biochem Flashcards
what two groups do AA contain
amino and carboxyl
amino group
NH2
the α-carbon of most AA is a chiral center. what is the exception?
glycine, it has a H as R
all chiral AA in us are ____-amino acids
L
in a Fischer of L-AA, what group is drawn on the left?
NH2
all AA have a S configuration except ________
cysteine
non polar, non-aromatic AA (7)
glycine, alanine, valine, leucine, isoleucine, methionine, proline
GAVLIMP
which AA forms a cyclic structure
proline
aromatic AA (3)
TPT
tryptophan, pheynalanine, tyrosine
which AA has a double ring structure?
tryptophan
what is phenylalanine side chain
benzyl ring + CH2
adding ____ to phenylalanine makes tyrosine
OH
which aromatic AA is polar
tyrosine
polar, non-aromatic AA (5)
serine, threonine, asparagine, glutamine, cysteine
STAGC
stage with a C
serine and threonine have _____ in their R
-OH
asparagine and glutamine have ______ side chains
amide
amide
NH2 - C = O
what is cysteine’s side group
thiol, -SH
which AA is particularly prone to oxidation? why
cysteine, thiol is weaker than OH
negative, acidic AA (2)
aspartate and glutamate
rather than amides of asparagine/glutamine, aspartate/glutamate have ______ group
COO-
aspartate/glutamate is the _________ form of aspartic/glutamic acid
deprotonated
positive, basic AA (3)
lysine, arginine, histidine
LAH
which AA has an imidazole
histidine
which AA are hydrophobic
long side chain AA
alanine, leucine, isoleucine, valine, phenylalanine
which AA are hydrophilic
charged
LAH + aspartate + glutamate
pKa
pH at which half of the molecules are protonated
[HA] = [A-]
if pH < pKa, most will be
protonated
all AA have at least _____ pKa values
2
which pKa is first
2, carboxyl
which pKa is usually second
9-10, amino
when pH is close to pKa, the solution acts as a
buffer
pH = isoelectric point (pI) when
every molecule in the solution is a zwitterion (neutral)
how do you find the pI of an uncharged AA
average of pKa of amino & pKa of carboxyl
~6
how do you find pI of a negatively charged (acidic) AA
average of pKa of side group + pKa of carboxyl
how do you find pI of positively charged (basic) AA
average of pKa of amino + pKa of R group
basic AA have ______ pI
high, > 6
acidic AA have ___ pI
low, < 6
amino acid subunits make up a
peptide
what type of reaction is a peptide bond formation
condensation/dehydration
how do trypsin and chymotrypsin break the peptide bond
add H to amide N and OH to carbonyl, add H2O
where does trypsin clave
C-terminus of arginine and lysine
where does chymotrypsin cleave
C-terminus of non polar aromatic AA (phenyl, tryptophan, tyro)
what stabilizes primary structure
covalent peptide bonds between AA
what stabilizes secondary structure
hydrogen bonding between AA
what stabilizes an α-helix
hydrogen bond between = O and and an amide H from four AA away
in an α-helix, the side chains point
away from core
what is the α-helix important in
keratin
what stabilizes a β-sheet
hydrogen bond between = O of one chain and amide H of the adjacent chain
in a β-pleated sheet, the side chains point
above and blow the plane
what is the β-sheet important in
fibroin, silk fibers
what AA is not found in α-helices? why?
