BIOCHEM Flashcards
1
Q
Which reactions within the citric acid cycle are considered stereospecific
A
production of (intermediates) D-isocitrate and L-malate
2
Q
Do synthases require energy/consume ATP to break/form new bonds
A
No
- synthases do not use ATP (use flow of protons)
3
Q
what is a hydrolysis reaction
A
the breaking apart of molecules using water
- release energy
4
Q
what is a condensation reaction
A
the building of molecules with a loss of water
- require energy
5
Q
what is conformational stability
A
the ability of a protein to maintain its three-dimensional fold
- can be measured by melting temperature
- a lower Tm indicates decreased conformational stability bc less thermal energy is required to denature the protein
6
Q
what is melting temperature (Tm)
A
the temperature at which half the proteins in solution are folded and half are denatured
7
Q
what is kcat
A
the turnover number of an enzyme
- represents the number of reactions catalyzed per second
- represents ability of an enzyme to catalyze a reaction
8
Q
what is apo vs holoenzyme
A
apoenzyme - enzyme’s catalytically inactive component (without cofactor)
holoenzyme - enzyme’s catalytically active form
9
Q
all flavoproteins use ______ as their coenzyme
A
FAD
10
Q
lysine
- abbreviations, qualities, and key structure
A
Lys - K
positively charged
4 CH2 groups in a chain
protonated amine at the end
11
Q
arginine
- abbreviations, qualities, and key structure
A
Arg - R
positively charged
3 CH2 groups in a chain
NH-C=NH2+(-NH)
12
Q
histidine
- abbreviations, qualities, and key structure
A
His - H
positively charged
CH2 followed by an imidazole (five-membered ring containing two nitrogens)
13
Q
aspartate
- abbreviations, qualities, and key structure
A
Asp - D
negatively charged
1 CH2 group followed by COO- (carboxylate)
14
Q
glutamate
- abbreviations, qualities, and key structure
A
Glu - E
negatively charged
2 CH2 groups followed by COO- (carboxylate)
15
Q
describe the Na+ - H+ exchanger
A
an antiporter in which the transport of one Na+ is coupled with the transport of one H+ in the opposite direction
- no net translocation of charge
16
Q
describe the Na+ - Cl- cotransporter
A
cotransporter that transports one Na+ and one Cl- in the same direction
- no net movement of charge, electroneutral process
17
Q
describe the Na+ - glucose cotransporter
A
transports Na+ cations and glucose into the cell
- electrogenic process
- results in net movement of positive ions into the cell
18
Q
what is glycosylation
A
the attachment of carbohydrates to the back of a protein
- crucial for the structural conformation of a protein
19
Q
insulin is released in response to ____________ by ___________
A
high blood glucose levels ; pancreatic beta cells
20
Q
glucagon is released in response to ___________ by __________
A
low blood glucose levels ; pancreatic alpha cells
21
Q
what is an ionophore
A
compound that binds to an ion and moves it across the cell membrane
- degrades ion gradient in process
22
Q
diaphragm contraction results in _________ thoracic volume and _________ intrathoracic pressure, which causes _________
A
increased ; decreased ; inhalation
23
Q
what are colonocytes
A
epithelial cells that line the colon
24
Q
in an enzyme-catalyzed reaction where enzyme concentration is constant and substrate concentration is relatively low, which kinetic parameter will increase with the addition of more substrate
A
Vo (initial velocity)
25
what are enterocytes
intestinal cells that produce enzymes that digest disaccharides (like lactase)
26
what are parietal cells
stomach cells that produce HCl
27
why would some DNA sequences be conserved among species
they are vital to an organism's life
28
what are lyases
enzymes that catalyze the cleavage of a single molecule into two products
- do not require water as a substrate
- can also catalyze the reverse of their specific reactions (synthesis of two molecules into one) but referred to as synthases
29
what are isomerases
enzymes that restructure the chemical formula of a compound
- rearrangement of bonds within a molecule
- do not break down chemical bonds
- catalyze reactions between stereoisomers and constitutional isomers
- can be classified as other kinds of enzymes based on their reaction-
30
what are transferases
enzymes that transfer chemical groups between compounds
- example: kinases (transfer a phosphate group, generally from ATP, to another molecule)
31
what are oxidoreductases
enzymes that catalyze oxidation-reduction reactions; the removal of hydrogen atoms and transfer of electrons
- often have a cofactor that acts as an electron carrier like NAD+
- enzymes with names like dehydrogenase or reductase are usually oxidoreductases
- enzymes where oxygen is the final electron acceptor are called oxidases
