mcat rev Flashcards
amino acids have four groups attached to a
central alpha carbon
the four groups that make up an AA?
carboxylic acid group, H atom, amino group, R group
R group function
chemistry and function of AA
how many AAs appear in eukaryotic organisms’ proteins?
20
ALL AAs are chiral except
glycine
ALL chiral AAs except cysteine have
S configuration
nonpolar/nonaromatic side chains:
glycine, alanine, valine, leucine, isoleucine, methionine, proline
aromatic side chains:
tryptophan, phenylalanine, tyrosine
polar side chains:
serine, threonine, asparagine, glutamine, cysteine
negative charged (acidic) side chains:
aspartate, glutamate
positively charged (basic) side chains:
lysine, arginine, histidine
amino acids w/ long alkyl chains are
hydrophobic
amino acids with short alkyl chains are
hydrophilic
amphoteric:
means AAs can accept or donate protons
pKa of a group is the
pH at which half the species is deprotonated
[HA] = [A-]
AAs exist in different forms at
different pH values
at low (acidic) pH, AA is
fully protonated
at pH near the isoelectric pt (pI) of the AA,
the AA is a neutral zwitterion
at high (alkaline) pH, AA is
fully deprotonated
isoelectric point (pI) is
calculated for an AA without charged side chains by averaging two pKa values
can AAs be titrated?
yes
titration curve is nearly flat at
pKa values of AA
titration curve is nearly vertical at the
pI of the AA
AAs with charged side chains have additional
pKa value
pI is calculated by averaging the two pKa values that correspond to the protonation and deprotonation of zwitterion
AAs w/o charged side chains have a
pI around 6
acidic AAs have a pI
below 6
basic AAs have a pI
above 6
dipeptides have two
AA residues
tripeptides have three
AA residues
oligopeptides have a (x) AA residues
FEW (less than 20)
polypeptides have
MANY AA residues
forming a peptide bond is a
condensation or dehydration rxn
nucleophilic amino group of one AA attacks
the electrophilic carbonyl group of another AA
amide bonds are rigid because of
resonance
breaking a peptide bond is a
hydrolysis reaction
primary structure of a protein is the
linear sequence of AAs in a peptide and is stabilized by peptide bonds
secondary structure of a protein is the
local structure of nearby AAs
stabilized by H-bonding b/w amino groups and nonadjacent carboxyl groups
alpha-helices are
clockwise coils around a central axis
beta-pleated sheets are
rippled strands that can be parallel or antiparallel
proline can interrupt
secondary structure b/c of its rigid cycle structure
tertiary structure is the
3D shape of a single polypeptide chain
what stabilizes tertiary structure?
hydrophobic interactions
acid-base interactions (salt bridges)
h-bonding
disulfide bonds
hydrophobic interactions
push hydrophobic R groups to the interior of a protein
increases entropy of the surrounding water molecules and creates a negative gibbs free E
disulfide bonds occur when
two cysteine molecules are oxidized and create a covalent bond to form cystine
quaternary structure is the interaction
between peptides in proteins that contain multiple subunits
conjugated proteins
proteins with covalently attached molecules
attached molecules on conjugated proteins is called
prosthetic group
what can the prosthetic group be?
metal ion
vitamin
lipid
carbohydrate
nucleic acid
denaturation is
when heat and increasing solute concentration can lead to loss of 3D protein structure
what do enzymes do?
lower activation energy
increase reaction rate
enzyme specificity states that a given enzyme will ONLY catalyze….
