full review - biochem mcat Flashcards
four groups on AAs
carboxylic acid
R group
H atom
amino group
R group on AA determines
functions
amino acids with long alkyl chains are
hydrophobic
AAs with charges are
hydrophilic
stereochemistry of alpha-carbon is (answer) for all chiral AAs
L configuration
carbohydrates are (answer) configuration
D config
all chiral AAs except (what) have S configuration
cysteine
all amino acids are chiral except
glycine
lower pH means
AA is FULLY protonated
when the pH is around the same value of the pI, that means the AA is a
neutral zwitterion
increased pH means that the AA is
FULLY deprotonated
what is pI?
pH at which AA is in zwitterion form
charges cancel out to make a neutral molecule
titration midpoint
pH = pKa
equivalence pt for a titration
pH = pI
dipeptide = how many residues
2
tripeptide =
3 residues
oligopeptides has less than
20 residues
polypeptides have greater than
20 residues
how to form a peptide bond
dehydration rxn
in a dehydration rxn, nucleophilic amino group of one AA attacks the
electrophilic carbonyl group of another AA
amide bonds
C-N bond of a peptide bond
RIGID due to resonance
breaking a peptide bond is a
hydrolysis rxn
primary structure of a protein
linear sequence of an AA in a peptide
what stabilizes primary structure
peptide bonds
AA sequence in primary structure is written
N-terminus to C-terminus
N-terminus is POSITIVELY charged due to -NH3+
secondary structure is the local structure of
neighboring AA
what stabilizes secondary structure
H-bonding between amino groups and nonadjacent carboxyl groups
alpha helices are found in what protein structure
secondary structure
clockwise coils around a central axis
beta-plated sheets are found in
2ndary structure
rippled strand that can be parallel or antiparallel
which AA can interrupt 2ndary structure
proline b/c of its rigid cyclic structure
what is denaturing
protein (or nucleic acid) loses quarternary/tertiary/2ndary structures
non-covalent interactions break
what non-covalent interactions break during denaturing
h-bonds
hydrophobic interactions
dipole-dipole interactions
tertiary structure is the
3d shape of a single polypeptide chain
what stabilizes tertiary structure
hydrophobic interactions
acid-base interactions
h bonds
disulfide bonds
hydrophobic interactions push r groups to the
interior of a protein
increases entropy of surrounding water molecules
negative gibbs free E created
disulfide bonds occur when two cystein molecules…
oxidize and create a covalent bond b/w thiol groups
when two cystein molecules are oxidized and create a covalet bond b/w thiol groups, what is formed
cystine
quarternary structure is the interaction between
peptides in proteins that contain multiple subunits
conjugated proteins are proteins with
covalently attached molecules
what is the attached molecule in a conjugated protein?
prosthetic group
what can a prosthetic group be?
metal ion
vitamin
lipid
carbohydrate
nucleic acid
what can cause denaturation
heat or solute concentration
monosaccharides are single carbohydrate units with…
glucose as the most commonly observed monomer
monosaccharides can undergo
oxidation/reduction
esterification
glycoside formation
aldoses oxidized into
aldonic acids
reduced to alditols
sugar that can be oxidized are
reducing agents
sugar that are reducing agents can be detected by
reacting with Tollen’s or Benedict’s reagents
in deoxy sugars, what replaces what
-H replaces -OH
in esterification, sugars react with…
carboxylic acids and their derivatives
forming esters
phosphorylation is a phosphate ester formed by….
transferring a phosphate group from ATP onto sugar
glycoside formation is the basis for building….
complex carbohydrates and requires anomeric carbon to link to another sugar
cyclization describes ring formation of
carbohydrates from straight-chain forms
anomeric carbon is the new chiral center formed in
ring closure
alpha-anomers have the -OH on the
anomeric carbon trans to the free -CH2OH group
beta-anomers have the –OH on the
anomeric carbon cis to the free CH2OH group
what represents 3D structure of a monosaccharide?
hawthorn projections
mutarotation is the spontaneous shift from one
anomeric form to another w/ the straight-chain form as an intermediate
disaccharides form as a result of
glycosidic bonding b/w two monosaccharide subunits
dissacharide examples
sucrose, lactose, maltose
polysaccharides are formed by repeated…
monosaccharide or polysaccharide glycosidic bonding
cellulose is the main structure component for
plant cell walls
cellulose is the main source of
fiber in a human diet
starches are the main energy storage form for
plants
amylose is unbranched or branched?
unbranched
amylopectin is branched or unbranched?
branched
lipids are insolube in
water
lipids are soluble in
nonpolar organic solvents
phospholipids are
amphipathic and form the bilayer of membranes
phospholipids contain a
polar head and nonpolar tails
polar head is attached by
phosphodiester linkage which determines the phospholipid function
saturation of the fatty acid tails determines
membrane fluidity
saturated fatty acid is less or more fluid than unsaturated
less
glycerophospholipids contain a
glycerol backbone
spingolopids contain a
spingosine backbone
many spingolipids are also phospholipids with a
phosphodiester bond
spingomyelines are the major class of
spingophospholipids
part of myelin sheath
glycosphingolipids are attached to sugar moieties instead of
a phosphate group
cerebrodies have how many sugars connected to the spingosine
1 sugar
globosides have how many sugars
2 connected to spingosine
gangliosides contain oligosaccharides with….