32
what are hydrolases
enzymes that catalyze hydrolysis (breaking of bonds) using the addition of water
- usually named for their substrate
- example: phosphatases, peptidases, nucleases, lipases
33
34
mutations to what regions of genes most specifically alter gene expression over gene function
promotor and enhancer regions
35
exocrine glands secrete substances through _______ while endocrine glands secrete substances __________
ducts onto your body's surfaces ; directly into your bloodstream
36
what is transformation
the process that transfers genetic material from the environment into bacteria
37
what is transduction
process by which nucleic acids are transferred from viruses to cells
38
what is conjugation
the exchange of nucleic acids between bacteria
39
what is the induced fit model
the theory that an active site changes its form when it comes into contact with a substrate in order to make the enzyme-substrate complex
- process of changing shape requires energy/is endergonic
- process of releasing product is exergonic
40
what is a prosthetic group
cofactor that is tightly bound to the enzyme
41
compare cofactors vs coenzymes
cofactors - inorganic molecules or metal ions that are often ingested as dietary minerals (example: Mg2+)
coenzymes - small, organic groups, usually vitamins or derivatives of vitamins like NAD+, FAD, and CoA
42
what are the fat-soluble vitamins
A,D,E, and K
43
what are the water-soluble vitamins
B complex and C
44
what does the Michaelis-Menten plot of enzyme kinetics tell you
as the amount of substrate increases, the enzyme is able to increase its rate of reaction until it reaches a maximum enzymatic reaction rate (saturation)
45
what is the Michaelis-Menten equation (when enzyme concentration is constant)
v = ( vmax [S] ) / ( Km + [S] )
when v = 1/2vmax --> Km = [S]
at very low substrate concentrations, you can take out the + [S] in the denominator
46
what is Km
the Michaelis constant
- the substrate concentration at which half of the enzyme's active sites are full
- also a measure of affinity (higher Km means lower affinity)
47
what is the equation relating max velocity to kcat
Vmax = [E]kcat
48
what is the catalytic efficiency of the enzyme
ratio of kcat / Km
- a large kcat (high turnover) or small Km (high affinity) will result in a greater catalytic efficiency
49
what is the value of the x-intercept of a lineweaver-burk plot
- 1 / Km
50
what is the value of the y-intercept of a lineweaver-burk plot
1 / vmax
51
what is T vs R state of an enzyme
T state = low-affinity tense state
R state = high-affinity relaxed state
52
what is Hill's coefficient
numerical value that quantifies cooperativity
- if Hill's > 1, positive cooperativity
- if Hill's < 1, negative cooperativity
- if Hill's = 1, no cooperative binding
53
the anaerobic process that replenishes NAD+ levels occurs in the
cytosol
54
what is the most important start codon for amino acids and which amino acid does it code for
AUG
methionine
55
how do you find the percent decrease of something
(old value - new value) / old value
56
lipid rafts tend to be rich in _________ and poor in ___________
sterols ; phospholipids
57
what are prostaglandins
nonhydrolyzable lipids that are involved in inflammatory responses
- not found in cell membranes
58
what are triglycerides
molecules in which 3 fatty acids are each linked to a glycerol molecule
- used for energy storage not structure, not found in cell membranes
59
what are waxes
lipid molecules that typically form soft solids that are malleable at room temperature
- composed of two sets of long chain hydrocarbons linked together through an ester group
60
which functional group is most common in waxes
ester groups
61
glycolysis uses ATP with which two enzymes
hexokinase and phosphofructokinase-1
62
are L or D amino acids degraded more quickly
L amino acids are more common in nature --> more easily recognized by proteins --> get degraded faster
63
T or F: for a reversible reaction, the same enzyme catalyzes both forward and reverse reactions
T
64
which metabolic process provides the necessary energy for sustained gluconeogenesis
fatty acid oxidation
65
which amino acids contain alkyl side chain groups
alanine, proline, leucine, isoleucine, valine
66
which amino acids contain branched alkyl side chain groups
isoleucine, leucine, valine
67
what are isoprene units and terpenes
isoprene units are branched 5-carbon molecules that are the basis for cholesterol synthesis
terpenes are at least 2/3 isoprene units linked together
68
sugars with the anomeric carbon at position 1 are called __________
aldoses
69
sugars with the anomeric carbon at position 2 are called ________
ketoses
70
how to distinguish which carbon is the anomeric carbon?
