Final Exam Flashcards
citric acid cycle products
3 NADH, 1 FADH2, 1 GTP/ATP, 2 CO2
regulatory enzymes in citric acid cycle
isocitrate dehydrogenase (+ for ADP, - for NADH and ATP)
alpha-ketoglutarate dehydrogenase (- for NADH, ATP, succinyl CoA)
high succinyl coA will slow down…
ETC
dehydrogenase catalyzes…
an oxidation step
oxidation steps in citric acid cycle
4; 1 produces FADH2, 3 produce NADH
high ADP means energy is…
low
can i keep selling seashells for money officer?
pneumonic for citric acid cycle
acetyl-CoA starts the…
citric acid cycle
dehydrogenases in citric acid cycle
I AcKnowledge, SUCky Men
Isocitrate
Alpha-Keto
SUCcinate
Malate
ETC: 1 NADH creates…
2.5 ATP
ETC: 1 FADH2 creates…
1.5 ATP
proton gradient from ETC is in…
intermembrane space
NADH and FADH2 comes from…
mitochondrial matrix
complex I
NADH
complex II
FADH2
what happens to electrons as they pass through ETC?
they become lower and lower in free energy hence why they are passed on
final electron acceptor
removes low energy electron and binds them to free H+ to form water
synthesis of ATP in mitochondria is driven by…
a protein gradient
reoxidation of NADH and FADH2 indirectly creates a protein gradient
ATP synthase
“complex V”
carnival ride (subunit C) - loads H+ and rotates to power the rest
beta subunit - ATP produced
alpha subunit - stabilize the beta subunits
loose: ADP and inorganic phosphate (Pi) are mingling (ADP + Pi)
tight: ADP and Pi bind to produce ATP
open: ATP released
conformations change by rotating of the gamma stalk caused by rotating of C subunit
stator
holds ATP synthase in place
E cell
E red - (E ox)
PLUG IN AS GIVEN
what is oxidized? what is reduced? spontaneous reaction?
OIL RIG - use this to figure out what goes on which side of balanced equation
pick the half reaction with more negative potential (lower E value) will be oxidized
greater E value will be reduced
g deg: phosphorylase action
MAIN ENZYME: asdjfa;dkj
cleaves alpha 1,4 linkages and creates glu-1-phosphate
will cleave 7-8 glucose monomers (whatever is 4 monomers away from the branch)
glu-1-phos –> glu-6-phos by phos
phosphoglucomutase
g1p –> g6p
branch of glycogen
alpha 1,6 linkage
g6p + water
glucose + inorganic phosphate
once glycogen cleaved by g1p…
4 glucose monomers still attached - NOT wanted!
transferase! takes 3 from the end and puts on end of glycogen chain
alpha 1,6 glucosidase cleaves using water to create FREE GLUCOSE with the one that remained after the transferase passed through
after degradation, phosphorylase…
keeps cleaving the glycogen chain until it reaches the core
glycogen synthesis
MAIN ENZYME: glycogen synthase
first, need to activate! with UDP glucose (glucose + UTP = UDP)
synthase transfers glucose from UDP glucose onto growing chain
glycogenin is the CORE - autoglycosylation can also transfer glucose (essentially, can participate in chain elongation)
adds 7-8 monomers to core
long chain isn’t convenient!! we must branch
branching enzyme! takes added glucose monomers and creates alpha 1,6 linkage to the 4th carbon from the right end of the core
next branching point much be at least 4 units away from the last branching points
a to b
covalent modification (something is getting phosphorylated)
T to R
allosteric modification (something about external factors will affect being pushed into these states)
most active
phosphorylase a (phosphorylated) in R state
least active
phosphorylase b in T state
T state
active site is covered
phosphorylase b
not phosphorylated
liver is source of…
glucose mobilized between meals; liver stores glucose
phosphorylase a is dominant
muscle…
energy reserve for muscle control; muscle CANNOT supply glucose because it does not contain glucose-6-phosphatase
phosphorylase b is dominant
high conc of glucose reverts…
R to T state since a high conc of glucose means that the liver doesn’t need to call on glycogen stores
high AMP means we need energy
R state which pushes forward glycogen degradation
high ATP means…
energy is needed
what does protein kinase A do?
phosphorylates!!
