytosol but can’t pass membrane
Acetyl CoA combines with oxaloacetate to form citrate which passes through membrane and is converted to oxaloacetate and acetyl CoA in cytosol
How do peroxisomes aid in fat metabolism
Extra long chain fatty acids are catabolized to smaller pieces here
What does beta oxidation require, and what does it produce?
Requires: 1 FAD, 1 H2O, 1 NAD+, 1 CoA-SH
Produces: 1 FADH2 (2 ATP), 1 NADH (3 ATP), 1 acetyl CoA (12 ATP)
How many cycles of beta oxidation require for 14-C FA? For 17-C FA?
14-C: divide by 2, subtract 1–> 6 rounds
17-C: 7 rounds, odd numbered C uses last 5 C to make acetyl CoA (2C) and succinyl CoA (3C)
What type of enzyme is used for oxidation of odd numbered FA?
Isomerase (enoyl-CoA isomerase)
Catalyzes movement of double bond to 2-3 position
4 steps of beta oxidation
Dehydrogenation
Hydration
Dehydrogenation
Thiolase (cleavage)
Which of these ketone bodies CANNOT be used for energy by the heart and the brain?
Acetone
Acetoacetate
3-hydroxybutyrate
Acetone CANNOT be used for energy
Transamination in protein metabolism
Exchange of amine group of one molecule for a carbonyl group on another
What fuel does heart prefer
Fatty acids
Like the endurance muscle it is
Can use ketones in fasting
Primary location of FA synthesis
Source of acetyl CoA?
Cytosol of liver cells
Always makes 16-C palmitic acid
Citrate shuttle provides acetyl CoA
Steps of FA synthesis
Condensation
Reduction
Dehydration
Reduction
Which provides more energy, glucose or glucose 1-phosphate?
G1P is product of glycogenolysis. G1P is converted to G6P (via phosphoglucomutase) and funneled into glycolysis. This skips the first step which requires ATP (glucose to G6P via hexokinase- the investment step)
So G16 is more efficient
Which requires ATP:
Alcohol dehydrogenase
Decarboxylases
Phosphofructokinase
Phosphofructokinase
Kinases needs ATP for phosphorylation
Other two options use NADH
Where does oxidative phosphorylation occur
Inner mitochondrial membrane and matrix to a degree (O is final e- acceptor, in matrix)
NOT intermembrane space
Where is coenzyme Q in ETC
Complex I gives e- from NADH to coenzyme Q (via NADH dehydrogenase)
Where does TCA take place
Mitochondria
Which of these is endergonic Glycolysis Gluconeogenesis Glycogenolysis Glycogen synthesis
Gluconeogenesis- requires coupling to ATP hydrolysis
How does insulin affect GLUT2?
Not directly. GLUT2 (liver and pancreas) is bidirectional glucose transporter- requires glucose release via gluconeogenesis at same time as glucose uptake towards glycolysis
What molecule connects glycolysis and PPP
Glucose 6-phosphate
What percentage of beta oxidation is redox reactions?
50%
- Dehydrogenation (oxidation)
- Hydration
- Dehydrogenation (oxidation)
- Thiolysis
When comparing 2 LB plots, enzyme that produced steepest slope will have:
Higher Km value, low Vmax value
Slope is Km/Vmax
How do peptide bonds form
Amino terminus of one amino acid attacks carbonyl terminus of another
Only amino acid without chirality center
Glycine (just an H R group)
Atomic oxygen is not found naturally because it is a free radical. It has 8 electrons. Why is it a radical?
E- configuration of oxygen:
1s2 2s2 2p4
4 e- in p orbital.
2 will be paired in -1
1 will be in 0
1 will be in +1
These unpaired electrons are free radicals
All monosaccharides are reducing sugars?
TRUE
T/F: a reaction step that follows second order kinetics MUST have only 2 reactants
TRUE
Oxidation number of C in
(NH2)2CO
N is -3 (look at periodic table)
2 x -3 = -6
H is +1
4 x 1 = 4
Oxygen is -2
-6+4-2 = -4 for carbon
For a buffer, the pH varies LEAST where?
Around the pKa
So a triprotic acid could be a buffer over several pH ranges because of 3 pKa’s
On a globular protein, where will leucine and phenylalanine each be?
Both interior- Hydrophobic side chains
Which will have a lower melting point, valine or ethanol?
Ethanol
Valine CAN hydrogen bond because of amino and carboxyl groups
And valine is bigger then ethanol
When tittering HCl with NaOH, what pH range should the indicator transition?
Strong acid + strong base will neutralize around pH7
Indicator for titration should have transition range around equivalence point
Uracil is purine?
FALSE. Uracil is pyrimidine
Can you separate enantiomers by physical properties?
