Biochem Flashcards
What is indirect assay
Uses a labeled secondary antibody
What is direct assay?
Uses a labeled primary antibody
What is competitive assay?
Used when the target antigen is small and has only one epitope. Consists of labeling purified antigen instead of the antibody
What is capture assay?
Analyte is bound between two antibodies, the capture antibody and the detection antibody
Higher NAD+/NADH ratio
Drives catabolism because having more of the oxidized form in the cell signals an energy need
Lower NAD+/NADH ratio
Drive fatty acid synthesis because having more of the reduced form in the cell can eventually provide the ATP required for synthesis
Lower NADH/NAD+ ratio
Drives catabolism because having more of the oxidized form in the cell signals an energy need
Higher FADH2/FAD ratio
Drive processes that result in energy storage
What is the absolute configuration of selenocysteine?
S
What is the absolute configuration of cysteine?
S
What is the equivalent RNA sequence of the DNA coding for 3’-ACT-5’?
5’-UGA-3’
What codon is the result of 3’-ACT-5’?
Stop codon
What amino acid has two atoms in its side chain?
Cysteine
How are the pyrimidines cytosine and uracil metabolized?
Cytosine and uracil are converted into beta-alanine and later to malonyl-CoA which is needed for fatty acid synthesis
How is glycogen involved in aerobic respiration?
Glycogen can be broken down into glucose, which can directly enter glycolysis
How are fatty acids like 3-ketoacyl-CoA involved in aerobic respiration?
Fatty acids like 3-ketoacyl-CoA can be broken down via beta-oxidation to produce two carbon units which are then fed into the citric acid cycle via acetyl-CoA
How is glycogen involved in aerobic respiration?
Glycogen can be broken down into glucose, which can directly enter glycolysis
What molecules are commonly used in detection or visualization of the antigen of interest in immunoassays that require labeling or conjugation with the antibodies?
Fluorophores, enzymes, radioisotopes, or biotin
Transmembrane proteins generally consist of a _______ portion within the lipid bilayer and two _______ portions that face the cytosol and extracellular space
hydrophobic; hydrophilic
What are the two primary determiners of protein tertiary structure?
Interactions between charged amino acid side chains and accumulation of hydrophobic side chains towards the inside of a globular protein, away from the charged solvent (water)
What are the two main effects of the activation of histone deacetylase?
Decreased rate of transcription of the affected DNA and DNA-histone attractions will become stronger
Insulin is a ______ hormone that promotes a _______ in blood glucose levels.
peptide; decrease
Peptide hormones are ________, ________, and ________.
short-acting; promote second-messenger cascades; and are soluble in water.
Steroid hormones ________, ________, and ________.
Bind to its receptor in the nucleus; impact transcription; share cholesterol’s fused-ring hydrocarbon structure
What enzyme catalyzes an irreversible step in glycolysis?
pyruvate kinase
What happens to a person’s fuel storage after fasting for several hours and then consuming a large meal?
Liver glycogen stores increase
The levels of what hormone peaks just prior to ovulation?
LH
Chymotrypsin is an intestinal enzyme that is synthesized as a ________, which is activated by other digestive enzymes in the presence of food
zymogen
What helps drive lymph through the lymphatic vessels?
one-way valves that prevent fluid backflow
What does the endosymbiotic hypothesis state?
Mitochondria began as small, independent prokaryotic organisms that entered into a symbiotic relationship with a eukaryotic cell
Mitchondria have a separate set of DNA, that unlike nuclear DNA, is inherited ________.
maternally
Mitochondria are able to replicate in a fashion that is _________ of cell replication
independent
In gluconeogenesis, the reverse of step 3 of glycolysis is catalyzed by what enzyme?
fructose 1,6-bisphosphatase
What protein structure is intricately involved in chromosome pairing, synapsis, and recombination?
Synaptonemal complex
What is glycogenolysis?
The breakdown of glycogen, a polymer of glucose that is stored by the body for future energy needs
Glycogenolysis occurs when
one has not eaten recently or exists in a state of increased ATP demand
Low blood glucose levels will increase the rate of what two pathways that make glucose in the body?
Glycogenolysis and gluconeogenesis
What is the reason why sodium ions are able maintain a more tightly-coordinated sphere of hydration?
they have a smaller atomic radius
Mitosis must be arrested during what phase as a result of the replicated chromosomes being retained within the original nucleus?
prophase
Both leucine and isoleucine are _______ molecules
chiral
glycine is an ______ molecule
achiral
What enzyme must be present within the viral capsid of a (-) RNA virus for successful infection and replication to take place?
RNA-dependent RNA polymerase
What must occur for eukaryotic cells to have direct contact with viral DNA?
Viral DNA must enter the nucleus
What do leucine and valine have in common?
They are both neutral and nonpolar amino acids
________ single-stranded RNA viruses need RNA replicase to create _________ RNA strands that can be translated using host cellular machinery
negative-sense; positive-sense
What microbe can only replicate inside cells?
Viruses
How are viral proteins synthesized?
They are synthesized using host ribosomes, which are found in the rough endoplasmic reticulum
Viral envelopes are mainly comprised of ________ and _______ that contribute to recognition and interactions with cell receptors.
phospholipids; glycoproteins
Microfilaments aid what process during mitosis?
cytokinesis
What are two possible ways to reduce membrane fluidity?
reducing temperature and adding more saturated phospholipids
What organelle is involved in the catabolism of proteins?
lysosomes
Peroxisomes perform functions related to the ____________ and the ___________
pentose phosphate pathway; neutralization of reactive oxygen species
What are the two ribosomal subunits of a bacteria?