at least 1 terminal acetylneuraminic acid
waxes contain long-chain fatty acids…
esterified to long chain alcohols
protection against evaporation/parasites in plants and animals
terpenes are
steroid precursors
terpenoids are derived from terpenes via
oxygenation or backbone rearrangement
odorous characteristics
steroids contain…
3 cyclohexane rings
1 cyclopentane
3 rooms and 1 basement
steroid hormones have high-affinity receptors, work at low…
concentrations
affect gene expression/metabolism
cholesterol is a steroid important to
membrane fluidity and stability
serves as a precursor to many other molecules
prostaglandins are what kind of signalling molecules
autocrine and paracrine signalling molecules
prostaglandins regulate
cAMP levels
prostaglandins affect
smooth muscle contraction
body temp
sleep-wake cycle
fever
pain
fat soluble vitamins
vitamins A, D, E, K
vitamin A
carotene
vision
vit D
cholecalciferol
bone formation
vit E
tocopherols
antioxidants
vit K
forms prothrombin (clotting factor)
phylloquinone and menaquinone
triacylglycerols are a storage form of
fatty acids
1 glycerol attached to 3 fatty acids by ester bonds is
triacylglycerols (very hydrophobic!)
adipocytes are animals cells used for
triacyglycerol storage
free fatty acids are unesterified fatty acids that
travel in bloodstream
salts of free fatty acids = soaps
saponification is the ester hydrolysis of
triacylglycerols using a strong base like sodium or KOH
micelle can dissolve a lipid-solube molecule in
its fatty acid core
washes away with water b/c of shell with carboxylate head groups
cerebroside is a type of
glycolipids
a glycolipid is a
lipid linked to any sugar
2ndary structure are interactions between bases within
the same molecule
2ndary structure in DNA, bases are held together by
h bonds
2ndary structure is responsible for the
shape of nucleic acid
quarternary structure is the interactions of
nucleic acids with other molecules
e.g. chromatin interacting w/ histones
nucleic acids are
polymers of nucleotides
DNA replication is the process of producing an
identical replica of a DNA molecule
occurs during S phase of cell cycle
oncogenes develop from mutations of
proto-oncogenes and promote cell cycling
may lead to cancer
oncogenes =
stepping on gas pedal
tumor suppressor genes code for
proteins that REDUCE cell cycling
promote DNA repair
mutated tumor suppressor genes =
cutting the brakes
proofreading is when DNA polymerase
proofreads its work and excises incorrectly matched bases
daughter strand is identified by its
lack of methylation and corrected accordingly
mismatch repair occurs during
G2 phase using MSH2 and MLH1 genes
nucleotide excision repair fixes helix-deforming lesions of
DNA such a thymine dimers
cut-and-patch process
excision endonuclease
base excision fixes nondeforming lesions of the
DNA helix such as the cytosine deamination by removing base
leaving AP site
AP endonuclease removes the
damaged sequence which can be filled in with the correct bases
what is DNA
macromolecule that stores genetic info in all living organisms
nucleoside is a 5-carbon sugar and
nitrogenous base
NO PHOSPHATE groups
nucleotides are
a nucleoside with 1 to 3 phosphate groups added
nucleotides in DNA contain
deoxyribose
nucleotides in RNA contain
ribose
name the nucleotides
adenine (A)
thymine (T)
guanine (G)
cytosine (C)
uracil (U)
in RNA, what replaces T
U replaces T
A paired with U via 2 H-bonds
watson-crick model is the backbone of
alternating sugar/phosphate groups
watson-crick model is always read
5’ to 3’
two strands with antiparallel polarity wind into a
double helix
nitrogenous bases
purines: adenine and guanine (2 rings)
pyrimidines: cytosine, thymine, uracil (1 ring)
chargaff’s rule states that
number of purines = number of pyrimidines
A = T
C = G
B-DNA means
a right-handed helix is formed
DNA is B-DNA
low concentrations of Z-DNA has what shape
zigzag shape
has a high GC content or high salt concentration
denatured DNA gets
pulled aparted
reannealed DNA gets
brought back together
how many chromosomes in human cells
46
DNA is wound around (what) to form…
histones to form nucleosomes
nucleosomes can be stabilized by
another histone protein
as a whole, DNA and its associated histones make up
chromatin in the nucleus
chromatin types
heterochromatin
euchromatin
heterochromatin is
dark, dense, silent
euchromatin is
light, uncondensed, expressed
where are telomeres
end of chromosomes
telomeres contain high GC-content to prevent
DNA unravelling
during replication, telomeres are
shortened
telomeres shortening can be partially…
reversed by telomerase
where are centromeres
middle of chromosomes