reciprocal regulation of glu deg and syn
protein kinase A and protein phosphatase 1
protein kinase A
phosphorylates through turning on kinases
glycogen phosphorylase (b–>a)
glycogen synthase (a–>b)
starts the breakdown of glycogen because we need energy in the form of free glucose
phosphorylase <3 phosphorylation
protein phosphatase 1
dephosphorylates!
glycogen phosphorylase (a–>b)
glycogen synthase (b–>a)
starts glycogen synthesis to make glycogen and remove stores of free glucose
hormones
act on kinases
insulin
means high glucose level
start glucose synthesis
glycogen synthase kinase!! will become inactivated when insulin is high to produce glycogen to keep synthase in the a state
inactivated by covalent modification through phosphorylation
glucagon and epinephrine
send out same signal
low glucose level (glucose is gone)
phosphorylatine
activates phosphorylase kinase BUT inactivates
glycogenesis enzymes
glycogen synthase
branching enzyme
glycogenolysis
glycogen phosphorylase
transferase
alpha 1,6 glucosidase
PPP phases/products
phase 1: oxidative phase - make NADPH
phase 2: non oxidative phase - makes 5C sugars (ribose-5-phosphate)
mode 1
when we need ribose 5 phosphate MORE than NADPH
non-oxidative phase
cell division since r5p is needed MUCH more
mode 2
need ribose 5 phosphate and NADPH equally
oxidative phase then an isomerase to transform ribulose to ribose
ex: when cell is rapidly dividing since r5p is needed for nucleotide materials and NADPH for biosynthetic needs - would more need r5p MORE but still “equal” - acceptable answer according to labrake
mode 3
need lots of NADPH»_space; r5p
oxidative state - easy
isomerase will create r5p but we do not need it!
end up with glycolysis intermediates that can go into further oxidative steps go into gluconeogenesis (??)
repeat until cell is happy
needed when synthesizing fatty acids
mode 4
need NADP and ATP
oxidative state
glycolysis intermediates and go forth with glycolysis
will create pyruvate for citric acid cycle and electron transport chain to make ATP
needed during oxidative stress
NADPH
reduces reactive oxidative species
PPP effectors
NADP+ (+)
fatty acid acyl CoA (-)
NADPH (-)
first step of PPP
dehydration of glucose-6-phosphate
how much more ATP is generated from glucose-6-phosphate, compared to glucose, when it is metabolized by the glycolytic pathway?
1
glycolysis: 4 ATP products- 2 ATP react = 2 net ATP
starting at g6p: 4 - 1 = 3
therefore 1 more is generated
why? we skip the first reaction that takes an ATP (????)
glutathione protects against
reactive oxidative species
fatty acid synthesis
- transport from mitochondria: acyl-conitine
- activation
acc1 and 2
regulated covalently and allosterically
acc1
cytosol
acc2
mitochondria
inhibition of acc2 will…
push forward beta oxidation; therefore, negative effectors of acc2 will push it forward
fatty acid synthesis
acetyl coA in mitochondria is converted to citrate and transported to cytoplasm where it is reconverted
insulin dephos….
acc1 and acc2 become active
activation of FA
acyl-coA synthetase - ATP is required
steps of beta oxidation
oxidation
hydration
oxidation
thiolase
products of beta oxidation
1 nadh, 1 fadh, 1 acyl coa
example where glucose in the body is low: prolonged starvation
ketone bodies can be used as alt source of energy!
especially important for the brain!
keto diet is meant for epilepsy
nutritional ketosis
not that bad but can’t last forever because it makes the blood acidic
ketoacidosis
dangerous for individuals with type 1 diabetes
which ketone body contributes the most energy
3-hydroxybutyrate
complex that does not contribute to proton gradient
complex ii
ribosome
site of protein synthesis
mitochondria
generates energy
cytoplasm
solution of water, nutrients, and proteins
nucleus
controls and regulates the activity of the cell
types of intermolecular forces present between h and o
van der waals forces, dipole-dipole, hydrogen bond
hydrogen bonds
special type of dipole-dipole attraction between molecules, NOT a covalent bond to a hydrogen atom
hydrogen bond acceptor
atom, ion, or molecule component of a hydrogen bond which does not supply the bridging hydrogen atom
amino group
nitrogen atom bonded to two hydrogen atoms
hydroxyl group
-OH
phosphate group
phosphorus atom bonded to four oxygen atoms
weak acids
weak acid with the lower pH will dissociate to a greater extent in water than the other acid
effective buffering range
+/- 1 of the pKa
ex: if the pKa = 6.5 and the effective buffering range is pH 5.5 to pH 7.5
at physiological pH, the carboxylic acid group of an amino acid will be _____, while the amino group will be _____, yielding the zwitterion form
deprotonated, protonated
what happens when proteins fold into their native conformation?