30S ribosome and 50S ribosome
The volume known during quiet breathing is known as what?
tidal volume
The volume left in the lungs after a maximal exhalation is known as what?
residual volume
What concept refers to the maximum amount of air we can have in our lungs?
total lung capacity
What is gluconeogenesis?
Generation of glucose from non-carbohydrate carbon substrates such as pyruvate, lactate, glycerol, and glucogenic amino acids like alanine and glutamine
What is the role of epinephrine in gluconeogenesis?
Epinephrine acts to increase the rate of substrate flux in liver cells through the gluconeogenic pathway and away from the glycolytic pathway by simulating a cAMP-regulated kinase, protein kinase A
What is the function of protein kinase A?
To phosphorylate and inactivate the phosphofructokinase-2 domain of the bi-functional enzyme responsible for the formation of fructose-2,6-bisphosphate
What enzyme is responsible for the hydrolysis of glucose-6-phosphatase to free glucose in the final step of gluconeogenesis and is required for export of glucose, via glucose transporter membrane proteins, from the renal cortex?
Glucose-6-phosphatase
What happens when there is an increased concentration of circulating blood glucose?
The osmotic pressure of the extracellular fluid rises, causing water to leave the cell
The juxtoglomerular cells in the kidney, small intestine muscle, and large intestine muscle are what kinds of muscle cells?
Smooth muscle cells
Membrane potential is always measured in terms of the ________ relative to the extracellular fluid
inside of the cell
What is the result of the change in amino acid from a glutamic acid into an aspartic acid?
Loss of a methylene group
Vasoconstriction _________ TPR whereas vasodilation _________ TPR
increases; decreases
How does the body shunt blood to working muscles to supply them with oxygen during excercise?
Through vasodilation in working muscles
In what blood vessel is blood pressure likely to be highest?
Aorta
An _______ in TPR would lead to _______ arteriole constriction restraining blood from entering the peripheral vascular system. The _______ arteriole constriction would therefore lead to a _______ cardiac output
increase; increase; increase; decrease
If TPR is known to _______ venous return, there would be a _______ in the amount of blood returning to the heart from the periphery via the ______ ______. This ________ in venous return would therefore lead to a _______ in ______ ______ _______.
decrease; decrease; right atrium; decrease; decrease; right atrial pressure
What is orthostatic hypertension?
Drop in pressure due to delayed constriction of lower body blood vessels, which is needed to maintain an adequate blood pressure when changing position from supine to standing
How does orthostatic hypertension cause reduced delivery of blood to the head?
Blood pools in the blood vessels of the lower extremities for a longer period, and less is returned to the heart
Cytochrome P450 belongs to what class of enzymes?
oxidoreductases
The turnover number is also known as ___________
kcat
What is kcat?
the time it takes one enzyme to turnover a maximum amount of substrate molecules per unit time
What is the equation for kcat?
kcat = Vmax / [Et]
If the turnover rate increases but the binding affinity (Km) remains the same, then it’s likely that the substitutions ________ entry of substrate into the active site without altering the site itself
increased
A heme group is classified as a ________, a ________, and a ________
cofactor; coenzyme; prosthetic group
What are zymogens?
inactive precursors of enzymes that require proteolytic cleavage prior to becoming active
What is positive cooperativity?
binding at one position or active site causes binding to take place more easily at the remaining active sites
A Hill coefficient greater than 1 reflects ________ _________
positive cooperativity
a graph of saturation versus substrate concentration for an enzyme that displays positive cooperativity would be _________
sigmoidal
Magnesium cations are classified as what?
cofactors
An uncompetitive inhibitor is an inhibitor of the _______ _______
enzyme-substrate complex
What enzyme is responsible for transferring a high-energy phosphate group from a donor molecule (typically ATP) to the substrate?
Kinase
What enzyme removes phosphate groups from their substrates?
phosphatase
What enzyme is responsible for binding together two smaller components?
ligase
What enzyme transfers functional groups from one molecule to another?
transferase
Many metabolic pathways, feedback loops, and cell growth and division rely on _______ _______
allosteric regulation
What is allosteric regulation?
a ubiquitous phenomenon in the physiology of multicellular eukaryotic organisms
The amino acids most likely to become phosphorylated are those which contain an ___ _____ on their side chains
OH group
What amino acids have an OH group on their side chains?
serine (S), threonine (T), and tyrosine (Y)
What is the function of SDS?
serves to disrupt the molecular forces which allow proteins to take their native conformation
Edman degradation _______ size of polypeptide
shrinks
treatment with an eluant of increasing ionic strength and pH could disrupt [statement]
the ionic bonding between polypeptide and column anions by influencing the charge state of the polypeptides, decreasing their likelihood of existing in the charged, cationic state
If polypeptide unfolding proceeds via a unimolecular mechanism, the rate law for the reaction must be _____ order with respect to only the polypeptide
first
What happens in an addition reaction?
the number of pi bonds declines, while the number of sigma bonds increases
Under _______ conditions, interactions between polypeptides is disrupted
reducing
glutamic acid is an _______ residue
acidic
Acidic side chains have ___ pKa values
low
Lysine is a ______ and [positively charged or negatively charged] residue
basic; positively charged
SDS applies a uniform _______ charge along the protein
negative
SDS is used to allow separation by ____ or _____
size; mass
What method uses antibody-protein affinity to retain the desired substrate on the solid-phase matrix?