centromeres hold
sister chromatids together until separation during anaphase in mitosis
high GC-content maintains what between chromatids
a strong bond
acrocentric chromosomes is located near one end of the
chromosome and not in the middle
recombinant DNA is DNA composed of
nucleotides from 2 different sources
hybridization is the joining of
complementary base pair sequences
what is the central dogma
statement that DNA is transcribed to DNA which is translated to protein
degenerate code allows for multiple codons to
encode for the same AA
start and stop codons
start codon: AUG
stop codons: UAA, UGA, UAG
start codon
AUG
stop codons
UAA
UGA
UAG
wobble is the
3rd base in the codon
allows for mutations to occur w/o effects in protein
wobble base pairings are less
stable
silent point mutations are…
mutations with no effect on protein synthesis
silent point mutations are usually found in the
3rd base of a codon
nonsense point mutations are…
mutations that produce a premature STOP codon
missense point mutations produce a codon that…
codes for a different AA
frameshift mutations result from a
nucleotide addition or deletion
frameshift mutations change the
reading frame of subsequent codons
RNA is similar to DNA except that
ribose sugar instead of deoxyribose
uracil instead of thymine
single stranded not double
3 types of RNA
mRNA
tRNA
rRNA
mRNA is transcribed from
DNA in nucleus
mRNA travels into
cytoplasm for translation
tRNA brings in AAs and…
recognizes the codon on mRNA using its anticodon
rRNA makes up the
ribosome and is enzymatically active
tRNA translates the…
codon into the correct AA
ribosomes are factories where
translation (protein synthesis) occurs
eukaryotes have which ribosomes
80s
prokaryotes have which ribosomes
70s
initiation in prokaryotes is when the
30S ribosome attaches to the Shine-Delgarno sequences
scans for a start codon
lays down N-formylmethionine in P side of ribosome
eukaryote initiation
when 40S ribosome attaches to 5’ cap
scans for start codon
lays down methionine in P site of ribosome
elongation is the addition of a new
aminoacyl-tRNA into the A site of ribosome
transfer of growing polypeptide chain from tRNA in P site –> tRNA in A site
uncharged tRNA pauses in E site before exiting ribosome
A site tRNA moves to P site
termination occurs when the codon in the
A site is a stop codon
release factors places a water molecule on the
polypeptide chain and thus releases the protein during termination
posttranslation modifications:
folding by chaperones
quarternary structure formation
cleavage of protein/signal sequences
covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
DNA ligase fuses what together to create…
fuses DNA strands to create one strand
helicase function
unwinds DNA double helix
RNA polymerase II function
binds to TATA box within promoter region of gene
25 base pairs upstream from first transcribed base
hnRNA is the collective term for
the unprocessed mRNA in nucleus
posttranscriptional modification is the process in which the
eukaryotic cells where primary transcript RNA is converted into mature RNA
introns cut out
exons exit the
nucleus and form mRNA
introns spliced out so they
stay in nucleus
introns also enable
alternative splicing
alternative splicing is when
introns cut away and exons remain
but in alternative splicing, a certain exon may be cut out or an intro may stay
alternative splicing allows for the
RNA segment to code for more than one gene
what are added to the mRNA
5’ cap and poly-A tail
what do the 5’ cap and poly-A tail do
stabilizes mRNA for translation
prokaryotic cells can increase variability of gene products from
one transcript through polycistronic genes
multiple translation sites within the gene which leads to
different gene products
jacob-monod model explains how
operons work
operons are inducible or repressible
clusters of genes transcribed as a single mRNA
inducible systems
under normal condition, IS bonded to a repressor
turned on when an inducer pulls the repressor off
e.g. Lac operon
repressible systems
transcribed under normal conditions
can be turned off by a corepressor coupling w/ the repressor
binding of complex to operator site
e.g. Trp operon
transcription factors search for promoter and enhancer
regions in DNA
bind to DNA and recruit RNA polymerase
promoters are within
25 base pairs of transcription start site
enhancers are more than
25 base pairs away from the transcription start site
modification of chromatin structure affects the ability of transcriptional enzymes to….
access the DNA thru histone acetylation (+ access)
or DNA methylation (- access)
what does the fluid mosaic model account for?