carbon bound to 2 oxygens
- if one of the oxygens is an OH, it is a hemi
71
what's the difference between a hemiacetal and hemiketal
hemiacetal - when an alcohol adds to an aldehyde (resulting product has 2 R groups and 2 H atoms)
hemiketal - when an alcohol adds to a ketone (resulting product has 3 R groups and 1 H)
72
which reactions of glycolysis are energy-investment and which are energy-payoff
the first 5 are energy-investment and the remaining 5 are energy-payoff
73
preincubation with an inhibitor enzyme allows for what to occur
covalent linkages
- typical of irreversible inhibitors
74
is an amino acid positive or negatively charged when the pH is below its pI
positive
75
what different information does boiling point vs heat of combustion tell you
boiling point measures the energy required to overcome intermolecular forces
heat of combustion tells you energy needed to break bonds (thermodynamic stability)
76
T or F: post-transcriptional modifications occur before translation
T
after transcription, before translation
77
what are transposons
DNA sequences that can insert and remove themselves from the genome, can exist in both prokaryotic and eukaryotic cells (no known active ones in humans)
- in prokaryotes, can act as a 'stress response' system, allowing for rapid inactivation of genes in response to environmental changes
- can regulate transcription (if they occur in the middle of a coding sequence, that gene will no longer be transcribed)
78
where does a repressor bind to an operon?
the operator
79
what is the structure of GPCRs?
a single subunit consisting of seven membrane-spanning a helices
80
what is the structure of enzyme-linked receptors
a single transmembrane protein with an extracellular ligand-binding domain and an intracellular catalytic domain
81
what is the structure of a ligand-gated channel
multiple subunits arranged around a central channel with a ligand-binding site on the subunits
82
competitive inhibitors increase _______
Km
- vmax stays the same
83
uncompetitive inhibitors do what to Km and vmax
decrease them both
84
noncompetitive inhibitors do what to Km and vmax
Km is unaffected
vmax is reduced
85
what does helicase do
enzyme responsible for unwinding DNA during replication, generating two single-stranded template strands ahead of the polymerase
- breaks the hydrogen bonds between nitrogenous bases
86
what do DNA topoisomerases do
alleviate torsional stress and reduce the risk of strand breakage by introducing negative supercoils
- work ahead of helicase, nicking one or two strands and then resealing them
87
how can you tell if a sugar is reducing or nonreducing
reducing if they contain a free anomeric carbon that can be oxidized
nonreducing if the anomeric carbon is linked to another molecule
88
adjacent sugars in RNA and DNA are joined by what bonds
phosphodiester bonds at the 5' and 3' carbon
89
the nitrogenous bases in RNA and DNA are bound to their sugar by what bond
glycosidic bonds (covalent)
90
what functional groups does cytosine have attached to its aromatic ring
amino group attached to carbon 4 and carbonyl at carbon 1
91
what functional groups does uracil have attached to its aromatic ring
carbonyl attached to carbon 4 and carbonyl at carbon 1
92
what functional groups does thymine have attached to its ring
carbonyl at carbon 4, carbonyl at carbon 1, amine branch, and methyl group at carbon 3
93
what functional groups does adenine have
amine group at carbon 4
94
what functional groups does guanine have
amine at carbon 1 and carbonyl at carbon 4
95
what is differential scanning calorimetry
technique that shows the rate at which proteins denature
- peak in the curve is the Tm (melting temperature)
96
what is palmitic acid
free fatty acid synthesized by cells
- can be incorporated into phospholipids
97
what is sphingomyelin
a phospholipid with a sphingosine backbone
98
the best competitive inhibitors are molecules that _____
bind tightly and resemble most closely the transition state
- have small Kd values
99
what is a futile cycle
when anabolic and catabolic metabolism occurs at the same rate, so there is no overall energy gain
- active or proliferating cells usually prefer one over the other
100
what is the rate-limiting enzyme of fatty acid oxidation
carnitine palmitoyltransferase I
101
what are anabolic hormones
generally stimulate anabolic processes and inhibit catabolic processes
- insulin, growth hormone, testosterone, estrogen
102
what are catabolic hormones
generally stimulate catabolic processes
- glucagon, cortisol, epinephrine
103
NADPH is used in fatty acid _______ not _________
synthesis ; oxidation
104
each PCR cycle amplifies DNA by how much?