immunoaffinity
“Salting in” refers to what?
the addition of a salt to a solution that does not yet contain very high salt concentrations
“Salting out” refers to what?
when salt concentrations are already high, addition of more salt decreases protein solubility
in cation-exchange chromatography, the stationary phase is designed to attract _______
cations
A protein rich in lysine (a basic amino acid) will have a [higher or lower] isoelectric point (pI) than a protein largely formed from hydrophobic residues
higher
A ______ pI means the protein will tend to be more ______ charged and will thus move closer to the ______ end of the gel
higher; positively; negative
In an electrolytic cell, the anode is _______ and the cathode is _______
positive; negative
in isoelectric focusing, a protein or amino acid always becomes ________ when it has reached the portion of the gel corresponding to its isoelectric point
stationary
What is mannitol?
a sugar alcohol that can be formed by reducing the C=O group in mannose
What occurs when adding bonds to oxygen?
Oxidation
True or False: α- and β-anomers of glucose interconvert under cellular conditions
True
What is Tollens’ reagent used for?
test for reducing sugars
Reducing sugars have free ________ groups that can be oxidized to ________ _____, with concomitant reduction of Tollens’ reagent
aldehyde; carboxylic acids
Tollens’ reagent contains what and is reduced to what?
an oxidized silver compound, which is reduced to elemental silver.
Fructose is what kind of sugar?
reducing
Specific rotation is an _________ value
experimental
Enantiomers have _____ but ________ specific rotation values
equal; opposite
Racemic solutions have a specific rotation of what?
0°
What makes L-glucose unique from D-glucose?
L-glucose does not exist in nature, and virtually no naturally-occurring enzymes are able to metabolize it unlike D-glucose
What happens to glucose prior to it being regulated to glycolytic or glycogenic metabolic pathways?
glucose is imported into the cell by GLUTs and trapped in the cell via hexokinase phosphorylation
Rate of production of G6P will [increase or decrease] with an increased accumulation of the enzyme hexokinase
increase
What is substrate-level phosphorylation?
the process by which a phosphate group is transferred from a phosphorylated compound to ADP or GDP, producing ATP or GTP
When does substrate-level phosphorylation occur?
During anaerobic glycolysis when ATP is produced from the breakdown of 1,3-BPG and PEP
Glycolysis involves what?
the oxidation (catabolism) of glucose to form two molecules of pyruvate, among other products
The investment phase refers to the first ____ steps of _________
five; glycolysis
_______ has been converted into two three-carbon _________ _-_________ molecules by the end of the first five steps of glycolysis
glucose; glyceraldhyde-3-phosphate
ATP is not produced until what phase of glycolysis?
payoff phase
The payoff phase refers to the last ____ steps of the overall pathway
five
What is the single most crucial reason for the use of anaerobic respiration?
it is capable of producing ATP at a significantly faster rate than oxidative phosphorylation
What does the cell do when tissue requires more ATP than aerobic respiration can produce?
turns to anaerobic methods
Lactic acid is a product of what?
fermentation
A facultative aerobe can undergo what metabolic process(es) and survive in what kind of environment?
can use oxygen as an electron acceptor in the presence of oxygen, but it can also survive in an anaerobic environment by deriving energy solely from glycolysis and subsequent fermentation
an _______ _________ would not be able to survive in the presence of oxygen, while an _______ _______ would require oxygen to survive
obligate anaerobe; obligate aerobe
Glucose 6-phosphate isomerase is involved in both __________ & ______________
glycolysis; gluconeogenesis
What is the function of glucose 6-phosphate isomerase?
interconverts glucose 6-phosphate and fructose 6-phosphate
Branch points in glycogen consist of what kinds of linkages?
α (1→6) linkages
α (1→6) linkages in branch points in glycogen are broken by what kind of enzyme?
glycogen debranching enzyme
Straight-chain glycogen is held together by what kinds of linkages?
α (1→4) linkages
α (1→4) linkages are broken through the action of what enzyme?
glycogen phosphorylase
What is the rate-limiting step of glycolysis?
phosphorylation of fructose 6-phosphate by the enzyme phosphofructokinase-1
Hexokinase transports ______ into the cell and is inhibited by high levels of its own product – ___.
glucose; G6P
when blood sugar is low, ________ is slowed, and when blood sugar is high, ________ as catalyzed by ________ occurs more rapidly
glycolysis; glycolysis; glucokinase
Peptidoglycan is specific to what kinds of organisms?
prokaryotes
What is a Gram stain?
a common biochemical technique in which a crystal violet dye is retained by a peptidoglycan (a sugar and amino acid polymer) cell wall
Cis-aconitate is a precursor of what molecule?
isocitrate
Activation of enzyme citrate synthase would cause an [increase or decrease] in the production of TCA intermediate citrate
increase
NADH is an inhibitor of what enzyme?
citrate synthase
ADP is an activator of what enzyme?
citrate synthase
What is the name of the enzyme that converts citrate to cis-aconitate?
aconitase
During gluconeogenesis, ___________ in the mitochondria is converted to ______ for export from the mitochondria
oxaloacetate; malate
Cytosolic malate is then re-oxidized to ___________ and converted to ___________________
oxaloacetate; phosphoenolpyruvate
The step in which cytosolic malate is re-oxidized to oxaloacetate and converted to phosphoenolpyruvate is the _____ ________ step in gluconeogenesis
rate-limiting
What is the function of Complex I?
removes 2 electrons from NADH which are then transferred to ubiquinone, or coenzyme Q. Complex I then translocates 4 protons across the inner mitochondrial membrane
One turn of citric acid cycle yields what?