a single rxn / class of rxns with these substrates
substrates
molecules upon which an enzyme acts
six types of enzymes
oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase
oxidoreductases catalyze
oxidation-reduction reactions
- transfer of electrons bw bio molecules
- often have a cofactor that acts as an electron carrier (NAD+ or NADP+)
in reactions catalyzed by oxidoreductases, the electron donor is the
REDUCTANT
in reactions catalyzed by oxidoreductases, the electron acceptor is the
OXIDANT
enzymes in which oxygen is the final electron acceptor
often includes oxidase in their names
transferases catalyze the movement of
a functional group from one molecule to another
kinases catalyze the transfer of a
phosphate group generally from ATP to another molecule
hydrolases catalyze the breaking of
a compound into two molecules using the addition of water
lysases catalyze the
cleavage of a single molecule intwo two products
lysases do not require
water as a substrate and do not act as oxidoreductases
because most enzymes can also catalyze the reverse of their specific reactions,
the synthesis of two molecules into a single molecule may also be catalyzed by a lyase
isomerase catalyze the rearrangement of
bonds within a molecule
isomerases catalyze rxns b/w
stereoisomers as well as constitutional isomers
some isomerases can also be classified as
oxidoreductases, transferases, lyases
ligases catalyze
addition or synthesis reactions (generally b/w large similar reactions) and often require atp
synthesis rxns with smaller molecules are generally done by
lyases
ligases are most likely to be involved in
nucleic acid synthesis and repair
what do lineweaver-burk plots display?
enzyme kinetic data in linear form
inverse of rxn velocity on y axis and inverse of substrate concentration on x axis
vmax is
the max possible rxn rate
km is the
concentration of substrate at which 1/2 vmax is achieved
y intercept of a lineweaver-burk plot is
1/vmax
x intercept of lineweaver-burk plot is
-1/Km
allosteric effectors are molecules that bind to
enzymes at a site other than the active site and either increase/decrease activity
allosteric effectors that increase activity
activators
allosteric effectors that decrease activity
inhibitors
lineweaver-burk plots created in the presence and absence of an allosteric effector can be compared to find out how
the effector alters Km and Vmax
x and y intercepts are related to the
inverse of Km and vmax
when presence of allosteric effector show y intercept increasing
vmax decreases, making effector an inhibtor
when x-int on lineweaver-burk plot is negative…
this shift moves intercept away from origin –> mag increases
(+) sign on lineweaver-burk plot means
allosteric effector is present
increasing y intercept =
decreased vmax
(-) means allosteric effector
is absent
left shifted x intercept means
decreased Km
which deoxyribonucleotides would move most slowly down an alkaline agarose gel during electrophoresis?
dGMP (pruine deoxyguanosine phosphate) would move the slowest as it’s the biggest
gel electrophoresis separates
molecules by molecular weight
DNA is composed of four
deoxyribonucleotides (dNMPs)
dGMP
purine deoxyguanosine phosphate is the largest
2nd largest deoxyribonucleotides (dNMPs)
deoxyadenosine monophosphate (dAMP)
3rd larges dNMP
deoxythymidine monophospate (dTMP)
smallest dNMP
deoxycytidine monophosphate (dCMPs)
oligonucleotide is a short strand of
DNA and its molecular weight is determined by its composition of dNMPs
metabolic pathways consist of both
reversible and irreversible reactions
opposing metabolic processes usually
use the same enzymes for reversible rxns (going in opp directions)
opposing metabolic processes must use
different enzymes to catalyze distinct rxns for the irreversible steps
many metabolic pathways are regulated by
allosteric effectors
allosteric effectors are
small molecules that bind to enzymes at sites other than the active site
upon binding, allosteric effectors induce
conformational changes in enzymes that alter enzyme activity
an effector that activates one metabolic pathways often
inhibits the opposing pathways
e.g. F2,6BP in glycolysis and gluconeogenesis
how many ntp produced during glycolysis
2 NTP
catabolic pathways degrade complex molecules into
simpler molecules to product high energy nucleotide triphosphates (NTPs such as ATP or GTP)
anabolic pathways use
simple molecules to synthesize more complex molecules (e.g. proteins, polysaccharides)
NTPs provide
energy for many bio processes
anabolism requires
energy input from NTPs
most catabolic processes are paired
with an opposing anabolic process
net ntp production or consumption refers to
the difference bw the numbers of NTPs produced and consumed in a process
ntp used in glycolysis
consumed 2 atps
produces 4 atps per glucose molecules
net production of 2 atps per glucose
glycolysis is what kind of process
catabolic
gluconeogenesis is what kind of process
anabolic
gluconeogenesis - ntps/atps
consumes a net total of 6 ntps (4 atps and 2 gtps) to produce one glucose molecule
glycolysis in the muscles is connected to
gluconeogenesis in the liver by the cori cycle
2 net ntps are produced when glucose becomes
pyruvate (glycolysis) partially offset the 6 net that are consumed later when pyruvate becomes glucose through gluconeogenesis
net number of ntps consumed by the first round of the cori cycle
6 - 2 = 4 net ntps consumed
ntps consumed in glycolysis/gluconeogensis
2 in glycolysis, 6 in gluconeogenesis = 8 total ntps consumes
4 ntps produced (glycolysis only)
8-4 = 4 new ntps consumed
catabolic processes lead to
energy production typically in the form of atp equivalents
anabolic processes consume
energy
glycolysis (catabolic) and gluconeogensis (anabolic) are connected by
the cori cycle
what metabolic process provides E necessary for sustained gluconeogenesis?