presence of lipids, proteins and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells
in the phospholipid bilayer, each phosphlipid has a
hydrophilic head + hydrophobic tail
heads of phospholipids are arranged so that they are
facing outward and the tails make up in the inside of the membrane
proteins are embedded in the
phospholipid bilayer
lipid rafts are made of
lipids moving freely in the plane of the membrane
flippases are specific membrane proteins that maintain the…
bidirectional transport of lipids b/w layers of the phospholipid bilayer in cells
proteins and carbohydrates may also move within the
membrane but are slowed by their large size
all transmembrane movement is based on
concentration gradients
concentration gradient tells us whether the process is
passive or active
osmotic pressure is what kind of property
colligative
osmotic pressure is the pressure applied to a
pure solvent to prevent osmosis
used to express solution’s concentration
what characterizes osmotic pressure
“sucking” pressure in which a solution is drawing water in
proportional to its concentration
passive transport does not require
energy b/c the molecule is moving down its concentration gradient
simple diffusion is a type of
passive transport
in simple diffusion, small nonpolar molecules move…
passively from an area of high to low concentration until equilibrium is achieved
osmosis is a type of
passive transport
osmosis describes diffusion of water across
a selectively permeable membrane
facilitated diffusion is a form of
passive transport
facilitated diffusion uses what to move…
transport proteins to move impermeable solute across the cell membrane
active transport requires
energy (ATP)
primary active transport uses what to…
ATP to power transport of molecules across a membrane
secondary active transport is known as
coupled transport
2ndary active transport harnesses energy released by
one particle going down electrochemical gradient to drive a different particle up its gradient
symport is when
both particles flow in same direction
part of 2ndary active transport
antiport is when
particles flow in opp direction
part of secondary active transport
endocytosis and exocytosis are the methods of
engulfing material into the cells or releasing material out of the cell
pinocytosis is the ingestion of
liquids aka vesicles
phagocytosis is the ingestion of
larger solid materials
lipids are the primary…
membrane component
both by mass and mole fraction
triaglycerols and fatty acids act as
phospholipid precursors and are found in low levels in the membrane
glycerophospholipids replace one fatty acid with a
phosphate group (often linked to other hydrophilic groups)
cholesterol is present in
large amounts in the membrane
cholesterol contributes to
membrane fluidity and stability
lower temp = decrease fluidity
increase temp = increase fluidity
waxes are present in very
small amounts
what are waxes most prevalent in?
in plants
function: waterproofing and defense
transmembrane proteins are a type of integral protein that…
spans the entire membrane
often glycoproteins
embedded proteins are most likely part of
catalytic complex or involved in cellular communication
membrane-associated proteins may act as
recognition molecules or enzymes
carbohydrates can form a
protective glycoprotein and also function in cell recognition
extracellular ligands can bind to
membrane receptors which function as channels/enzymes in second messenger pathways
gap functions allow for rapid exchange of
ions and other small molecules b/w adjacent cells
tight junctions prevent solutes from leaking into
the space b/w cells via a paracellular route
do NOT provide intercellular transport
desmosomes bind adjacent cells by
anchoring to cytoskeletons
hemidesmosomes are similar to desmosomes but
their main function is to attach epithelial cells to underlying structures
GLUT-2 is found in
liver for glucose storage and pancretic b-islet cells (as a part of the glucose sensor)
INCREASED Km
GLUT-4 is found in
adipose tissue and muscle
stimulated by insulin
LOWERED Km
mechanical digestion of lipids occurs…
primarily in the mouth and stomach
chemical digestion of lipids occurs in the
small intenstine
chemical digestion is facilitated by
bile, pancreatic lipase, colipase, cholesterol esterase
upon entry into the duodenum, what occurs
emulsification which is the mixing two liquids don’t mix usually (fat + water)
emulsification increases the
surface area of the lipid
increasing surface of the lipid via emulsification permits
greater enzymatic interaction and processing
what aids emulsification?
bile salts
micelles are
water-soluble spheres w/ a lipid soluble interior
digested lipids may form micelles to be carried to
the intestinal epithelium where they are absorbed across the PM
short chain fatty acids are absorbed across
the intestine into the blood
long chain fatty acids are absorbed as
micelles and assembled into CHYLOMICRONS for release into lymphatic system
fatty acids are
carboxylic acids w/ a long chain
saturated fatty acids have
NO double bonds
unsaturated fatty acids have
one or more double bonds
five steps of fatty acid synthesis
activation
bond formation
reduction
dehydration
second reduction
where are fatty acids formed
cytoplasm from acetyl-COA that is transported out of the mitochondria
arachidonate is the precursor to
eicosanoid signalling mollecules
leukotrienes
eicosanoid signalling molecules:
prostaglandins
prostacyclins
thromboxanes
fatty acid oxidation occurs in the
mitochondria following transport by the carnitine shuttle
beta-oxidation uses cycle of
oxidation, hydration, thiolysis cleavage
fatty acid chain is shortened by
two carbon atoms in fatty acid oxidation
in fatty acid oxidation, what is generated
FADH2
NADH
acetyl CoA
ketogenesis is the process by which
ketone bodies form due to excess acetyl-CoA in liver (during prolonged starvation)
ketolysis regenerated
acetyl-CoA for energy use in peripheral tissues
brain can derive up to
2/3 of its energy from ketone bodies during starvation
where does protein digestion usually occur
small intestine
catabolism of cellular proteins occurs ONLY under
conditions of starvation
amino acids released from proteins usually…
lose their amino group through deamination
in protein catabolism, remaining carbon skeleton can be used for
energy
glucogenic AAs can be converted into
glucose through gluconeogenesis
all amino acids except (which ones) can be converted into glucose via gluconeogenesis
leucine and lysine
ketogenic can be converted into
acetyl-CoA and ketone bodies
which AAs are the only ones that are solely ketogenic?