NO- same physical properties, just polarize light in opposite directions
What is Ksp expression for
Ca3(PO4)2
Ksp = [Ca2+]^3[PO4]^2
How will an isotope differ in electron configuration?
It won’t
The only elements that are exceptions to filing order in electron configurations
Transition metals
solvents should solubilize all compounds of reaction, and can also act as reagents of reaction. How could you tell if a solvent acts as a reagent? how could you tell if it acts as a catalytic base?
if solvent is used as reagent, its functional groups will be present in products
if solvent acts as catalytic base, reaction will begin with abstraction of a proton
pKa 1 represents __
pKa1 represents __
pKa1 = carboxyl pKa2 = amino
on LB plot, inverse of x-intercept represents
Km
intravenous sucrose (C12H22O11) solutions contain 0.34 mol of sucrose per liter. how many grams of sucrose are in 500mL (MW sucrose ~350g/mol)
- 34mo/L = 0.17mol/0.5L
0. 17mol/0.5L x 350g/mol = 60g / 500mL
pKa of citric acid 3.13, what is pH of buffer made of 0.005M citric acid and 0.5M sodium citrate?
pH = pKa + log[base/acid] pH = 3.13 + log[0.5/0.005] pH = 3.13 + log(100) pH = 3.13 + log(1x10^2) pH = 3.13 + (2) = 5.13
how to find enthalpy change of a reaction
enthalpy change of rxn = enthalpy(products) - enthalpy (reactions)
if Ksp of Cu2S is 5x10^-29, what is [Cu]?
Ksp = [Cu2+]2[S2-] = (2x)^2(x) = 4x^3 5x10^-29 = 4x^3 (->divide by 4) 12.4x10^-30 = x^3 cube root of 12.5 somewhere between 2 and 3 x ~ 2.3x10^-10
what does Keq < 1 mean
Keq = kforward/ kreverse
Keq < 1 means reverse rate is larger than forward rate
how can you tell if a sugar is the beta anomer
all substituents are equatorial
on a cyclic sugar, which is C1 and which is C6
C1 is CW to ring oxygen C6 is CCW to ring oxygen
which is least likely to form ionic bond: iron, sodium, helium, magneisum
helium- noble gas
compare position of oxygen on anomeric carbon in alpha and beta anomers
beta- anomeric C on same side of ring as CH2OH
Alpha- anomeric C Anti to CH2OH
break starch down to its smallest component
starch (poly) - > maltose (di) -> glucose (mono) via pancreatic amylase
lactose and its linkage
lactose = galactose + glucose
beta linkage
exception to the rule that humans cannot hydrolyze beta-linkages (via lactase)
explain how to go from Fischer to Hawthorn projection
all groups on RIGHT are DOWN
all groups on LEFT are UP
NEXT TO LAST C (on bottom of Fischer) isn’t included because this hydroxyl becomes ring oxygen upon closure
facilitated diffusion uses or releases energy?
releases. molecule moves down concentration gradient and does not require energy
how does partial pressure of oxygen at high altitude vary, and how does this affect blood pH?
partial pressure of O is reduced at high altitude
does not directly affect blood pH
might make you breathe rapidly, which would cause you to blow of CO2 and blood would become more basic (but this is indirect)
acetycholinesterase does what?
catalyzes hydrolysis of ester functional group
ATP is an effective source of energy coupling because hydrolysis of phosphoanhydride bond occurs at low energies. why?
resonance stabilized
how can there be 63 codons and only 20 amino-acyl tRNA synthase enzymes?
- wobble allows for +1 amino acids to be paired to same tRNA molecule
- wobble allows for same amino acid to be paired with +1 tRNA molecule
wobble allows for same amino acid to be paired with +1 tRNA molecule
same amino acid can be loaded onto multiple tRNA molecules with different anticodons
bonds of cellulose
beta(1-4), why we can’t digest it
only beta sugar we can digest is lactose
why does Bohr effect cause more oxygen to be released in active muscle tissue?
- active muscle consumes CO2, causes local decrease in pH
- active muscle produces CO2, causes local decrease in pH
- active muscle produces CO2, causes local increase in pH
- active muscle consumes CO2, causes local increase in pH
active muscle produces CO2, causes local decrease in pH
TCA produces CO2, which shifts bicarbonate equilibrium left towards H+
decrease in pH leads to decreased affinity for O2, facilitating oxygen release
what is the purpose of washing with cold solvent in recrystallization
removes soluble inpurities
which of these amino acids is nonpolar: T Q F S
T = threonine = polar Q = glutamine = polar F = phenylalanine = nonpolar S = serine = polar
in muscles, action potential triggers calcium channels to open in ___
sarcoplasmic reticulum
D and L convention, and how to distinguish
D/L distinguishes enantiomers of chiral monosaccharides and amino acids
most oxidized position at top, D will have OH on right, L will have OH on Left
stearic acid is C17H35CO2H requires how many beta oxidation steps
18 C total
(18/2)-1 = 8 rounds
what does increase in Km indicate when an inhibitor is present
inhibited binding, decreased substrate binding
Zn2+ forms quaternary coordination compound- what is bond angle?