fatty acid oxidation
fatty acid oxidation produces
atp equivalents
fatty acid degradation to acetyl-CoA yields
NADH and FADH2 (both enter ETC = ATP)
resulting acetyl-CoA can enter the
citrtic acid cycle to produce more NADH and FADH2 as well as gtp (atp equivalent)
glycogenesis produces
glucose
when glycogen is present, gluconeogenesis is
not required
gluconeogenesis generally occurs
after glycogen stores have been depleted
fermentation is the conversion of
pyrute to lactate
resulting lactate from fermentation can enter gluconeogenesis after
being converted back to pyruvate
pentose phosphate pathway converts g
glucose and glycolysis intermediates to ribose-5-phosphate
process doesn’t consume/produce ATP
gluconeogenesis is an
anabolic process that requires energy from atp equivalents
necessary E for gluconeogenesis is provided by
catabolic processes such as fatty acid oxidation
blood glucose levels are primarily controlled by
peptide hormones insulin and glucagon
when blood glucose levels are high…
pancreas releases insulting –> induces glucose uptake into cells
insulin also induces
glycolysis and glycogen synthesis
helps remove glucose from bloodstream
when blood glucose is low…
pancreas releases glucagon
when glucagon binds to receptors on liver cells…
i.t. induces an intracellular response that ends up upregulating glycogenolysis and gluconeogenesis
releases glucose into blood
glucagon decreases
rate of glycolysis
increases gluconeogenesis
histones are nuclear proteins that…
help in the organization of eukaryotic DNA
serve as structural support for DNA to wind tightly around
allows genomic DNA to be condensed into the nucleus
histones can also help…
regular gene expression
depending on strength of the binding interaction bw histone and its associated DNA
strong interactions inhibit the
DNA’s accessibility and prevent transcription/gene expression
weaker binding interactions bw histone and its DNA
promote transcription and gene expression
lysine residues are charged…
positively
play an important role in histones due to their electrostatic interaction w/ neg charged phosphate groups on sugar-phosphate backbone
rxn with BHB neutralizes the…
lysine side chain
replaced charged amine w/ a neutral and non-ionizable amide
DNA-histone interaction weakens –> upregulation of gene expression
protein function is related to
structure and affected by temp
primary protein structure
linear AA sequence
secondary structure
results from H bonding in polypeptide backbone
quaternary structure
28 C
results from assembly of 1+ polypeptide chain
tertiary structure
37 C
results from AA side chain (R group) interactions
protein in quarternary structure binds…
DNA at lower temp
blocks transcription
protein in tertiary structure does not bind…
DNA at higher temp so transcription occurs
what links AAs?