proline, it can make it kink
where is proline found in secondary structures
turns of a β-sheet or start of an α-helix
proteins that resemble sheets or strands are _______
fibrous
proteins that are spherical are ______
globular
what stabilizes tertiary structure
hydrophilic and hydrophobic interactions between R groups
what type of bond is important in tertiary structure
disulfide bonds
cysteine + cysteine =
cystine
what do disulfide bonds do
create loops in the chain
there is a _____ change in entropy when a hydrophobic solute is in water
negative, water surrounds in to maximize hydrogen bonding
what makes solvation more favorable after a solute is initially dropped
the hydrophilic move towards water, hydrophobic move to anterior
this allows water to spread out and increases entropy
quaternary structure only exists for proteins with
more than one chain
conjugated proteins
get some function from covalently attached prosthetic groups
oxidoreductase
catalyze oxidation-reduction reactions
oxidoreductaases often have
cofactors that carry electrons (NAD+, NADP+)
reductant
molecule that gives electrion
oxidant
molecule that receives electron
ΔG and ΔH _________ by catalysts
stay the same
enzymes active site is in appropriate conformation for substrate to bind, no alteration occurs. this is the __________ theory
lock and key
the shape of the active state becomes a good fit after the substrate begins to bind. this is the _________ theory
induced fit
apoenzymes
enzyme without their cofactor
holoenzymes
enzymes with their cofactor
cofactors
inorganic molecules or metal ions
coenzymes
organic groups
water-soluble enzymes (2)
vitamin B and ascorbic acid (vitamin C)
fat-soluble enzymes
A, D, E, K
vitamins and derivates are co__________
enzymes
thiamine
B1
riboflavin
B2
niacin
B3
pantothenic acid
B5
pyridoxal phosphate
B6
biotin
B7
folic acid
B9
cyanocobalamin
B12
Vmax = __________ of enzyme
saturation
how do you increase Vmax at saturation
increase concentration of enzyme
write the Michaelis-Menten equation
K1 Kcat
E + S ES –> E + P
K-1
velocity of MM equation
v = Vmax * [S]
__________
Km + [S]
when at 1/2 Vmax, Km =
[S]
what is Km
Michaelis constant, the concentration where half of the active sites are full
a higher Km = _________ affinity
lower
you ______ change Km
cannot
Vmax equation
Vmax = [E]kcat
kcat
of substrates converted to product per enzyme in a second
catalytic efficiency
Kcat / Km
an efficient enzyme will have a ____ Kcat and ____ Km
large, small
when will a enzyme show a sigmoidal curve on MM plot
when it has cooperativity
Hill’s coefficient > 1
positive cooperative binding
Hill’s coefficient < 1
negative cooperative binding
Hill’s coefficient = 1
no cooperative binding
feedback regulation
enzymes regulated by products produced later in the pathway
feedforward regulation
enzymes regulated by intermediates preceding the enzyme in a pathway
four types of reversible inhibition
competitive, noncompetitive, uncompetitive, mixed
competitive inhibition
substrate cant bind if something is blocking the site
how do you overcome competitive inhibition
add more substrate to outcompete
competitive inhibition
Vmax ____________
Km _____________
Vmax stays the same - there is enough enzymes
Km increases - need more substrate to outcompete
noncompetitive inhibition
inhibitor binds to an allosteric site, which induces an unfavorable change in conformation
inhibitor can bind the enzyme or enzyme-substrate complex, but binds them both equally
noncompetitive inhibition
Vmax ____________
Km _____________
Vmax decreases - less enzyme available
Km stays the same - affinity doesn’t change
mixed inhibition
inhibitor can bind to either enzyme or enzyme-substrate complex, but prefers one or the other
if a mixed inhibitor prefers the enzyme
Vmax ____________
Km _____________
Vmax decreases - less enzyme available
Km increases - makes the enzyme not want substrate
if a mixed inhibitor prefers the enzyme-substrate
Vmax ____________
Km _____________
Vmax decreases - less enzyme
Km decreases - makes the enzyme want substrate so it can bind
uncompetitive inhibition
bind only to enzyme-substrate complex and prevents release of substrate
uncompetitive inhibition
Vmax ____________
Km _____________
Vmax decreases - less enzyme free
Km decreases - want substrate there
motif
repetitive organization of secondary structures
collagen structure
trihelical, three left-handed helices forming a secondary right-handed helix
collagen function
strength and flexibility
elastin function
restores shape of connective tissue, acts like a spring
keratin function
mechanical integrity of cell
regulatory protein
primary protein in hair and nails
actin function
make up microfilaments
actin structure
positive and negative side, polarity allows motor proteins to travel unidirectionally
tubulin function
makes up MT
tubulin structure
negative end next to nucleus, positive end in periphery
motor protein involved with actin
myosin
motor proteins involved with tubulin
kinesin and dynein
kinesin function
align chromosomes during metaphase
depolarize MT during anaphasa
dynein function
sliding movement of cilia and flagellaa
kinesin & dynein also play a role in vesicle transport. how?
kinesin bring vesicle towards + end of MT
dynein bring vesicle towards - end of MT
CAMS are all ________ membrane proteins
integral
CAMs
bind cell to ECM or other cells
three families of CAMs
cadherins, integrals, selectins
cadherin
glycoprotein groups mediating calcium-dependent cell adhesion
caherins usually hold
similar cells together
integrin structure
β and α chains
integrin function
bind to/communicate with ECM cellular signaling (apoptosis, division)
selectin structure
bind to carbs that project from other cells
weakest adhesion molecule bond
selectin bond
which two CAM families play a role in defense
selectin and aherin
what hold the chains of Ig together
disulfide linkages and noncovalent interactions
how do you isolate proteins and biomolecules from tissue
lysis or homogenization
how do you isolate proteins from smaller molecules
centrifugation
how do you isolate proteins from other proteins
electrophoresis and chromatography
migration velocity equation
v = Ez / f
z = net charge of molecule f = frictional coefficient
a small, highly charged molecule in a strong E will have a _____ migration velocity
larger
in electrophoresis, anions will move towards the ______
anode
in electrophoresis, cations will mov towards the ______
cathode
anode is ___ charged
positive +
cathode is ___ charged
- negatively
PAGE analyzes proteins in ________ state
native
what is the limitation of PAGE
you should know their size to be able to compare their charge
since a small positive molecule can move the same distance as a large negative
how does SDS-PAGE improve on PAGE
it adds sodium dodecyl sulfate, a detergent
it adds net negative chains to the protein
so, they move only based on size! not charge.