most of the non-polar, hydrophobic amino acid residues are found buried in the protein core
most of the polar, charged, and hydrophilic residues are found on the exterior surface of the protein
proteins adopt their lowest energy state form
secondary protein
folded regions stabilized by backbone hydrogen bonding
primary protein
sequence of amino acids
quaternary protien
association of several protein chains
tertiary protein
three-dimensional shape of the protein stabilized by side chain interactions
the amino acid side chain residues in an alpha helix point _____ from the center of the helix
outward
motifs and domains of proteins
separate proteins with similar domains are likely to have similar functions
what structure does myoglobin have?
tertiary
lyase
can catalyze reactions that link two compounds together through the formation of a new chemical bond and without the use of water
Km in the Michaelis-Menten equation
equal to the [S] (substrate concentration) required to achieve 1/2 Vmax
on a lineweaver-burk plot, what does the x-intercept represent?
-1/Km
transferase
catalyze the transfer of groups among substrates
isomerase
catalyze conversion between isomers
oxidoreductase
catalyze redox reactions
hydrolase
catalyze hydrolysis reactions
ligase
catalyze synthesis reactions between substrates
deltaG of a spontaneous reaction is…
< 0
how do enzymes speed up reactions?
they lower the activation energy of the reaction
as Km increases, the measured affinity of an enzyme for its substrate will…
decrease
what rate constant is negligible when measuring the initial velocity of an enzyme-catalyzed reaction?
k-2
ideal enzyme characteristics
small Km and large kcat
what amino acid performs the nucleophilic attack in the chymotrypsin mechanism?
Ser
the binding of a competitive inhibitor to an enzyme will cause the Vmax to _____ and the apparent Km to _____
remain unchanged, increase
in hemoglobin, the heme group is _____ when oxygen is bound
planar
competitive inhibitor
reversible inhibitor that binds the active site
how do uncompetitive inhibitors alter the kinetics of an enzyme-catalyzed reaction?
decreased Vmax and decreased Km
chymotrypsin mechanism (general)
deprotonation of Ser by His
nucleophilic attack by Ser
cleavage of peptide bond
deprotonation of water by His
Ser acts as leaving group and is cleaved from peptide fragment
diffusion of peptide fragment out of active site
how does the oxyanion hole stabilize the tetrahedral intermediate?
hydrogen bonding with the backbone of the peptide chain
myoglobin characteristics
acts as oxygen storage in tissue
has a higher affinity for oxygen than hemoglobin
hemoglobin characteristics
acts as an oxygen transporter in the blood
exhibits cooperativity
has quaternary structure
positive hemoglobin effectors
carbon monoxide
oxygen
negative hemoglobin effectors
2,3-BPD
carbon dioxide
hydrogen ions
according to the bohr effect, as the concentration of carbon dioxide increases, the concentration of H+…
increases
the oxygen binding curve for fetal hemoglobin lays ______ adult hemoglobin
to the left of
what molecules can form hydrogen bonds?
nitrogen, oxygen, or fluorine in the form of covalent compounds
substitution of leucine for which of the following amino acids would be least likely to have an observable effect on the activity and structure of a protein?:
valine
arginine
tryptophan
glutamic acid
valine
enzymatic catalysts affect ______ of a chemical reaction
only the rate
michaelis-menten equation
Vo = Vmax*[S] / (Km + [S])
what exerts its effects on hemoglobin by forming a carbamate ion when combined with the N-terminus of the globin chains?
CO2 (carbon dioxide)
what amino acid increases the basicity of His in the catalytic triad of chymotrypsin?