leucine and lysine
cholesterol may be obtained through
dietary sources or through de novo synthesis in liver
HMG-CoA reductase synthesizes
mevalonate
rate limiting step of cholesterol synthesis
LCAT catalyzes formation of
cholesteryl esters for transport with HDL
CETP catalyzes transition of LDL by
transferring cholesteryl esters from HDL
open system is where matter and E can be
exchanged with the environment
closed system is where
ONLY energy can be exchanged w/ the environment
no work is performed during a closed system because
pressure and volume remain constant
entropy is the measure of
energy dispersion in a system
chain in free energy
delta G that occurs at 1 M concentration, 1 atm, 25 C
ATP is a
mid level energy molecules
ATP contains high energy phosphate bonds that are
stabilized via hydrolysis by resonance, ionization, loss of charge repulsion
ATP provides energy through
hydrolysis and coupling to energetically unfavorable reactions
ATP can donate a
phosphate group to other molecules
in glycolysis, ATP donates a
phosphate group to glucose = G6P
bio oxidation and reduction reactions can be broken down into
component half-reactions
half-reactions provide useful info about
stoichiometry and thermodynamics
high energy electron carriers may be
soluble or membrane-bound
high energy electron carriers include
NADH2
NADPH
FADH2
ubiquinone
cytochromes
glutathione
flavoproteins is a subclass of electrons carriers…
dervied from riboflavin (vit B2)
e.g. FAD and FMN
insulin is secreted by
pancreatic b-cells
insulin is regulated by
glucose
insulin decreases
blood glucose by increasing cellular uptake
insulin increases rate of
anabolic metabolism
what secretes glucagon
pancreate a-cells
glucagon is stimulated by
low glucose and high AA levels
glucose increases
blood glucose by promoting gluconeogensis and glycogenolysis in liver
glucocorticoids increase blood glucose in response to…
stress by mobilizing fat stores and inhibiting glucose uptake
glucocorticoids increase impact of…
glucagon and catecholamines
e.g. cortisol
catecholamines promote glycogenolysis and….
increases basal metabolic rate through sympathetic NS activity
“adrenaline rush”
e.g. epinephrine and noriepinephine
thyroid hormones increase
basal metabolic rate
due to increased oxygen consumption and heat production when thyroid hormones are secreted
T3 is more potent than
T4 b/c i.t. has a shorter half-life
t3 is available in lower concentrations in the blood
T4 is converted to
t3 at tissues
thyroid hormones are what-based
tyrosine
equilibrium is a (what) state for most biochemical rxns
undesirable state for biochemicals rxns b/c organisms need free energy to survive
postprandial state is when body is
well-fed + absorptive
insulin increases
anabolism prevails
postabsorptive state is when body is
fasting
lowered insulin
increased glucagon and catecholamine
transition to catabolism
starvation leads to increased
glucagon and catecholamine
most tissues rely on
fatty acids
calorimetry measures
metabolic rates
respiratory quotient estimates
composition of fuel actively consumed by body
RQ =
Co2 produced / O2 consumed
ghrelin increases
appetite
regulatory hormone
orexin increases
appetite
regulatory hormone
leptin decreases
appetite by suppressing orexin production
BMI =
mass / height^2
liver is the most
metabolically diverse tissue
hepatocytes are responsible for the maintenance of blood glucose levels…
by glycogenolysis and gluconeogenesis to pancreatic hormone stimulation
liver process what materials
lipids, cholesterol, bile, urea, toxins
adipose tissue stores lipids under the influences of…
insulin and releases them under the influence of epinephrine
skeletal muscle metabolism will differ depending on
current activity level and fiber type
resting muscle conserve carbohydrates in…
glycogen stores and uses free fatty acids from bloodstream
active muscle may use anaerobic metabolism and…
glucose phosphorylation
direct phosphorylation from creatine phosphate
or
fatty acid oxidation
depending on fiber type + exercise duration
cardiac muscle uses fatty acid oxidation in…
both the well-fed and fasting states
brain and nervous tissue consume only glucose in
all metabolic states except for prolonged fasts (where 2/3 of brain’s fuel will come from ketone bodies)
name the branched alkyl side chains
leucine
isoleucine
valine
protein domains are
distinct regions in a polypeptide chain that fold independently
each protein domain carries out
a separate function (may assist another domain in performing its function)
one of the most common functions of a protein domain is to
bind a ligand (small molecule)
what does Kd measure
Kd = dissociation constant / affinity of a protein
small Kd =
high binding affinity (low tendency of complex to dissociate)
what does DNA determine?
sequence of AA in proteins
blueprint for living organisms passed from one gen to the next
main difference b/w prok or euk cells?
NUCLEUS
which of the following is found in prokaryotes:
mitochondria
nucleus
chloroplasts
ribosomes
more than 1 of these
ribosomes
where are ribosomes found?
rough ER
smooth ER does what?
makes lipids
rough ER does what?
makes ribosomes from mRNA
what can capture light energy and turn it to sugar?
chloroplast
what does the golgi apparatus involved in
sorting and modifying
spontaneous reaction is exer or endergonic?
exergonic
speed of spontaneous process?
FAST
heat of reaction at constant pressure is marked by
its change in enthalpy
hydrolysis of ATP involves
release of energy
monomers of proteins are
amino acids
what kind of compounds are more likely to dissolve in nonpolar solvents?
covalent compounds
ionic compounds and polar covalent compounds tend to dissolve in water because of
on-dipole and dipole-dipole interactions
hydrogen bonds can only form within a single molecule. T or F?
false
max number of H bonds a single water molecule can form?