1 GTP, 3 NADH, 1 FADH₂, and 2 CO₂
What is the irreversible, rate-limiting step of the citric acid cycle?
Decarboxylation of isocitrate, forming α-ketoglutarate
What enzyme catalyzes the decarboxylation of isocitrate, forming the five-carbon molecule α-ketoglutarate
isocitrate dehydrogenase
True or False: Complex II directly contributes to the gradient
False, Complex II does not directly contribute to the gradient
Complex IV removes how many protons from the mitochondrial matrix? How many of these protons are given to molecular oxygen along with four electrons to form water? How many of these protons are translocated across the membrane and contribute to the gradient?
8 protons; 4 protons; 4 protons
What is the name of the enzyme that catalyzes the rate-limiting step of glycolysis?
phosphofructokinase
Cytochrome c is a ___________
hemeprotein
Because cytochrome c contains a heme group, it also contains what metal atom?
Fe
Amides are [more or less] reactive than carboxylic acid derivatives
less
Ethoxide & NaOH are highly reactive _____ ______ & are conjugates of extremely ____ _____
strong bases; weak acids
Hormone-sensitive lipase is highly expressed in what two types of tissues?
adipose tissues and steroidogenic tissues
What is the function of hormone-sensitive lipase in adipocytes?
catalyzes the breakdown of triacylglycerols to fatty acids and glycerol through hydrolysis of ester linkages
Where does beta-oxidation occur?
the matrix of the mitochondrion
What is fatty acid oxidation?
process by which fatty acids are broken down
Where does fatty acid oxidation occur?
the mitochondria
Ketone bodies enter where after being converted to acetyl-CoA?
the TCA cycle directly
Prostaglandins & steroids are __________ molecules
signaling
Biological waxes are composed of what?
long-chain fatty acids esterified to long-chain alcohols
A phospholipid molecule generally consists of what?
a glycerol backbone covalently bound to two fatty acids and a phosphate group
The third glycerol hydroxyl group is bound to what?
a single phosphate group
What is required to permit phospholipids to move between the inner and outer leaflets?
enzymatic activity
Enzymatic promiscuity refers to what?
the case in which a single enzyme can exercise catalytic effects on a wide variety of structurally diverse substrates
What is the major transporter of cholesterol to the tissues of the body?
LDL
What transports cholesterol to the liver?
HDL
What two molecules primarily transport triglycerides?
Chylomicrons and VLDL
What is Chargraff’s rule?
a rule stating that the ratio of purine nucleotides to pyrimidine nucleotides in DNA is 1-to-1
The following picture is a structure of what nucleobase?
adenine
Phosphodiester bonds connect individual _________ monomers to form _______ ____ polymers
nucleotide; nucleic acid
Polypeptides are composed of ______ _____ joined by _______ bonds
amino acids; peptide
polysaccharides are composed of _____________ monomers joined by ___________ ________
monosaccharide; glycosidic linkages
What is the primary function of DNA?
transmitting genetic information
True or False: RNA is capable of a greater diversity of functions than DNA
True
Compared to ribose, deoxyribose lacks an OH group on what carbon?
2’
What is a pentose?
a structure that has 5 carbons
What is a furanose?
a five-membered ring where four atoms of the ring are carbon and one is oxygen
What is the template for PCR?
DNA
What is the template for RT-PCR?
RNA
What are lipid rafts?
regions of the plasma membrane that are very rich in cholesterol
What is required for Ca²⁺ ions to be transported across the hydrophobic cell membrane?
sodium-calcium exchanger
What is the sodium-calcium exchanger and what form of transport does it use?
an antiporter and it uses secondary active transport
There is [high or low] fluidity in plasma membrane at 20℃
low
What is the role of cholesterol at low temperatures?
acts to prevent stacking or clustering of the fatty acyl chains in the membrane’s interior, maintaining a normal amount of fluidity
The lumen of the lysosome has a pH of what?
about 4.5
Antiporters typically utilize what form of transport as a means of transporting molecules against their concentration gradients?
active transport
What does the fluid mosaic model state?
transmembrane proteins are able to freely diffuse within the membrane
Proteins generally [do or do not] spontaneously reverse their orientation within the membrane
do not
Electrostatic interactions involve [charged or uncharged] amino acids
charged
glutamate and lysine are examples of [charged or neutral] amino acids
charged
alanine is an example of a [charged or neutral] amino acid
neutral
At high temperatures, cholesterol increases membrane ________ through attractive ___ ___ _____ interactions with neighboring lipids preventing the membrane from becoming excessively fluid
stability; van der Waals
At low temperatures, the steric bulk of cholesterol increases membrane ________ by preventing tight packing of phospholipid tails
fluidity
Potassium channels contain a _______ ______ filled with water
central cavity
The local polar environment of potassium channels has what effect?
reduces the energetic penalty incurred by passage through the membrane core
What form of transport does GLUT2 use for transport of glucose?
facilitated diffusion
Small, polar molecules like urea and fructose generally cross the cell membrane through what kinds of proteins?
transmembrane proteins
How is insulin internalized for degradation by its target cells?
through endocytosis of insulin and its receptor
The following picture is a structure of what amino acid?
serine
True or False: Serine is an amino acid that can be phosphorylated
True
What amino acid has a negatively charged R group and is very hydrophilic?
aspartate
When are peptide bonds formed?