doubles it
105
what is the rate-limiting enzyme of glycolsis
phosphofructokinase-1
106
what is the rate-limiting enzyme of fermentation
lactate dehydrogenase
107
what is the rate-limiting enzyme of glycogenolysis
glycogen phosphorylase
108
what is the rate-limiting enzyme of glycogenesis
glycogen synthase
109
what is the rate-limiting enzyme of gluconeogenesis
fructose-1,6-biphosphotase
110
what is the rate-limiting enzyme of the pentose phosphate pathway
glucose-6-phosphate dehydrogenase
111
how does the reaction rate of enzyme kinetics change with substrate concentration
michaelis-menten kinetics : reactions are approximately first-order at low substrate concentrations ; under saturating concentrations it reaches zero-order kinetics (rate does not increase with increasing concentration)
112
what does it say about the substrate if the enzyme is operating at vmax
the substrate is bound to every enzyme active site in solution
113
how can molecules that pertain to the citric acid cycle be easily identified
with the exception of succinyl-CoA and acetly-CoA, they are all flanked by carboxylate ions on both ends of the main carbon chain
114
How does prokaryotic DNA differ from eukaryotic DNA?
I. Prokaryotic DNA lacks nucleosomes.
II. Eukaryotic DNA has telomeres.
III. Prokaryotic DNA is replicated by a different DNA polymerase.
IV. Eukaryotic DNA is circular when unbound by centromeres.
I, II, and III only
Prokaryotic DNA is circular and lacks histone proteins, and thus does not form nucleosomes. Both prokaryotic and eukaryotic DNA are replicated by DNA polymerases, although these polymerases differ in identity. Eukaryotic DNA is organized into chromatin, which can condense to form linear chromosomes; only prokaryotes have circular chromosomes. Only eukaryotic DNA has telomeres.
115
T or F: the light emitted by fluorescence is always lower in energy than the light that was absorbed
True
116
what is the equation for glucose combustion
C6H12O6 + 6O2 --> 6CO2 + 6H2O
117
an isotopic substitution requires ______
a radioactive 15N
118
what is the basic central dogma
DNA -->(transcription)--> RNA -->(translation)--> protein
119
what is reverse transcription
making of DNA from RNA
- reverse transcriptase: enzyme that generates complementary DNA (cDNA) from an RNA template
120
retroviruses like HIV use what kind of transcription
reverse transcription
- use reverse transcriptase to reverse transcribe their RNA genome into DNA so it can be integrated into the host genome and replicated
121
what are RNA viruses
viruses that only use RNA as their genetic information
- the RNA can be used as is for translation or used as a template for transcription and then translation
- example: coronavirus, influenza, paramyxo (measles)
122
what is noncoding RNA (ncRNA)
a functional RNA molecule that skips the last step of being translated into a protein and can directly perform functions within the cell
- example: transfer RNA (tRNA) and ribosomal RNA (rRNA) - both used in translation
123
what is epigenetics and what are some ways it happens
the study of heritable changes in gene activity that are not caused by changes in DNA sequence ; mechanisms where the same DNA sequence can be modified in a way that results in different phenotypes without changes to the underlying DNA sequences
- examples: DNA methylation, histone modification
- explains why each cell in your body has the same DNA but doesn't perform the same function (only certain genes are expressed)
124
what's the structural difference between deoxyribsoe and ribose
deoxyribose - has OH group on 3' carbon and H group on 2' carbon
ribose - has OH groups on both 2' and 3' carbon
125
what does RNA polymerase II do
uses a DNA template to make a complementary RNA strand (mRNA transcript)
126
what are the two phases of mRNA processing
protection
- nucleotide sequences are added to each end of the transcript to protect it from degradation
- 5' cap: 5' end of a single G nucleotide is attached ot the 5' end
- poly-A tail : a long sequence of A nucleotides are attached to the 3' end
- protect from exonuclease attacks
splicing
- removal of introns from RNA using spliceosomes
- parts that remain are called exons
- pre-mRNA (before splicing) and primary or mature RNA (after splicing)
127
what are exonucleases
enzymes that specifically target RNA molecules with exposed 5' ends
128
what are introns and exons
introns - sequences of RNA that don't contain any information on how to construct a protein
exons - sequences of RNA that do contain information
129
what are spliceosomes
enzyme that locates introns in mRNA, cuts them out, and fuses the remaining parts together
130
what is the idea of RNA interference
promising class of medical therapy that disrupt the production of harmful proteins by intercepting and incapacitating mRNA transcripts before they make it to the ribosomes
- used in Ebola treatment
- siRNA (short interfering RNA) - class of engineered molecules that capture and destroy harmful mRNA transcripts
131