peptide bonds link AAs
form proteins
sequence in which AAs are linked defines a
protein’s primary structure
chem characteristics (e.g. side-chain charge) of AAs in sequence
protein structure
function
environmental factors can change
protein structure (denaturation) and protein function
at lower temperatures, less protein was…
produced
transcription was repressed
allow dimerization
at higher temps, dimerization does…
not occur
transcription increases
mRNA is translated
into protein by ribosomes
CODING RNA
rRNA associates with
specific proteins to form ribosomes
NONCODING RNA
tRNA pairs
mRNA codons w/ specific AAs during translation
NONCODING RNA
snRNA associates with
specific proteins to form small nuclear ribonucleoproteins (snRNPs)
building block of spliceosomes
NONCODING RNA
siRNA (small interfering RNA)
functions in RNA interference
binds complementary mRNA and signals for its degradation
NONCODING RNA
miRNA (microRNA)
functions in RNA interference
binds target complementary sequence on mRNA molecule to silence gene expression
microRNAs bind
complementary sequences on target mRNA
inhibit expression at translational level
following binding, miRNA-mediated silencing occurs either by
promoting endonuclease activation
subsequent cleavage of target mRNA
or prevents target mRNA from binding to ribosomes (blocking translation)
rRNA pairs with specific proteins to form
ribosome, a molecular complex that brings mRNA and tRNA together
enzymatically manufacture polypeptides during translations
polymerase chain reaction (PCR) measures
DNA amplification after all the thermal cycles are complete
real time PCR quantifies
product amplification as rxn progresses in real time
oncogene is a
mutated/overexpressed gene that induces uncontrolled cell growth
promote cell cycle progression + inhibition of apoptosis
key feature of a tumor suppressor gene
inhibition of cell cycle progression
tumor suppressor genes regulate DNA repair by
rrepressing/pausing cell cycle to ensure that only normal cells proceed to divise stage
programmed cell death induced if repair fails
nucleic acid structures with more (x) pairs are more stable
G-C
A-U have how many H-bonds?
2
G-C bonds have how many H-bonds?
3
as beta-sheets form, the R groups
become aligned
glutamine is a
polar uncharged AA w/ an amide side chain
amides contain both a
carbonyl oxygen and an amide -NH2 group
amide -NH2 group can act as a
h-bond donor
carbonyl oxygen can act as a
h-bond acceptor
because side chains are aligned in beta-sheet and because glutamine side chain can simultaneously act as an acceptor and donor,
polyQ beta-sheets can form networks of H-bonds
in addition to the h-bonds b/w peptide backbone amide groups, glutamine-mediated h-bond networks…
further strengthen and stabilize beta-sheet conformation
having a stronger effect as polyQ length increases
stacking interactions stabilize which protein structure
secondary
occur between aromatic side chains such as Phe, Tyr, Tryp
which is more flexible: glutamine or glycine?
glycine
flexibility is favorable for beta-turns
proline’s ridigity is
conducive to tight turns
is glutamine rigid?
no
hydrophobic effect drives
protein folding
hydrophobic effect causes proteins to
adopt a conformation that hides as many hydrophobic residues in protein’s interior
changes that cause a protein to misfold often expose…
hydrophobic residues to the aqueous environment
misfolded proteins often
aggregate (group togther) to hide exposed residues
aggregation often results in a significant decrease in
protein’s solubility
glutamine has an uncharged
polar side chain
no ionic interactions to disrupt
interaction of glutamine side chains with each does not…
prevent interaction w/ water
h-bonds b/w side chains can transiently…
break to bond w/ water and vice versa
peptide backbones are not very hydrophobic because
they have both a carbonyl and an amino group that can form h-bonds
proteins that adopt non-native conformations are generally forced to…
more hydrophobic residues to the aqueous environment
hydrophobic residues cannot interact with water and therefore tend to
aggregate to minimize exposure due to hydrophobic effect
inability to interact with water results in
precipitation out of solute
how can beta-sheets be oriented?
parallel or antiparallel manner
parallel strands run in the same direction so the N-terminal of one strand aligns….