Asp
based on the mechanism of chymotrypsin, it would best be categorized as which class of enzyme?
hydrolase
globular protein that performs its biological function as a single independent polypeptide chain
myoglobin
its tertiary structure is stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain
it could contain α-helices that are stabilized by hydrogen bonding
non-covalent forces are the primary source of stability for the secondary and tertiary structure
tyrosine and tryptophan are less hydrophobic when compared to phenylalanine because…
phenylalanine lacks a polar group in its side chain
kcat
represents the turnover number
can be calculated by Vmax/[E]total
which of the following statements best describes the thermodynamics of protein folding as it nears its native state?
protein folding is primarily driven by the aggregation of hydrophobic residues in an aqueous solution
a research study finds that inducing severely low blood phosphate levels in rats decreases the release of oxygen from the hemoglobin in red blood cells (RBC) to their tissues. which of the following conditions will most likely cause the same physiologic effect on hemoglobin oxygen release as seen in the study?
exposure to carbon monoxide
in hemoglobin, the ________ stabilizes oxygen when it is bound and protects the iron from oxidation in the absence of oxygen
distal histidine
substitution of which amino acids for Gly and Ser in the oxyanion hole of chymotrypsin would preserve the function of the oxyanion hole? ignore any changes to the overall structure and folding of the protein that may be caused by substitutions
any amino acid may be substituted
slope of a lineweaver-burk plot
Km/Vmax
the interior of an alpha helix contains ________________
atoms from the protein backbone in close contact
anomeric carbon
the one with the double bond to oxygen and next to the carbon that is next to the end -OH
triacylglycerol formation
droplets
carbohydrate definition
1 carbonyl group and 2 hydroxyl groups
enantiomers
nonsuperimposable mirror images
alpha linolenic acid
humans can convert this into EPA and DHA; ALA is essential because we cannot synthesize it
saturated fatty acids
solidifies easily, relatively high melting temperature
dispersion forces occur in nonpolar condensed form
need electron clouds to be close in space to get dispersion forces
what types of bonds exist in glycogen?
alpha 1-4 and 1-6 bonds only
anomers
subtype of diastereomers that differ at a new asymmetric carbon atom formed on ring closure (anomeric carbon)
glucose is a _______ sugar
reducing
proteoglycans
polysaccharide w/ small protein core that is covalently linked with N or O glycosidic bonds (around 5% protein)
how is deoxyribose different from ribose?
deoxyribose has one less oxygen atom
wax
long chain fatty acid esterified to long chain alcohol
what factors determine the melting point of fatty acids?
the number of double bonds (sites of unsaturation)
free fatty acid formation
micelle
phospholipid formation
phospholipid bilayer; bilayer formation is largely driven by the hydrophobic effect
isomers
same molecular formula but different structures
constitutional isomers
differ in the order of attachment of atoms
stereoisomers
atoms are connected in the same order but differ in spatial arrangement
diastereomers
isomers that are not mirror images
epimers
subtype of diastereomers that differ at one of several asymmetric carbon atoms
anomeric carbon
the new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form; ether linkage
only ring carbon covalently attached to 2 oxygen atoms
pyranose
carbohydrates that have a chemical structure that includes a six-membered ring system consisting of five carbon atoms and one oxygen atom
furanose
carbohydrates that have a chemical structure that includes a five-membered ring system consisting of four carbon atoms and one oxygen atom
alpha form
hydroxyl at C-1 is below the plane of the ring
beta form
the hydroxyl at C-1 is above the plane of the ring
glycosidic bond
linkage between monomer units
O-glycosidic bond
bond formed between the anomeric carbon atom and a hydroxyl group of another molecule
N-glycosidic bond
bond formed between the anomeric carbon atom and an amine
what kind of bond do carbohydrates form with phosphates?
ester linkages
fucose
one of few biological molecules active in the L-state
common to add on to obtain new properties due to its interesting structure
glycoproteins
mostly protein
examples: antibodies or membrane proteins w/ bound oligosaccharides for some kind of cell-cell signal
mucins
glycoprotein that is about 1/2 protein and polysaccharide
how are carbohydrates attached in all glycoproteins?
attached to the nitrogen atom in the side chain of Asn (N-linkage) or to the oxygen atom of the side chain of Ser or Thr (O-linkage)
fatty acid nomenclature
18:3(delta^9,12,15)
18: number of carbons
3: number of double bonds (unsaturated sites)
9, 12, 15: carbons where double bonds are; start count at C-1 (anomeric carbon)
omega nomenclature
18:3(omega^1,3,6)
18: number of carbons
3: number of double bonds (unsaturated sites)
1, 3, 6: carbons where double bonds are; start count at end of carbon chain (opposite C-1)
unsaturated fatty acids
acyl chains are liquid and solidify at relatively low temperature
no/low dispersion forces so cannot pack tightly together
triacylglyerol
storage form of energy
typically saturated but can be unsaturated
glycerol + 3 fatty acids
glycerol
three-carbon alcohol to which fatty acids are covalently bonded to make fats
why are triacylglycerols contained in adipocytes?