4
what makes for a good H bond acceptor?
high electronegativity
nonbonding pair of electrons
h bonds explain which of the following properties of water?
water is a good solvent for ionic/polar molecules
water has a high melting pt and boiling pts for its small size
ice expands when frozen
bases are
proton acceptors
what has a greater Ka: weak or strong acid?
strong acid
small pkA means
strong acid
dissociation cosntant (Ka) for an acid with a pKa value of 6.0 is
1 x 10^-6
how to calculate pH from H+ ion concentration
pH = -log[H+|
how to calculate H+ concentration
[H+] = 10^ -pH
buffering capacity refers to the
extent to which a buffer solution can counteract the effect of added base or acid
main intracellular buffer system
H2PO4- / HPO4
stereoisomers are
nonsuperimposable mirror-image molecules
which AA takes on a negative charge when the R group loses a proton?
glutamic acid
true or false: Thr and Ser have hydroxyls as side chains
true
Asn has a polar or nonpolar side chain?
polar
pKa values of the amino groups of common AAs are around
pH 9
alpha-helices only use
intrachain H bonds
beta-sheets can use
intrachain or interchain H bonds
in the alpha-helix, there are
h bonds parallel to the helix axis
which forces are important in tertiary structure
disulfide bonds
h bonds
hydrophobic interactions
bonds involved in disulfide bonding
covalent bonds w/ R groups
what can cause protein denaturation?
heat
extreme pH
detergents
what maintains quarternary structure of a protein?
h bonds
ionic interactions
hydrophobic interactions
what does catalyst do to deltaG?
catalyst lowers deltaG
what does increased temperature do to enzyme-catalyzed reactions?
rate of enzyme rxns increases until heat denatures enzymes
true or false: all catalysts work by lowering the activation energy for a rxn
TRUE
active sit of an enzyme
substrate binds via noncovalent forces
substrate binding site
reactive group catalyze rxn here
sigmoidal curve suggests that
the characteristics of a multi-subunit enzyme
what type of enzyme display sigmoidal kinetics
ALLOSTERIC
allosteric enzymes have what curve shape
sigmoidal
e.g. hemoglobin
mechanism of an enzyme-catalyzed reaction makes which assumption about the conversion of production into substrate
product is not converted to substrate to any appreciable extent
lineweaver burk plot is useful for
seeing whether points deviate from a straight line than from a curve
lineweaver burk plot is not affected by
presence of inhibitors
lineweaver-burk plot can be used whether or not
the enzyme displays michaelis-menten kinetics
what does the michaelis constant determine
Km
michaelis constant describes the
affinity between enzyme and substrate
dimension (units) for the michaelis constant is
concentration such as molarity
Km is the substrate concentration necessary to
reach 1/2 vmax
lower Km =
HIGHER affinity
which inhibitor binds to the enzyme at a site other than the active site?
noncompetitive inhibitor
what inhibitor has an unchanged Vmax?
competitive inhibitor
what happens to the vmax with noncompetitive inhibitor?
vmax is altered
behavior of allosteric enzymes depends on
changes in quaternary structure upon binding of substrate or effectors
according to the concerted model of allosteric behavior, an allosteric activator favors the
relaxed form of the enzyme
main distinguishing feature of the concerted model for the behavior of allosteric enzyme is the
conformation of all subunits changes simultaneously
phosphorylation and allosteric control of enzymes can be combined to
afford a high degree of control over enzymatic reactions
in zymogen activation, an inactive protein is converted to
an active one by bond cleavage
how are cofactors bound to their enzymes
either covalently or non-covalently
examples of coenzymes
NAD+
FAD
biotin
what often functions as coenzymes in redox reactions?
NAD+ and FAD (nicotinamide adenine dinucleotides)
what does amphipathic mean?
there are hydrophilic and hydrophobic regions
fatty acids in both (x and y) vary
triacylglycerols and phospoacylglycerols
cholesterol has some degree of what nature
amphipathic
true or false: lipids differ from most biomolecules b/c they are defined on basis of solubility rather than chemical structure
TRUE
what does cholesterol do for membrane fluidity?
prevents extremes (too fluid or too firm)
association of integral membrane proteins w/ lipids in the membrane bilayer always involves
hydrophobic interactions
plants oils have more unsaturated or saturated fats?
UNSATURATED (less cholesterol)
distribution of lipids in membrane is
uneven w/ bulkier molecules on exterior
where can membrane proteins be located?
entirely within membrane
on surface of membrane
properties of membrane proteins
transport of substances into and out of cell
catalysis (enzymatic activity)
acting as a receptor
is energy storage part of the functions for membrane proteins?
no
lipid vitamins found in membranes
vitamins A and E
vitamin needed for blood coagulation
vitamin K
if a single strand of DNA contains 2100 A residues and 1800 T residues, what will be on the complementary strand?