isoelectric focusing separates proteins based on ______
pI
PAGE separates proteins based on ______
size and charge
SDS-PAGE separates proteins based on ______
size
how does isoelectric focusing work
the gel is a pH gradient
the protein stops moving at its pI
when is chromatography preferred
when large amounts of protein are present
components with high affinity for absorbent/stationary phase will move _____
very little
retention time
amount of time a component spends in the stationary phas
column chromatography uses
silica or aluminum beads
column chromatography separates proteins based on ______
size and polarity
less polar = _________ retention time
short
if non polar, it moves really fast
ion-exchange chromatography separates proteins based on ______
charge
ion-exchange chromatography uses
charged beads, attracts opposite charge
size-exclusion chromatography uses
beads with pores of different sizes, small compounds get stuck in beads
affinity chromatography uses
beads with a receptor that has affinity for a protein
affinity chromatography can be followed by washing the column with (2)
a free receptor, outcompetes beads and binds protein
pH or salinity fluid
how to determine protein structure
XR crystallography or NMR spectroscopy
how to determine AA composition
hydrolysis then chromatography
how to determine AA sequence
sequential digestion
how to determine AA of a small protein (50-70 AA)
edman degradation
edman degradation
removes N-terminal AA of the protein
what follows Edman degradation
mass spectroscopy
how to determine AA sequence of a large AA (>70 AA)
chymotrypsin, trypsin, cyanogen bromide
selectively clave at specific Acs to create smaller fragments
what follows digestion of large proteins
Edman or electrophoresis
how to determine concentration of a protein
spectroscopy
UV spectroscopy can analyze
proteins with aromatic side chains
what is UV spectroscopy sensitive to
contamination
how to determine concentration of a single protein
assays, specific color changes in reactions
Bradford protein assay
mixes a protein with Coomassie blue
coomassie blue is
protonated, green-brown in color
in Bradford assay, the more blue = the more
protein
how does Coomaassie blue turn blue
gives H+ to AA of protein
aldoses
carbs that contain an aldehyde as their most oxidized functional group
ketoses
carbs that contain a ketone as their most oxidized functional group
glucose aldehyde substituted with a ketone makes
fructose
stereoisomer
compounds with same formula different arrangement of atoms
enantiomers
mirror image stereoisomers
any molecule with ________ and no plane of symmetry has _______
chiral carbons
an enantiomer
of stereoisomers =
2^n
n = # of chiral centers
how to determine D or L
look at chiral center furthest from carbonyl
if OH is on the right - D
if OH is on the left - L
diastereomers
two sugars with same # of carbons but aren’t identical or mirror images
epimers
a type of diastereomer that differs at one chiral center
five-membered rings of carbs
pyranose
six-membered rings of carbs
furanose
anomeric carbon
carbonyl carbon that forms a ring
anomers
two molecules that differ at the anomeric carbon
α-anomer
-OH of C1 trans to CH2OH
β-anomer
-OH group of C1 cis to CH2OH
mutarotation
interconversion between α and β anomie’s via ring opening and closing
occurs in water, faster if acid or base is present
aldonic acid
oxidized aldoses
reducing sugar
any sugar with a hemiacetal ring (aldehyde)
oxidation of an aldose yields
a lactone
lactone
looks like sugar but with = O instead of CHOH
what reagents test for reducing sugars
Tollen’s and Benedict’s
[Ag(NH3)2]+
Tollen’s reagent
what does Tollen’s reagent do in the presence of aldoses
produces a silvery mirror
Cu(OH)2
Benedict’s reagent
what does Benedict’s reagent do in the presence of aldoses
form a red Cu2O
glucose oxidase
can be used to test presence of just glucose, only oxidizes it
nitric acid
oxidizes aldehyde and the primary OH on C6
tautomerization
rearrangement of bonds in a compound
do ketoses react with Tollen’s/Benedict
yes, they tautomerize to aldehydes
carbohydrates can react with carboxylic acids through
esterification
hemiacetal + alcohol =
acetal/glycosides
glycosidic bonds
C - O bond at the anomeric carbon of an acetal
glycoside formation is a _________ reaction
dehydration
maltose
glucose-α-1,4-glucose
lactose
galactose-β-1,4-glucose
sucrose
glucose-α-1,2-fructose
cellulose structure
homopolysaccharide
β-1,4 bonds
cellulose function
fiber, draws water into our gut because we cannot digest it
starch (amylose) structure
homopolysaccharide
linear α-1,2
amylopectin structure
homopolysaccharide
linear α-1,2
+ branches of α-1,6 (1/25)
what detects the presence of starch