when the carboxylic acid of one amino acid reacts with the amine group of another amino acid
NADPH is an example of a _____ _______ _____
strong reducing agent
What is 2-mercaptoethanol?
a reducing agent that is commonly used to denature proteins for SDS-PAGE analysis
How does 2-mercaptoethanol break disulfide bonds?
acts as an electron donor to reduce the sulfur-sulfur bond to two sulfhydryl groups disrupting quaternary structure
What is an apoenzyme?
an inactive enzyme that lacks a necessary cofactor
What are coenzymes?
small organic molecules that bind to coenzyme-dependent enzymes
What is Km?
the substrate concentration required to achieve Vmax/2
Enzymes [do or do not] affect the rate of reactions but [do or do not] affect their spontaneity
do; do not
What are hydrolases?
a class of enzymes that catalyze the breaking of bonds through addition of a water molecule
What kind of reaction is used to convert an unsaturated fatty acid into a saturated fatty acid?
hydrogenation
What is the isoelectric point?
the pH at which a protein or amino acid has no net charge
What is pepsin?
an enzyme released in stomach that catabolizes proteins to smaller peptides & amino acids
What is amylase?
an enzyme that catalyzes the hydrolysis of starches to sugars and is produced by the salivary glands and pancreas
What is hexokinase?
an enzyme that catalyzes the phosphorylation of sugars
What is lactase?
an enzyme that catalyzes the hydrolysis of lactose to glucose & galactose
Denaturation of proteins involves the disruption and destruction of what two types of protein structures?
secondary and tertiary structures
What is supersaturation?
a state where a solution contains more of the dissolved material than could be dissolved by the solvent under normal circumstances
What happens when a supersaturated system is perturbed?
the excess solute will crystallize out of solution
Le Chȃtelier’s principle states that the abundance of a substrate will cause the [forward or reverse] reaction to be favored
forward
Le Chȃtelier’s principle states that the abundance of a substrate will cause the [forward or reverse] reaction to be favored
forward
What amino acid is negatively charged and can draw away the separate hydrogen atom that is already connected to an oxygen in the OH group?
glutamic acid
What is the one letter code for glutamic acid?
E
What amino acid is very similar to threonine except that it lacks the extra methyl group that threonine has?
serine
True or False: CO₂ can bind hemoglobin and can dissolve to some degree in the plasma
True
True or False: Both kcat and the turnover number refer to the same thing
True
What is the formula for calculating the turnover number?
kcat=Vmax/[Et]
What is the turnover number defined as?
the maximum number of chemical conversions of substrate molecules per second that a single catalytic site will execute for a given enzyme concentration
[Et] refers to what?
the total enzyme concentration
Vmax refers to what?
the maximum reaction rate
Which carbon is the anomeric carbon for D-glucose?
C1
What is one key difference between the ɑ-anomer and ꞵ-anomer of D-glucose?
the ꞵ-anomer has the hydroxyl group in the equatorial position, while the ɑ-anomer has the hydroxyl group in the axial position
What is the one letter code for aspartic acid?
D
Is aspartic acid a neutral, positively charged, or negatively charged amino acid?
a negatively charged amino acid
What amino acid contains a methyl side chain, which is not considered a branched alkane?
alanine
When does the influx of Na⁺ across motor end plate occur?
Na⁺ ion channels bind the ligand acetylcholine
A Southern blot uses what to differentiate between mutant and wild-type alleles?
a restriction digest
What is required in a mutation for a Southern blot to be useful?
the mutation should either create or eliminate a restriction site, most of which are palindromes and 4 to 6 base pairs long
AAGCTT is a _______ sequence and is the recognition sequence for ______
palindromic; HindIII
Insulin promotes ___ storage because cells experiencing an insulin-mediated influx of glucose can obtain energy from that glucose
fat
What is driving force behind protein folding?
increased entropy made possible by the sequestration of hydrophobic residues in the protein core
Ribosomes in conjunction with peptidyl transferase are responsible for the synthesis of what macromolecules?
proteins
The reaction catalyzed by phosphofructokinase is [reversible or irreversible] under cellular conditions
irreversible
The reverse reaction catalyzed by phosphofructokinase during gluconeogenesis is bypassed by what enzyme?
fructose 1,6-bisphosphatase
What is the change in free energy of a reaction?
a thermodynamic value that depends only on the chemical identity of the reactants and products
True or False: Enzymes can only alter reaction kinetics, not thermodynamics
True
Which complex catalyzes the oxidation of NADH (formed during the TCA cycle) to NAD+ with the concomitant translocation of protons across the inner mitochondrial membrane?
Complex I
The movement of protons back into the matrix is coupled with what?
ATP production
Elevated [AMP] and low [ATP] indicate what?
inadequate ATP production
What is one mechanism to correct an ATP shortage?
upregulation of glycolytic activity
What is the principal product of glycolysis?
pyruvic acid
What is the function of G6P?
an allosteric inhibitor of hexokinase in order to prevent unchecked glucose phosphorylation
Hemoglobin has the characteristics of what type of enzyme?
allosteric enzyme
allosteric enzymes [do or do not] exhibit classical Michaelis-Menten kinetics
do not
True or False: the structure of threonine contains rings
False, the structure of threonine does not contain any rings
What are aromatic compounds?
compounds that contain planar, conjugated rings and follow Hückel’s rule (system possesses 4n + 2 π electrons)
Increased expression of protease enzymes would further [increase or decrease] SREBP levels in the cell
increase
How does the synthesis of LDL receptors allow the cell to import cholesterol?
by binding circulating LDL and taking it in via endocytosis
For a water-permeable cell to lose water via osmosis, its contents must be [hypotonic, isotonic, or hypertonic] relative to its environment
hypotonic
What molecule cannot be directly incorporated into gluconeogenesis?