2100 T (threonine) residues and 1800 A residues (alanine)
supercoiled helix can be untwisted by
helicase
production RNA from a DNA template is
transcription
mRNA base sequence directs AA sequence of a protein is called
translation
DNA replication in a prokaryote begins at a
unique site and proceeds in one direction all the way around a typically circular chromosome
when the synthesis of new DNA is directed by an original template DNA molecule…
two DNA molecules are formed
each w/ one new strand and the other from original DNA
functions of DNA polymerase III
polymerization
clamping on to the DNA template
proofreading
what activity of DNA polymerase I is most important in removing the primer?
3’ to 5’ exonuclease activity
strands in double helix are
anti-parallel
have their 3’ to 5’ directions opposed
DNA synthesis direction
5’ to 3’ end on one strand and 3’ to 5’ end on the other strand
which enzyme is responsible for bulk of DNA synthesis during replication
DNA polymerase I
okazaki fragments are
short DNA pieces that explain how DNA is synthesized on lagging strand
why is a primer strand needed in DNA replication
DNA polymerases require a preexisting strand w/ a nucleotide having a 3’-OH
why is telomerase needed
one major difficulty in replicating linear DNA molecules is replacing DNA segment that is occupied by the RNA primer on telomeres at DNA ends
hydrolysis of a nucleoside triphosphate drives the
reaction
direction of RNA synthesis
5’ to 3’ end
RNA base pairing includes
A to U
G to C
promote site is
site on DNA at which RNA polymerase bind to start transcription
which RNA has a cloverleaf structure
tRNA
ends of eukaryotic mRNA protected from degradation
3’ end only (polyA tail)
5’ end of mRNA is the
5’ cap
which ends of prokaryotic mRNA are protected from degradation
neither end
TRUE OR FALSE: single codon can coded for more than one AA
false
best linkage describes covalent bond b/w an AA and its tRNA
carboxyl group fo AA linked to 3’ –OH of tRNA
codons known for each AA?
depends on AA
TRUE OR FALSE: in bacterial, each mRNA will bind to only one ribosome at a time?
TRUE
necessary step after peptide bond formation takes place to continue protein synthesis
dissociation of ribosomal subunits
in protein synthesis formation of new peptide bonds is catalyzed by
peptidyl transferase
translation of mRNA in bacteria begins
during transcription of mRNA
first tRNA (bearing fmet) binds to
“P” site on the ribosome
production of larger to smaller molecules is called
catabolism
what kind of process is catabolism
oxidative
what kind of process is anabolism
reduction
smaller to larger molecules is
anabolism
oxidation refers to the
loss of electrons
reduction refers to the
gain of electrons
TRUE OR FALSE: molecular oxygen is always the substrate in oxidation rxns
true
TRUE OR FALSE: oxidation of food molecules supplies energy used to separate ATP
TRUE
to drive the synthesis of ATP, hydrolysis of an organic phosphate substrate must
have a HIGHER free energy than ADP + Pi –> ATP
TRUE OR FALSE: in order to initiate a metabolic pathway it is sometimes necessary to activate the starting materials
TRUE
mechanisms used to activate substrates for further metabolism
making an isomer that is more reactive
addition of a phosphate group
combination with a vitamin (i.e. coenzyme A)
metabolism takes place in stages to:
- allow for efficient production and use of E and regulation of process
- b/c large free energy changes cannot occur in living organisms
in the absence of oxygen, pyruvate can be converted to
lactate IN HUMANS
in glycolysis, how many actual steps involve electron transfer
1 step
enzyme glucokinase does what?
phosphorylates a number of different sugars:
glucose, fructose, mannose
which molecule allosterically control the enzyme phosphofructokinase?
ATP
isomerization of dihydroxyacetone phosphate (DHAP) to G3P is favored because
G3P is being continuously drained off subsequent rxn in glycolytic pathway
ATP is synthesize by what in glycolysis
both substrate-level and oxidative phosphorylation
can the citric acid cycle be used as both an anabolic and catabolic pathway?
NO
which enzyme uses coenzyme FAD as an e- acceptor?
succinate dehydrogenase
conversion of malate to oxaloacetate has a high/pos gibbs free E yet it can take place b/c
the oxaloacetate product is used up in the subsequent rxn
when mitochondria are actively carrying out aerobic respiration…
the pH of the matrix is greater than the pH of the intermembrane space
TRUE OR FALSE: synthesis of ATP in mitochondria is driven by a proton/pH gradient
true
ultimate electron acceptor in ETC is
oxygen
what is an advantage of the multiple steps in electron transport?
more E can be captured to synthesize ATP by using small steps
ATP is more efficiently generated through
substrate level phosrylation than oxphos
main purpose of TCA
generate reduced coenzymes NADH and FADH2 to be used in ETC = ATP
net yield of ATP per glucose molecule during aerobic respiration
max 28
reduction of pyruvate to lactate
allows for recycling of NAD+
lactate fermentation
alcohol dehydrogenase resembles lactate dehydrogenase in that it
uses NADH as a coenzyme
does fermentation make any ATP?