iodine
β-amylase
cleaves amylase at nonreducing end (acetal)
amylose + β-amylase –>
maltose
α-amylase
cleaves randomly along amylose
amylose + α-amylase –>
glucose and maltose
glycogen structure
homopolysaccharide
linear α-1,2
+ branches of α-1,6 (1/10, a lot more)
glycogen phosphorylase
cleaves glucose from acetal end of a glycogen and phosphorylates it to make glucose 1-phosphate
branching of glycogen benefits
makes it energy efficient, stored in body more
allows enzymes cleaving glucose to work at a lot of sites
fully saturated fatty acid
has only single bonds
strong van Der Waals, very stable
saturated FA form _______ at room temperature
solids, ex: butter
unsaturated FA
has one or more double bonds
introduce kinks
unsaturated FA are ________ at room temperature
liquids, ex: olive oil
glycerophospholipids/phosphoglycerols
have a glycerol backbone
what do the phospholipids of a phosphoglycerol bind to
ester linkage to two FA
phosphodiester linkage to a head
what kind of lipids are cell-surface antigens
sphingolipids
ceramide
sphingolipid with H as head group
sphingomyelin
sphingophospholipids
phosphocholine or phosphoethanolamine as head group
what are sphingomyelins involved in
plasma membranes of myelin producing cells
sphingomyelin head groups are ______ charged
0
glycosphingolipids
sphingolipids with sugar as had group
are glycosphingolipids phospholipids
no, there is no phosphodiester linkage
cerebrosides
glycosphingolipids with a single sugar
globosides
glycosphingolipids with two or more sugaars
gangliosides
glycosplingolipids with polar head groups of oligosaccharides + NANA (sialic acid)
what do gangliosides play a role in
cell interaction, recognition, and transduction
waxes
esters of long-chain FA with long-chain OH
in plants, waxes
are secreted to prevent excessive evaporation and to protect from parasites
in animals, waxes
prevent dehydration and act as a lubricant
terpenes
lipid built from isoprene (C5H8)
terpenes are mostly produced from
plants, protection and smell
monoterpenes contain ____ isoprenes
2
sequiterterpenes contain ____ isoprenes
3
diterpenes contain ____ isoprenes
4
vitamin A is a ___________ from which retinal is derived
diterpene
triterpenes can become
cholesterol and steroids
tetraterpenes can become
carotenoids
terpenoids
terpenes that have undergone oxygenation or rearrangement
steroids
metabolic derivatives of terpenes
steroid structure
four cycloalkane rings fused together
steroid has ___ cyclohexane + _____ cyclopentane
3 + 1
what determines function of steroid
oxidation and functional groups of rings
cholesterol
a steroid responsible for mediating membrane fluidity
at high temperatures, cholesterol prevents the membrane from
becoming too permeable
at low temperatures, cholesterol prevents the membrane from
solidifying
prostaglandin structure
20-carbons, unsaturated carboxylic acids
derived from arachidonic acid
contain one 5-carbon ring
what do prostaglandins do
act was paracrine or autocrine signals
vitamin A = ___________
carotene
vitamin A functions
vision, growth, immune
vitamin A produces _______ metabolite. what does it do
retinal, it senses light in the eye
vitamin A is stored as _________. what does it do?
retinol, it oxidizes to retinoid acid that regulates gene expression during epithelial development
vitamin D = ___________
cholecalciferol
in liver/kidneys, vitamin D becomes _________. what does it do?
calcitriol, it increases calcium and phosphate uptake to promote bone production
rickets
underdeveloped, curved long bones due to impeded growth
vitamin E structure
aromatic ring with a long isoprenoid side chain
vitamin E = ____________
tocopherols and tocotorienols
what do tocopherols do
antioxidants, prevent oxidative damage
vitamin K = ________
phylloquinone and menaquinone
what does vitamin K do
post translational modification to form prothrombin
introduces calcium-binding sites on several proteins
animals store large amounts of fat in
adipocytes
plants store large amounts of fat in
seeds
how do free FA move around
bound to albumin
saponification
ester hydrolysis of triacylglycerols using a strong base
lye
Na/KOH
triacylglycerol + lye =
glycerol + soap (FA salt)
flippass
assist flipping of lipids in the membrane
what transports FA from diet
chylomicrons
which fats are more unhealthy
saturated
tight junctions
prevent paracellular transport of water and solutes
where are tight junctions found
epithelial cells
desmosomes
bind adjacent cells by anchoring their cytoskeleton
hemidesmosomes
attach cells to underlying structure (epithelial to basement membrane)
which mitochondrial membrane is more permeable
outer
what does the inner mitochondrial membrane have a lot of? what does it not have?