quaternary = tertiary = 109.5*
octahedral = 90*
trigonal planar = 120*
what do NADH/NADPH donate
hydride ions (H-)
what does SDS page do
coats proteins in negative charge so they migrate towards positive terminal
it’s also a pseudo detergent, so it will denature noncovalent bonds but covalent bonds (so not disulfide bonds)
once all proteins are negatively charged, separation will be based on size of protein only
what direction does gel electrophoresis run
negative to positive (proteins coated in negative charge by SDS page or other substance)
carboxylation often use which cofactor
biotin
buildup of AMP would:
decrease rate of triacylglycerol synthesis
increase rate of enzymatic breakdown of triacylglycerol?
buildup of AMP would decrease triacylglycerol synthesis (enzymatic breakdown doesn’t involve phosphate group transfers)
myelin acts as conductor T/F?
FALSE: myelin is insulator (from outside of axon)
how do fat soluble vitamins travel through body
DEAK: fat soluble vitamins
travel attached to binding protein (does not need vesicle because it can freely diffuse through cell membrane)
compare roles of PCT and DCT
PCT- reabsorption of caloric substances (glucose, amino acids, proteins) and secretion of non-ionic substances
DCT- concentration of urine, some ion regulation (acid-base)
T/F PPP is stimulated by NADPH
FALSE, PPP generates NADPH from NADP+
what types of vascular are low pressure systems
capillaries and veins
heterozygote advantage
tendency of carrier of dangerous condition to have survival advantage
ex- sickle cell anemia conveys advantage to malaria
substituent of sphingomyelin?
phosphocholine
what causes menstruation, what causes ovulation?
ovulation (day 14)- LH surge
menstruation (end and beginning)- period of lowest FSH/LH secretion
aspartate transaminase
transfers amino group to alpha-ketoglutarate to form glutamate and oxaloacetate
muscarinic acetylcholine receptors
throughout CNS and postsynaptic parasympathetic nervous system
only two amino acids that are ketogenic but not glucogenic
leucine and lysine
what do molecule scavengers do
inhibit, like sponges- consume molecule
if mitochondria is malfunctional, how will CO2 concentration in cell change
will rely on anaerobic metabolism- glycolysis
decrease in CO2 because CO2 is product of TCA, which is part of aerobic respiration (takes place in mito matrix)
Triglycerides undergo base-catalyzed transesterification with either methanol or ethanol, involving:
a. Attack of carbonyl carbon by alcohol proton
b. Attack of carbonyl carbon by methoxide or ethoxide ion
b. Attack of carbonyl carbon by methoxide or ethoxide ion-> correct. During transesterification, base extracts a proton to generate RO- ion (methanol-> methoxide or ethanol-> ethoxide). RO- ion is nucleophile that attacks carbonyl carbon. Product is 3 fatty acid esters and glycerol
(a not correct because protons are not nucleophiles capable of attacking a carbonyl)
adrenal medulla releases ___ hormones, posterior pituitary releases ___ hormones
adrenal medulla- steroid
posterior pituitary- peptide
state of amino acids at physiological pH
carboxylic acid deprotonated, amine group positively charged, net charge of 0
to do RT-PCR, you need to lyse the cells, then:
isolate and stabilize genomic DNA
or
isolate and stabilize RNA, and generate cDNA
isolate and stabilize RNA, and generate cDNA
its RT-PCR! so RNA is reverse transcribed to form cDNA, upon which PCR is performed
which is true in skeletal muscle:
- reduced ATP results in high intracellular Ca2+
- Ca+ binds calmodulin
- shorter sarcomere length is stronger contraction
only true that reduced ATP results in high intracellular Ca2+–> persistent contraction
(Ca2+ binds calmodulin in cell signaling, but not in muscles- binds troponin)
(sarcomere length follows length-tension relationship, if it’s shorter there’s less space to create potential energy by overlap)
exogenous corticosteroids would do what to the hypothalamic-pituitary-adrenal axis?
decrease CRH (hypothalamus) and ACTH (anterior pituitary) due to negative feedback
where does FADH2 donate its electrons in the ETC
ubiquinone (CoQ)
what effect will changing FA tails in bilayer from saturated to unsatruated?
kinks due to unsaturation increases membrane fluidity and decreases melting point because they can’t pack as tightly
how many calories do you get per gram of carb, protein, fat?
carb- 4kcal/g
protein- 7kcal/g
fat- 9kcal/g