no - it uses NAD+ when oxygen is not present
an uncompetitive inhibitor binds only with the
enzyme-substrate complex
allosteric effector binds at (where) and does what
allosteric site
induces a chance in enzyme shape so substrate can no longer bind to the active site
what happens with positive effectors
activity goes up
negative effectors
activity goes down
secondary structure of nucleic acids is made up of
interactions between bases within same molecule
secondary structure is responsible for the
shape that the nucleic acid assumes
RNA secondary structure has 4 basic elemetns
loops
helices
bulges
junctions
what fixes helix-deforming lesions of DNA such as thymine dimers
nucleotide excision repair
cut and patch process
oncogenes develop from
mutations of proto-oncogenes and promote cell cycling
may lead to cancer
DNA ligase function
joins DNA strands by catalyzing formation of phosphodiester bonds
pyrimidines
C, T, U
purines
A and G
during replication, telomeres are shortened and this can
be partially reversed by telomerase
recombinant DNA is composed of
nucleotides from two different sources
created only in labs
base excision repair fixes
nondeforming lesions of DNA helix by removing base and leaving an AP site
AP endonuclease then removes the
damaged sequence which can be filled in w/ the correct bases
bonds between nucleotide bases
h bonds
DNA backbone is held together by
phosphodiester bonds
form b/w sugar and phosphate groups
saturated fatty acid has how many double bonds in its tail and is more/less fluid
NO double bonds
less fluid
prostaglandins are
lipid compounds that are signalling molecules and regulae cAMP levels
prostaglandins affect the following functions
smooth muscle contraction
body temp
sleep-wake cycle
fever
pain
3 parts of a nucleotide
phosphate group, nitrogenous base, pentose sugar
irreversible inhibitor is any inhibitor that
covalently binds to the active site of some enzyme (eliminates any activity)
vmax and Km in noncompetitive inhibition
vmax goes down
Km has no change
vmax and Km in uncompetitive inhibition
vmax and Km go down
vmax and Km in competitive inhibition
vmax - no change
Km goes up
feedback inhibition of an enzyme is when
an enzyme is inhibited by high levels of a production from later in the same pathway
translation occurs in the
cytoplasm at the ribosomes
translation steps
initiation
elongation
termination
in prokaryotic translation, the 30S ribosome subunit attaches to the
Shine-Delgarno sequence and scans for a start codon
in translation elongation, the new tRNA enters ribosome at
A site
in elogation, the polypeptide chain is transferred from the
P site to A site to meet the new tRNA
in elogation, before leaving the ribosome, the tRNA stops in the
E site
order of sites for tRNA is
A P E
in translation, termination will occur when the
codon in the A site is a stop codon
release factor places a water molecule on the
polypeptide chain and thus releases the protein
post-translational modification can happen at
any time of protein’s lifespan
commonly phosphorylation
what are operons
found in prok DNA
contain groups of genes regulated together
operons contain
activators
inducers
repressors
advantage of operons
group of genes whose products are all needed for a common function can be transcribed together
operon promoter is the
binding site for RNA polymerase (enzyme that performs transcription)
operon operation is a
short region of DNA that lies partially within the promoter
interacts w/ a repressor that controls transcription of the operon
operation repressor does what
turns operon off
repressor binds to the
operator
blocks movement of RNA polymerase down DNA
when lactose is absent, the lac repressor
binds tightly to the operator
gets in RNA polymerase’s way
prevents transcription
with lactose, the lac repressor
is bound to allolactose and operator is released
RNA polymerase can now transcribe operon
operon activator does what
turns operon on
lac operon uses
catabolite activation protein (CAP)
when glucose levels are low, what is produced
cAMP
cAMP attaches to CAP –> binding DNA
RNA polymerase binds to promoter –> high levels of transcription
when glucose levels are high,
no cAMP is made
CAP cannot bind DNA w/o cAMP –> low levels of transcription
operon inducer
small molecule that triggers gene or operon expression
lac operon is considered an
inducible operon b/c its default state is to be turned off/repressed
but can be turned on w/ allolactose
inducible operon under normal conditions is
bonded to a repressor
inducible operons are turned on when an inducer
pulls the repressor from the operator site
e.g. lac operon is an inducible operon
repressible operon under normal conditions will
proceed w/ transcription
repressible operons can be turned off by a
corepressor coupling w/ the repressor and
the binding of this complex to the operator site
e.g. Trp operon
in the absence of tryptophan, the trp repressor
dissociated from operator and RNA synthesis proceeds
when trp is present, the trp repressor binds the operator and
RNA synthesis is blocked
transcription factors are proteins that
help turn specific genes “on” or “off” by binding to nearby DNA
enhancers are sequences of DNA that function
to enhance transcription
more than 25 base pairs away from transcription start site
histone acetylation increases accessibility of chromatin and allows
DNA binding proteins to interact
activates transcription
DNA methylation decreases the
accessibility of chromatin and stops DNA binding proteins from interacting
inhibits transcription
lac operon contains genes that code for proteins in
charge of transporting lactose into the cytosol and digesting into glucose
glucose used to make energy
INDUCIBLE operon
genes in the lac operon will be expressed if
lactose is available
glucose is low
when lactose is available, the inducer
binds to the repressor and the repressor detaches from the DNA