a lot of cardiolipin
no cholesterol
how are nucleotides joined
3’-5’ phosphodiester bonds
DNA and RNA are overall ____ ly charged
negative
which nitrogenous base has two rings
purine
purines
adenine and guanine
which nitrogenous base has one ring
pyrimidines
pyrimidines
cytosine, thymine, uracil
four roles of aromaticity
- cyclic
- planar
- conjugating
- 4n+2 pi electrons (Huckels rule)
Watson and Crick model describes
DNA structure
Adenine:Thymine by ____ hydrogen bonds
2
Guanine:Cytosine by ___ hydrogen bonds
3
what provides stability for the double helix
hydrogen bonds and hydrophobic interactions btwn bases
B-DNA structure
right-handed
turns every 3.4nm, 10 bases in turn
Z-DNA structure
zigzag, left-handed
turns every 4.6nm, 12 bases in turn
what do the major and minor grooves of DNA do
provide binding sites for regulatory proteins
what breaks in DNA denaturation? what doesn’t?
hydrogen bonds do
phosphodiester bonds do not
5 histone proteins
H2A x2, H2B, H3, H4
H1
seals off DNA as it enter/leaves nucleosome, stabilizes
DNA + histones =
nucleosome
heterochromatin
compacted chromatin, often repetitive sequences
does not get transcribed
euchromatin
dispersed chromatin, genetically active DNA
TTAGGG
telomere sequence
telomere contributions
aging
knots off end to prevent unraveling
what kind of DNA makes up centromeres
heterochromatin
replisome
set of proteins helping DNA polymerase
origins of replication
where DNA unwinds
helicase
unwinds DNA
single-stranded DNA binding proteins
bind to the unraveled strands to prevent them from binding back together
nucleases
degrade DNA
DNA topoisomerase
reduces torsional stress but introducing negative supercoils
break and reseal strand
semiconservative model
one parental strand, one daughter strand
DNA polymerase III (α, δ, ϵ - eukaryotes)
read the parent and make the daughter
DNA polymerase reads __’ to ____’ and makes ___’ to ____’
reads 3’ to 5’
makes 5’ to 3’
Okazaki fragments
small strands made on the lagoon strand
primase
makes a short RNA primer in the 5’ to 3’ direction to start replication
DNA polymerase I (RNAase H - eukaryotes)
removes RNA primers
DNA polymerase I (δ - eukaryotes)
adds DNA where RNA primer was
DNA ligas
seals DNA fragments into a complete strand
DNA polymerase γ
replicates mitochondrial DNA
DNA polymerase δ and ϵ
forms a sliding clamp with PCNA, strengthens interaction between polymerases and template
DNA polymerase β and ϵ
DNA repair
DNA gyrase
removals supercoils to reduce torsional stress in PROKARYOTES
which strand has is more methylated
parent, been there longer
what proofreads DNA
DNA polymerase, checks for unstable bonds between bases
matches the more methylated strand
mismatch repair occurs
during G2
what do mismatch repair enzymes do
(MSH2 and MLH1)
detect errors missed during S phase
whaat does nucleotide excision repair remove
thymine dimers
steps of nucleotide excision repair
- proteins scan DNA and notice a bulge
- excision endonuclease cuts pieces of the phosphodiester backbone on bond sides of the thymine dimer
- it removes the messed up nucleotide
- DNA polymerase replaces it
- DNA ligase seals it
what causes thymine dimers
UV light
what causes cytosine deamination
heat
what happens when cytosine is deaminated
it becomes uracil
steps of base excision repair
- cytosine is recognized as uracil
- the base is removed by glycosylase enzyme
- apurinic/apyrimidic (abasic) site is left
- AP endonuclease recognizes site
- it removes the sequence of DNA
- DNA polymerase and ligase refill it
recombinant DNA
DNA multiplied by gene cloning or PCR
restriction endonucleases
enzymes that recognize specific dsDNA sequences
palindromic
two strands are identical
how are restriction enzymes used
cut at palindromic sequences to take sticky ends that can be used to recombine with a vector
what must DNA vectors have (3)
- a sequence recognized by restriction enzyme
- origin of replication
- gene for antibiotic resistance - allows selection of colonies
DNA vs cDNA
DNA has introns and exons
cDNA is made from mRNA so only has exons
hybridization
combining complementary sequences (DNA-DNA or DNA-RNA)
PCR can clone DNA without
bacteria amplification
Southern blot
detects presence and quantity of DNA strands
mRNA
carries AA sequence to the ribosome
mRNA is transcribed from _________ by _________
from a template DNA strand
by RNA polymerase