Acetyl-CoA
Describe the process of endocytosis
external molecules/pathogens first engulfed in a vesicle → vesicles deliver their contents to early endosomes → contents then progress to late endosomes
In an oxygen-poor environment, the ______ ____ _____ will slow while ___________ is activated further
citric acid cycle; glycolysis
Glycolysis utilizes ___, ___, & ______ to form ___ & ____
ADP; NAD⁺; glucose; ATP; NADH
What are the reactants and products of glycolysis?
reactants: one glucose, two NAD⁺, two H⁺, and two ATP molecules
products: two pyruvate, four ATP, and four NADH
How is Acetyl-CoA formed?
from the pyruvate dehydrogenase before the citric acid cycle
An eight-carbon fatty acid chain would require how many acetyl-CoA molecules?
four acetyl-CoA molecules
Each glucose molecule yields how many acetyl-CoA units?
two acetyl-CoA units
Which two amino acids have a carboxylic acid side chain?
aspartic and glutamic acid
What is melting temperature?
a measure of DNA stability
When fewer hydrogen bonds connecting the two DNA strands are present, the melting temperature of the DNA [increases or decreases]
decreases
The __ end of ssDNA often loops back onto itself due to complementary base pairing, which serves as a ______ for DNA polymerase I, providing a free __ __ _____ necessary for enzyme to initiate synthesis
3’; primer; 3’ OH group
This picture is the structure of what amino acid?
L-alanine
Transamination of L-glutamate & pyruvate results in the formation of what two products?
ɑ-ketoglutarate and alanine
Transamination of L-glutamate & pyruvate is catalyzed by what enzyme?
alanine amino transferase
When does transamination occur?
when an amino group is transferred from one species to another, often to form new amino acids
What is one key difference between saturated and unsaturated fats?
unsaturated fats have C=C bonds whereas saturated fats have no C=C bonds
Why are unsaturated fats more flexible and fluid than saturated fats?
their C=C double bonds introduce a kink into the hydrocarbon tail
Cholesterol stabilizes membranes by making [more or less] fluid at low temperature & [more or less] fluid at high temperature
more; less
What is beta oxidation?
the process by which long hydrocarbons are oxidized to acetyl-CoA by enzymes in the mitochondria
What is the critical concentration?
the point at which no net polymerization or depolymerization occurs
What enzyme is responsible for catalyzing the reaction to form glyceraldehyde 3-phosphate and fructose-6-phosphate?
transketolase
Both glyceraldehyde-3-phosphate and fructose-6-phosphate are part of what process?
glycolysis
Is arginine a basic, neutral, or acidic amino acid?
basic
Is glutamate a basic, neutral or acidic amino acid?
acidic
What is produced in the final step of beta-oxidation?
acetyl-CoA
How can the number of acetyl-CoA molecules produced from a complete reaction of a fatty acid be determined?
divide the number of carbons by 2
Denaturation via SDS & mercaptoethanol effectively removes all forces that hold together what kinds of protein structures?
secondary, tertiary, & quaternary structures
Only [L or D] amino acids are produced in cells and used to form protein
L amino acids
The tertiary structure of a protein is driven by what?
the tendency of hydrophobic residues to bury themselves inside the molecule, away from water, as well as interactions between side chains
Extended cardiac arrest leads to a decrease in what in the cells of vital organs?
ATP concentration
It is extremely [easy or difficult] for an organism to alter the temperature of a specific subcellular component
difficult
Gluconeogenesis and the pentose phosphate pathway both share the molecule, ______________, a glycolytic intermediate
glucose-6-phosphate
The pentose phosphate pathway begins with the production of __________________, which can be fed into the ______ _____ _____ and the _______ ______ _____
glyceraldehyde-3-phosphate; citric acid cycle; electron transport chain
____________ is important in the production of nucleic acids
ribose-5-phosphate
The formation of a polypeptide takes place via what kind of reaction?
dehydration reaction
Pinocytosis is a specific form of what?
endocytosis
Endocytosis requires large amounts of ___ and is classified as ______ ________
ATP; active transport
To proceed, gluconeogenesis must overcome the _____ ____________ _____ that occur during glycolysis
three irreversible steps
Step 10 of gluconeogenesis indicates the conversion of ________________ to ________
phosphoenolpyruvate; pyruvate
The reverse of the conversion of phosphoenolpyruvate to pyruvate requires catalysis by what two enzymes?
PEP carboxykinase; pyruvate carboxylase
_________ must undergo further modification before entering into glycolysis, D-_______ can enter into that series of reactions right away
galactose; glucose
In the electron transport chain, what is reduced to form water?
O₂
Protein is generally [more or less] dense than cholesterol?
more
Protein is generally [more or less] dense than cholesterol
more
HDL molecules would have relatively more ______ than LDL molecules
protein
What is the one letter code of asparagine?
N
The residue of asparagine contains an extra nitrogen atom in the form of an _____ functionality
amide
Amides are overall [acidic, neutral, or basic]
neutral
What happens when a G protein-coupled receptor (GPCR) binds a ligand?
Associated protein’s ɑ subunit exchanges a bound GDP molecule for GTP, thus transitioning to an active conformation
Sucrose disaccharide is made up of what monomers?
one D-glucose and one D-fructose unit
Yes or No: Will both D-glucose and D-fructose be able to enter into the glycolytic cycle once they are phosphorylated?