free fatty acids are charged and need a safe way to be stored
simple hydrolysis/dehydration is used to store molecules
phospholipid components
fatty acids (2+), a platform, a phosphate, and an alcohol
platforms: glycerol or sphingosine
sphingosine
palmitate + serine
backbone: CH - CH - CH2
head group: OH
amine group: site of attachment for the fatty acid that will get swapped out
cholesterol
most common steroid that plays a role in maintaining membrane fluidity
structure of steroids
3 cyclohexane rings and 1 cyclopentane ring
transverse diffusion
outer to inner layer; flip-flop, very slow, requires enzyme (flipases)
lateral diffusion
movement within the same layer; rapid
integral membrane protein
can be used for signaling; extends through all or part of membrane/can form a tunnel
tend to have a higher concentration of hydrophobic amino acids on their surface
peripheral membrane protein
attaches only at surface of the membrane
anchored proteins can exist (anchored via lipid and covalent bond)
can move hydrophobic molecules to active site
nonmediated transport
no special protein needed to complete
rapid: hydrophobic (lipophilic) solutes
slower: polar/charged solutes (membranes are effective barriers to the diffusion of polar/charged molecules)
diffuses CO2 and O2
facilitated (passive) transport
does not require energy other than the concentration gradient; diffusion of certain solutes is accelerated by specific transporter proteins
pore, channel, carrier
facilitated (active) transport
transporter proteins that achieve transport against a concentration gradient
uniport
membrane transport process that carries one type of solute
symport
membrane transport process that carries two substances in the same direction across the membrane
typically, one species moves with the gradient and another moves against it (accounts for energy balance)
antiport
membrane transport process that carries one substance in one direction and another in the opposite direction
ex: Na+ and Ca2+ // Na+ moves with the gradient and causes structural change which causes Ca2+ to move against its gradient
pump
moving against the gradient
ex: sodium-potassium pump; energy of hydrolysis of ATP pushes energy
channel
first entry is large enough for the solute + hydrogen sphere to enter
selectivity filter: water molecules are forced to shed and the carbonyl oxygens of the polypeptide are at the right geometry and distance to cause a bond and polar attraction to potassium
how do channels become specific for certain ions?
channel narrows to prevent large ions from passing through
ions that are too small are unable to interact with the selectivity filter backbone carbonyl groups in the protein, meaning they cannot shed their hydration shell
when the specific ion passes through, it replaces its hydration interactions with those of the peptide carbonyls
glycosaminoglycan
composed of repeating units of a disaccharide: one is a derivative of an amino sugar and the other carries a negative charge (ex: carboxylate or sulfate)
how does negative charge contribute to glycosaminoglycan structure?
negative charge can be used to pull water into the tissue (ex: cartilage), allowing for tissue to withstand compressive forces and sustain tension to become flexible
flow of K+ ions out of the cell through channels is…
spontaneous
transport of K+ ions into the cell via pump is…
non-spontaneous
formula for simple carbohydrate
Cn(H2O)n
ex: C6H12O6
when numbering carbons…
start from the end that will give the carbonyl the lowest number
hemiacetal
alcohol + aldehyde (R-CH=O)
hemiketal
alcohol + ketone (R2-C=O)
reducing end
the end of a chain with a free anomeric carbon
signaled by hemiacetal or hemiketal
function of triacylglycerols in animals include
storage for long-term energy and thermal insulation of body temperature
glycerol and fatty acid linkage
ester linkage
fluidity of a bilayer is generally increased by…
an increase in the number of double bonds in the fatty acid hydrocarbon chains
membranes are a fluid mosaic of what components?
phospholipids, proteins, and cholesterol
in the hydrophobic environment of a membrane, the alpha helix of a protein folds such that the outer surfaces contain mostly ________ amino acids, while _______ amino acids are mostly buried on the inside
non-polar on outside
hydrophilic on inside
the most _______ molecules will be the most permeable
hydrophobic
phosphatidate
glycerol-3 phosphate and two fatty acid chains
acetal
functional group that contains a carbon atom bonded to two -OR groups, an alkyl chain, a hydrogen atom
ketal
functional group that contains a carbon atom bonded to two -OR groups and two alkyl chains
fatty chain length’s relation to melting point
longer chains can withstand higher temps
shorter chain can withstand cooler temps