with the N-terminal portions of the others
in antiparallel sheets, the individual strand run in directions opposite each other so the…
N-terminal portion of one strand lines up w/ C-terminal portion of neighboring strands
secondary structure always includes
H-bonds b/w amide carbonyls and NH groups in the polypeptide backbone
parallel and antiparallel sheets differ in their
hydrogen bond geometries with bond pairs directly aligned in antiparallel sheets and slightly offset in parallel sheets
antiparallel strands run in
opposite directions
antiparallel strands may be linked by a
short sequence of AAs called a beta-turn
induces 180 degree bend in polypeptide chain
parallel beta strands do not reverse
directionality
neighboring strands must be linked instead by
longer loops that makes 360 degree turns to align N-terminal regions of neighboring strands
parallel strand can never be liked by
beta turns
beta-turns are
a short sequence of amino acids that induce a 180 degree bend in the polypeptide chain
molecular chapterones are proteins that
facilitate the proper folding of other proteins
chaperones ensure protein folds properly by binding
hydrophobic regions of nascent/misfolded/aggregated proteins
exposure to aqueous solvent is prevented
chaperons prevent or reverse
aggregation by blocking interactions b/w hydrophobic regions of separate polypeptides
disruption of interactions b/w beta-sheets could help disaggregate
amyloid fibers which may increase solubility and reduce toxicity
where are globular domains found?
oxidizing environment of the Golgi apparatus and its vesicles
bonds that most likely form between cysteine residues?
disulfide bonds
stabilizes tertiary structure
peptide bonds are covalent bonds formed between
amino acids to make proteins and peptides
contribute to a protein’s primary structure but not its tertiary structure
electrostatic interactions are frequently involved in
tertiary protein structure
DO NOT involve shared electrons and covalent bonds
thioester bonds form between a
sulfur atom and a carbonyl carbon
what are thioester bonds important for
coenzymes and metabolites such as acetyl-CoA and succinyl-CoA
do not participate in tertiary protein structure
3D folded form of a protein includes
secondary and tertiary structure
DETERMINED BY primary structure (AA sequence)
proteins with similar AA sequences often…
fold similarly
AAs with similar folds have similar AA sequences
proteins with different sequences are likely
to adopt distinct folds
domains with a protein behave as
individual units and typically fold indepedently from each other
low Kd means
few ligands required for binding
HIGH AFFINITY of a protein
high Kd means
many ligands required for binding
LOW AFFINITY
3rd base in a codon can
wobble and break standard Watson-Crick rules but STILL code for intended protein
wobble is caused by
redundancy found in genetic code
are wobble base pairings stable?
LESS STABLE
what mutation results from a nucleotide addition/deletion that changes reading frame of subsequent codons?
frameshift mutation
where are silent mutations usually found?
3rd base of a codon
missense mutation produces a
codon that codes for a different AA
nonsense mutation produces a
premature stop codon
first step of gene expression
transcription
transcription is the when
segment of DNA is copied into RNA by enzyme RNA polymerase
tRNA brings AAs to the ribosome and recognizes the
codon on the mRNA using its own anticodon
rRNA makes up the
ribosome and is enzymatically active
what is a segment of DNA wound in sequence around 8 histone protein cores
nucleosome
introns are
segments of DNA/RNA molecule that does NOT code for protein
introns stay in the
nucleus since they are cut out and not included in mRNA
exons exit the
nucleus and form mRNA
what process in eukaryotic cells have primary transcript RNA converted into mature RNA?
post-transcriptional modification
introns are cut out
alternative splicing is a
regulated process during gene expression resulting in a single gene coding for multiple proteins
in normal gene expression, introns are
cut away and exons remain in sequence
in alternative splicing, a certain exon may be
cut out or an intron may stay
alternative splicing allows for the
RNA segment to code for more than one gene
chromatin packages DNA into a
smaller volume to fit in the cell
heterochromatin is
dark, dense and silent
euchromatin is
light, uncondensed, expressed
segment of prokaryotic mRNA that encodes several proteins
polycistronic gene
purpose of 5’ cap and poly-A tail on mRNA is that they
protect mRNA for translation
start codon also codes for
methionine
in translation, a succession of tRNAs add their
AAs to the polypeptide chain as mRNA is moved through ribosome one codon at a time
acrocentric chromosome is one in which the
centromere is located near one end of the chromosome and not in the middle
what is transcribed from DNA in nucleus?
mRNA
mRNA travels into
cytoplasm for translation