what occurs in the nucleus before mRNA leaves
transcribed from DNA –> mRNA
+ posttranscriptional modifications
monocistromic
mRNA translates to one protein
polycistromic
mRNA translates to different proteins, depending where it starts
tRNA
converts nucleic acid sequence to amino acids
anticodon
pairs with specific codon on mRNA in the ribosome
where is mature tRNA found
cytoplasm
what sequence does AA bind to tRNA at
CCA
aminoacyl-tRNA synthetase
binds AA to 3’ end of tRNA, requires ATP be broken down twice into AMP
what supplies the energy to create a peptide bond during translation
aminoacyl-tRNA (it has a lot of energy)
rRNA
part of ribosomal machinery, made in nucleolus
help catalyze formation of peptide bonds & splices its own introns
each codon represents ____ AA
one
the codon of mRNA is recognized by
an anticodon on tRNA
what is the start AA
methionine
start codon
AUG
three stop codons
UAA u are annoying
UGA u go away
UAG u are gay
degenerate
an AA can be coded for by more than one codon
what does degeneracy allow
for mutations in DNA that are silent, mutation in wobble position codes for same AA
what strand does mRNA copy from
template strand of DNA (antisense)
what enzymes transcribes mRNA
RNA polymerase II
what must RNA polymerase II recognize
promotor regions
what part of the promoter region does RNA polymerase bind
TATA box, lots of thymine and adenine
transcription factors
help RNA polymerase find the TATAA and bind
RNA polymerase I
synthesizes rRNA
RNA polymerase II
synthesizes hnRNA (preprocessed) and snRNA (small nuclear)
what strand matches the mRNA strand
coding/sense DNA strand, the one not being copied from
it will just have T instead of U
what number is the TATA box
about -25
DNA –> __________ –> mRNA
hnRNA
RNA polymerase III
synthesizes tRNA and rRNA
what are the three post transcription processes that must occur for hnRNA to become mRNA
- intron/exon splicing
- 5’ cap
- 3’ poly-A tail
spliceosome
snRNA + snRNP, cuts 5’ and 3’ ends of introns
how are introns excised
as a lariat
7-methylguanylate triphosphate cap
added to 5’ end of hnRNA
what does the 5’ cap do
serves as binding site to ribosome
protects mRNA from degradation when it leaves
polyadenosyl tail
added to the 3’ end of hRNA
what does the 3’ polyA tail do
protects mRNA against degradation, adds a ton of As that are like a ticking bomb
assists export from nucleus
three subunit sizes of prokaryotic ribosome
30S + 50S = 70S
three subunit sizes of eukaryotic ribosome
40S + 60S = 80S
where does the small ribosome bind in prokaryotes
shine-delgarno
where does the small subunit bind in eukaryotes
5’ cap
where does the initiator tRNA bind
AUG, start codon
what part of the ribosome does tRNA bind to mRNA
P
after the small unit binds to mRNA, what happens
the large subunit binds to the small subunit
what helps the small and large subunits bind
initiation factors
order of sites in the ribosome
APE
A site
holds incoming amino-tRNA
next AA being added, determined by codon in the A site
P site
holds tRNA carrying the chain
where Met binds
what site does a peptide bond form
when a polypeptide is moving from P to A
what forms the peptide bond in ribosome
peptidyl transferase, requires GTP
E site
inactivated tRNA passes before exiting
what helps locate and recruit amino-tRNA and GTP
and remove GDP
elongation factors
release factor
binds to termination codon, causing a water to be added to the polypeptide chain
what hydrolyzes the peptide chain from tRNA
peptidyl transferase and termination factors
once water is bound
chaperones
assist folding of protein
operon
a cluster of genes that are transcribed together in bacteria
Jacob-Monod model
operons contain structural genes + operator + promotor + regulator
structural gene
codes for protein
operator
non transcribable region of DNA that binds a repressor protein
promotor
provides a place for RNA polymerase to bind
regulator
codes for repressor
operons offer
an on and off switch for gene control in prokaryotes
inducible system
repressor is bound to operator and blocks RNA polymerase from binding to the promotor region
OFF but can be turned ON
how do you remove repressors
add an inducer to remove it
how does the lac operon work
- drop in glucose
- increase in cAMP
- cAMP binds to CAP
- CAP binds to promotor of operon
- transcription increases
lac operon is __________