Yes
The rate of the reaction is dependent on what two factors?
concentration of the reactants and the rate constant
As the pyruvate dehydrogenase complex is created and bound with substrate, the amount of unbound enzyme and substrate [increases or decreases]
decreases
The pushing of protons from the mitochondrial matrix into the intermembrane space can only be seen during what?
the establishment of the proton gradient
During regeneration of ATP, H⁺ ions will instead flow from the _____________ _____ back to the _____________ _____ through ATP synthase
intermembrane space; mitochondrial matrix
This picture is a structure of what amino acid?
proline
This picture is a structure of what amino acid?
tryptophan
How can proline be identified?
the amino terminal that is directly attached to its side chain in the form of a heterocyclic ring causing proline to promote “kinks”
NAD is an example of a what?
a coenzyme
What are coenzymes?
a subset of cofactors that tend to bind loosely to their associated enzymes
Coenzymes are known for what?
transferring functional groups between species
NAD donates its hydrogen to what complex in the ETC?
Complex I
What is the primary function of the pentose phosphate pathway?
To produce NADPH
What is the first molecule that is involved in the pentose phosphate pathway?
glucose-6-phosphate
The formation of a disulfide bond involves ________, so it can be coupled with a ________ reaction
oxidation; reduction
What is the name of the molecule depicted?
acetaldehyde
What is the oxidized form of ethanol called?
acetaldehyde
All amino acids have a ______ and an ______ group, corresponding to pKa values of about _ and _-___, respectively
carboxyl; amino; 2; 9-10.5
What is the function of carnitine?
to transport fatty acids into the mitochondria
Fatty acids are utilized to create what for the citric acid cycle?
acetyl-CoA
Fatty acids are utilized to create what for the citric acid cycle?
acetyl-CoA
The Na⁺/K⁺ pump brings _ potassium ions into the cell for every _ sodium ions it expels
2; 3
The act of coupling [would or would not] change the activation energy of a process
would not
What is the goal of reaction coupling?
to make the total of the two reactions exergonic in nature
Which three complexes in the ETC pump protons from the mitochondrial matrix into the intermembrane space?
Complexes I, III, and IV
What is SDS?
a denaturant and a charged molecule with a long hydrophobic tail
What is the purpose of SDS having a charged molecule with a long hydrophobic tail?
to coat proteins with a uniform charge density
What is the purpose of SDS being a denaturant?
to prevent proteins from running through the gel according to their cross-sectional profiles rather than their masses
A typical enzyme-catalyzed reaction at low substrate concentration is _____ order with regard to substrate. However, as [S] increases and the reaction velocity reaches Vmax, it undergoes a shift to become ____ order
first; zeroth
The plasma membrane is a lipid bilayer made of phospholipids w/ _____ “heads” & ________ “tails”
polar; nonpolar
Nitrogen gas is extremely [reactive or unreactive]
unreactive
Insulin allows a patient to take in ______ and produce ___ through glycolysis, while also stimulating the citric acid cycle and the electron transport chain
glucose; ATP
Pyruvate is a product of what process?
glycolysis
Increased levels of ATP correlates with a [rise or drop] in AMP concentration
drop
Regulation of _____ ____ ___________ occurs once nutrients have been taken up into the bloodstream and cells
fatty acid digestion
Enzyme evidently binds its substrate more effectively when ATP levels are [high or low]
low
acetyl-CoA is a product that is exclusive to _______ __________
aerobic respiration
___ is a product of both anaerobic & aerobic respiration through glycolysis
CO₂
Aerobically, _ pyruvates & _ molecules of CO₂ will be generated
2; 2
Anaerobically, in yeast fermentation, _ molecules of ethanol & _ molecules of CO₂ will be generated
2; 2
In anaerobic lactic acid fermentation, no ___ is produced
CO₂
Complex IV adds ___ protons to the intermembrane space per oxygen-reducing reaction
two
Complex III pumps ____ protons
four
A typical rate vs. pH curve is _________ in shape
parabolic
What macromolecules are typically inserted in cytosolic leaflet of ER after synthesis?
lipids
What is the name of the proteins positioned between the two leaflets that move lipids into the inner leaflet?
flippases
What organelle is continuous with the ER?
nuclear membrane
__________ occurs in all cells, while ______________ only occurs in the liver and cortex of the kidney
glycolysis; gluconeogenesis
Cysteine is a _____ amino acid with the ability to participate in __________ _______
polar; disulfide bridges
Glycine is a ________, _______ residue that lacks ______
nonpolar; neutral; sulfur
Glycine is a ________, _______ residue that lacks ______
nonpolar; neutral; sulfur
The rigidity of the proline ring disrupts the formation of what?
alpha helices and beta sheets
For lysine to bind to Na⁺ and not to Cl⁻, it must contain only __________ charged groups and no __________ ones
negatively; positive
The electron transport chain is present on the _____ ____________ _______ and pumps protons from the ______ into the ____________ _______
inner mitochondrial membrane; matrix; intermembrane space
What is DNP?
an uncoupling agent which allows proteins to leak back across the inner mitochondrial membrane, therefore destroying the gradient
Le Chȃtelier’s principle states that, with a decrease in product concentration, the system will shift [left or right] to reestablish equilibrium
right
Reaction quotient Q is calculated as what?