what are the three germ layers formed by gastrulation
ectoderm (outermost layer) ; mesoderm ; endoderm (innermost layer)
132
what does the ectoderm differentiate into
form epithelial cells/tissues and neuronal tissues (neuronal plate and tube)
- neural tube will later give rise to brain and spinal cord
- stimulated by growth factors
- epidermis; cornea and lens of eye; nervous system; sensory receptors in skin; adrenal medulla; teeth enamel
133
what does the mesoderm differentiate into
develops into the circulatory system (blood cells, vessels, heart) and various connective tissues (bone, muscles, tendons, and dermal layer) and kidney
- reorganized into groups of cells called somites which have spaces in between them and develop into the ribs, lungs, and spine muscles
- notochord ; skeletal system ; muscular layer of stomach ; excretory system ; reproductive system (except germ cells)
134
what does the endoderm differentiate into
forms the epithelial lining of the whole of the digestive tube (except part of mouth and pharynx) and the end part of the rectum
- forms internal organs like stomach, colon, liver, pancreas, bladder, lungs, intestines, thyroid glands
135
a nucleotide contains ______
a phosphate group, a pentose sugar, and a nitrogenous base
136
why are the nitrogenous bases called bases
the electronegative N has an extra lone pair that can take up protons if needed
137
what are phosphodiester linkages
ester bonds that connect phosphate groups to sugars and make up the DNA backbone
- phosphate is connected to 5' carbon of sugar below it and 3' carbon of sugar above it (for 5-3')
- opposite way for 3'-5' strand
138
what's the difference between the 5' and 3' end of DNA
5' end - has free phosphate group attached to 5' carbon
3' end - has free hydroxyl group attached to 3' carbon
139
what are telomeres and what do they do
little caps at the end of chromosomes that protect them from degradation
- act as a buffer zone (very tips of chromosomes cannot be reached by replication enzymes so telomeres are there to ensure all the important genes are replicated)
- prevent chromosomes from sticking to each other
140
what does telomerase do
enzyme that lengthens telomeres and brings them back to their original length
- telomeres shorten each time DNA gets replicated
141
what is single copy vs repetitive DNA
single copy DNA
- one sequence of DNA that does not repeat itself
- usually contains the most important genes
- gets highly translated and transcribed with low rates of mutation
repetitive DNA
- found mainly near the centromeres (centers) of DNA
- contains both genes and sequences that are not genes
- higher rate of mutation
- highly repetitive DNA has no genetic information and is not transcribed/translated (telomeres are an example of this highly repetitive DNA - TTAGGG)
142
you can only add nucleotides to DNA in which direction
5' --> 3'
- can only add nucleotides on to 3' end
143
what is leading vs lagging strand of DNA
leading is 3'-5' end (so its complementary sequence is 5' - 3' and bases can easily be added in the same direction
lagging is opposite direction so bases cannot be directly added on
- DNA primase puts RNA primers on small sections of DNA so they can be transcribed at a time (gives you Okazaki fragments)
144
what does DNA primase do
adds RNA primers (usually around 10 nucleotides) so that transcription can begin
145
what does DNA ligase do
seals up all the Okazaki fragments on the lagging strand
146
what does DNA polymerase I do
uses its 5'-3' exonuclease activity to remove RNA primers and replace them with DNA
147
western blotting detects _______ while southern blotting detects ________
specific proteins ; specific DNA sequences
148
the stereochemical designators a and B distinguish between
epimers at an anomeric carbon
149
which ideal solution exhibits the greatest osmotic pressure
0.1 M MgCl2
0.2 M NaCl
0.2 M CaCl2
0.5 M glucose
0.2 M CaCl2
this would dissociate into 3 ions so concentration becomes 0.6 M
150
what kind of mutation is necessary for a southern blot to be useful
the mutation needs to create or eliminate a restriction site (palindromes usually 4-6 bases long)
151
proteolytic cleavage is a _________ reaction
hydrolysis
152
what is native vs SDS page
native page - electrophoresis method of analyzing proteins ; keeps them in their native shape ; results are limited bc mass-to-charge ratio can get in the way
SDS page - electrophoresis method that compares proteins ONLY based on molecular mass
- denatures proteins through addition of a detergent which disrupts the non-covalent interactions and masks the charge (only size matters)
- functional protein cannot be regained
153
what is isoelectric focusing electrophoresis
separates proteins by their isoelectric point (pI)
- the protein migrates toward an electrode in a pH gradient until it reaches a region of the gel where pH = pI of the protein. Positively (+) charged proteins will move towards the cathode and negatively (-) charged proteins will move towards the anode.