inducible, it is off unless lactose levels are higher than glucose
repressible systems allow
constant production of a gene
in a repressible system, how does the repressor act
it is not bound to the operator site unless bound to a corepressor
trp operan is __________
repressible, tryptophan acts as a corepressor and causes the cell to stop making more tryptophan
enhancer
response elements outside the promotor regions, fear away so DNA must bend
histone acetylase
acetylate lysine on the amino terminal of histone proteins
what does histone acetylation do
decreases positive charge of histones, make them bind less strongly to DNA
this opens chromatin to allow for transcription of DNA
DNA methylation
add methyl to cytosine and adenine, silences gene
GLUT2 is located
in liver and pancreatic cells
GLUT2 function
captures excess glucose traveling through hepatic portal vein when levels are HIGH
Km of GLUT2 is _______
high, so liver/pancreatic cells have low affinity for glucose
GLUT4 location
fat tissue and muscle
GLUT4 reaches the membrane when
insulin is released
Km of GLUT4 is __________
close to glucose, so really sensitive to glucose
how can cells increase glucose reuptake with GLUT4
increase the # of GLUT4 on the membrane
by releasing insulin
_____ cells carry out glycolysis
ALL, doesn’t require mitochondria
GLUT transporters are specific to
glucose alone, not glucose-6-phosphate
hexokinase located in
tissues, inhibited by Glu6Phosphate
glucokinase located in
liver and pancreatic B cells, induced by insulin
what inhibits PFKI
ATP and citrate
what activates PFK1
AMP
insulin activates _______, which will indirectly activate PFK1
PFK2, which makes Fru6BisP –> Fru26BisP which activates PFK1
glucagon _____ PFK2, which inhibits PFK1
glucagon lowers P26BisP which inhibits PFK1
where is PFK2 mostly found
liver
substrate level phosphorylation
ADP phosphorylated to ATP by a high-energy intermediate
what activates pyruvate kinase
Fructose16BisP
what does lactate DH do
prevents the cell from running our of NAD+ for glycolysis
in yeast, what does pyruvate become
ethanol and CO2
in animals without oxygen, whaat does pyruvate become
lactate
____ –> Fru1,6BisP –> glycerol 3P –> glycerol
DHAP
what three enzymes catalyze irreversible reactions
hexo/glucokinase
PFK1
pyruvate kinase
net ATP for glycolysis
2
BPG mutase
makes 1,3BPG -> 2,3BPG
2,3BPG binds to Hgb and decreases affinity for oxygen (right shift)
allows oxygen to be unloaded at tissues, so increase this when oxygen levels are low
epimerase
catalyze conversion of one sugar epimer to another
what activates pyruvate DH
insulin
three fates of pyruvate
- lactate by lactate DH
- acetyl coA by pyruvate DH
- oxaloacetate by pyruvate carboxylase
what factors does pyruvate DH require
thiamine pyrophosphate, lipoid acid, CoA, FAD, NAD+
what inhibits pyruvate DH
acetyl CoA
how is glycogen stored
in granules in the cytoplasm
glycogen granules of liner chairs have highest density of glucose
near the protein core
glycogen granules that are branched have highest density of glucose at
periphery, allows rapid release
glycogen in liver is for
release of glucose when insulin levels are low
glycogen in muscle is for
release of glucose when muscles are exercised
glycogenesis
synthesis of glycogen granules
glycogenin
core protein of glycogen granule
what stimulates glycogen synthase
insulin and Glu6P
what inhibits glycogen synthase
glucagon and epinephrine
what introduces the α-1,6 branches to the granule
branching enzyme
what bonds does glycogen phosphorylase braak
α-1,4
cannot break 1,6 so stops at branches
what activates glycogen phosphorylase
glucagon, epinephrine, AMP
what inhibits glycogen phosphorylase
AMP
how does debranching enzyme work
one enzyme moves the branch point chain to the end of another chain
one enzyme breaks the single glucose from the branch
what process increases after 12 hours of fasting
gluconeogenesis, glycogen stores have depleted
gluconeogenesis
making glucose from things other than glucose/glycogen
glucogenic AA
can be converted into intermediates that can enter gluconeogenesis
all AA except leucine and lysine
ketogenic AA
converted into ketone bodies, used as alternative fuel
three substrates for gluconeogenesis
glycerol 3 phosphate from fats
lactate from glycolysis
glycogenic AA from muscle proteins
acetyl coA from ________ activates ___________ to convert pyruvate to OAA