[products]/[reactants]
Q＜Keq corresponds to an [increase or decrease] in ΔG
decrease
Q＜Keq corresponds to an [increase or decrease] in ΔG
decrease
During gluconeogenesis, the conversion of glucose to glucose-6-phosphate is bypassed by what enzyme?
glucose-6-phosphatase
During gluconeogenesis, the conversion of glucose to glucose-6-phosphate is bypassed by what enzyme?
glucose-6-phosphatase
By reducing the activation energy, the rates of the forward & reverse reaction [increase or decrease]
increase
Secondary hyperparathyroidism can be caused by what three factors?
elevated blood phosphate levels, chronic kidney disease, and decreased dietary calcium intake
Extracellular calcium is required for what?
neurotransmitter release
Extracellular calcium is involved in the mechanism of what?
contraction of the cells of all muscle types
PTH levels [increase or decrease] in response to low blood calcium concentrations
increase
What are the thyroid hormone (T₃) and its prohormone (T₄)?
modified amino-acid hormones that behave much like steroid hormones in their global regulation of metabolism
ACTH is a [peptide or steroid] hormone
peptide
Peptidoglycan is formed from amino acids and sugar and is thus [hydrophilic or hydrophobic]
hydrophilic
Methyl violet 10B is [hydrophilic or hydrophobic] because it is charged
hydrophilic
Destruction of reactive oxygen species is a form of __________ __________
antioxidant protection
What is one function of osteoclasts?
bone resorption
What is bone resorption?
the destruction of bone to release its component minerals and ions into the blood
Downstream means _______ ____ the body
farther down
The three parts of the small intestine are ordered _______ → _______ → _____
duodenum → jejunum → ileum
The three parts of the large intestine are ordered _____→ _______ → _____
cecum → colon → rectum
Glutamate decarboxylase is an enzyme that catalyzes the removal of a __________ _____ from glutamate
carboxylate group
This picture is a structure of what molecule?
glutamate
This picture is a structure of what molecule?
GABA
Totipotent stem cells are typically found in ________ tissue
zygotic
Pluripotent stem cells are typically found in ___________ tissue
embryonic
MSCs are _____ stem cells
adult
Adult stem cells give rise to one of several cell types and are thus ___________
multipotent
What is a negative control group?
a control that does not provide a treatment response
What is a negative control group?
a control that does not provide a treatment response
G1 phase is characterized by what?
cell growth
By passing the G1/S checkpoint the cell commits to _______, check that it is [large or small] enough, and that ___ is not damaged
dividing; large; DNA
This picture is the structure of what amino acid?
threonine
____ is oxidized by Complex I while ____ is oxidized later by Complex II
NADH; FADH₂
If a mutation rendered NAD+ coenzyme nonfunctional, if a mutation rendered NAD+ coenzyme nonfunctional, ____ still provides e- needed to facilitate oxidative phosphorylation; just that the process slows down
FADH₂
Changing amount of enzyme affects what?
how fast the reaction can occur
What is a mixed inhibitor?
one that has effects that are a mix of both competitive and noncompetitive effects affecting both Vmax & Km
Antibodies of different isotypes differ in their [constant or variable] region
constant
Antibodies of different isotypes differ in their [constant or variable] region
constant
Cells will [swell or shrink] as water flows down its concentration gradient from low to high solute
swell
Each unique order of amino acids represents a distinct __________
tripeptide
What are disulfide linkages?
those that form between two free -SH groups, yielding S-S bonds
What can be used to break disulfide linkages?
a reducing agent
What can be used to break disulfide linkages?
a reducing agent
Disulfide linkages form between two ________ residues
cysteine
Which complex does not contribute to the proton gradient and instead oxidizes FADH₂ and reduces ubiquinone?
Complex II
What two amino acids contain aromatic rings?
tyrosine and phenylalanine
What two amino acids contain aromatic rings?
tyrosine and phenylalanine
What is the one letter code for tryptophan?
W
What is the one letter code for tyrosine?
Y
What is the one letter code for phenylalanine?
F
What enzyme mediates the first step in glycolysis?
hexokinase
What enzyme mediates the first step in glycolysis?
hexokinase
What enzyme mediates the first step in glycolysis?
hexokinase
How does hexokinase mediate the first step in glycolysis?
adds a phosphate group to the sixth carbon to trap glucose within the cell
What is glucokinase?
an isoenzyme of hexokinase that is used in liver and pancreatic beta cells
Acetyl-CoA is fed into the Krebs cycle to produce what?
three NADH, one FADH₂, and one GTP molecule
Acetyl-CoA is fed into the Krebs cycle to produce what?
three NADH, one FADH₂, and one GTP molecule
One NADH is used to produce how many ATP molecules?
3
One FADH₂ is used to produce how many ATP molecules?
2
How many molecules of ATP are produced in total from one molecule of acetyl-CoA?
12
What is the Michaelis-Menten equation?
What is the Michaelis-Menten equation?
The following picture is a structure of what molecule?
deoxyadenosine triphosphate
This hyperbolic curve is a characteristic of what type of kinetics?
Michaelis-Menten kinetics
This is the structure of what amino acid?
histidine
This is the structure of what amino acid?
lysine
This picture is the structure of what molecule?
citrate
This picture is the structure of what molecule?
pyruvate
This picture is the structure of what molecule?
oxaloacetate
This picture is the structure of what molecule?
ɑ-ketoglutarate
What is the name of the molecule depicted?
GTP
This picture is the structure of what amino acid?
lysine
This picture shows the structure of what molecule?
cytosine that has been methylated at the C5 position