lipids
pyruvate carboxylase
what induces PEPCK
glucagon and cortisol
OAA –> PEP by
PEPCK
pyruvate –> PEP by
pyruvate carboxylase and PEPCK
what is the rate limiting step of gluconeogenesis
F-1,6-bisphosphatase
where is glucose 6 phosphatase found
ER
Glu6P –> ER –> glucose –> _____
cytoplasm
what does gluconeogenesis depend on
Beta oxidation of FA to produce acetyl-coA
what are the two functions of the PPP
to make NADPH
to make ribose 5-phosphate for nucleotide synthesis
Glucose6P –> 6phosphogluconate by
glucose6P dehydrogenase
NADP –> NAPH
fructose6P / GAP -> ribose 5P by
rtanektolaase and transaldolase
where does the TCA cycle occur
mitochondria
how does pyruvate enter the mitochondria
active transport
activation
thioester bond formation between carboxyl of FA to CoA-SH
carnitine
FA-carnitine, allows fatty acyl to cross inner membrane
in the matrix, ______ can convert FA-carnitine to
FA-CoA, which can be oxidized to Acetyl CoA
alcohol is converted to acetyl coA by
alcohol dehydrogenase and acetaldehyde dehydrogenaase
when alcohol produces acetyl coA
it builds up NADH, which inhibits Krebs
how many ATP does NADH make`
2.5
how many ATP does FADH2 make
1.5
new ATP per glucose
30-32, 7 from glycolysis & 25 from citric acid
net ATP per pyruvate
12.5
what inhibits citrate synthase
ATP, NADH, succinylcoA, citratae
what inhibits citrate synthase
ATP, NADH, succinylcoA, citratae
what inhibits pyruvate DH
acetylCoA, ATP, NADH
what inhibits isocitrate DH
ATP and NADH
what inhibits AKGDH
NADH ATP and succinylcoA
what does succinylcoA Inhibit
AKGDH and citrate synthase
what stimulates AKGDH
ADP and calcium
when do lipids start being digested
in the duodenum
triacylglycerol –> 2-monoacylglycerol by
emulsification by bile and pancreatic lipase
free FA, 2-monoacylglycerol, and bile salts form
micelles
how are bile salts reabsorbed
active transport
triacylglycerol is reformed in
the mucosal cells
phospholipids, cholesterol, fat-soluble vitamins, and triacylglycerol make up
chylomicrons
chylomicrons leave the intestine via
lacteals
chylomicrons enter the blood via
thoracic duct
water-soluble short-chain FA reabsorption
just diffuse simply into blood
glucagon effect on fat tissue
none
insulin effect on fat tissue
low insulin activates hormone-sensitive lipase that breaks down triacylglycerols
what activates HSL
epinephrine, cortisol, and low insulin levels
in VLDL and chylomicrons, how are triacylglycerols broken down
lipoprotein lipase (LPL)
how are free FA transported in blood
with albumin
how are triacylglycerols and cholesterol transported in blood
as lipoproteins
chylomicrons are the least dense meaning
high fat, low protein
chylomicrons and VLDL carry
triacylglycerols and cholesteryl esters
LDL and HDL carry
cholesterol
chylomicron carries from _____ to _______
intestine
tissue
VLDL carries from ______ to ________
liver
tissues
IDL picks up
cholesteryl esters from HDL in liver to become LDL
LDL delivers
cholesterol
HDL picks up
cholesterol from blood, delivers to liver and steroidogenic tissues
IDL lacks
triacylglycerols
HDL helps
clean up cholesterol from blood for excretion
where does de novo synthesis of cholesterol occur
liver
citrate shuttle
carries acetylCoa from mitochondria into cytoplasm, uses NADPH from PPP
rate limiting step of cholesterol synthesis
HMG-CoA reductase, produces mevalonic acid in SER
insulin promotes cholesterol _______
synthesis
LCAT is found
in blood
LCAT is activated by
HDL apoproteins
LCAT function
adds FA to cholesterol, producing cholesteryl esters
CETP
transfers cholesteryl esters to other lipoproteins (IDL)
acetyl-CoA shuttling
- Krebs inhibited by too much citrate
- citrate accumulates
- citrate crosses into cytosol
- in cytosol, it is broken into acetyl-CoA and OAA by citrate lyase
acetyl-CoA –> malonyl coA by __________
acetyl-CoA carboxylase (biotin)
malonyl CoA –> FA palmitic acid by
fatty acid synthase
rate limiting step of FA synthesis
acetyl-coA carboxylase
what activates acetyl-CoA carboxylase
citrate and insulin
what vitamin is required for FA synthase
B5
what energy carrier Is required for FA synthase
NADPH
rate limiting step of FA oxidation
carnitine acyltransferase I
ΔU =
Q - W
heat - work (W is change in pressure/volume)
in closed systems, W is constant
ΔU = Q
enthalpy
change in heat
at constant pressure and volume, ΔH =
ΔQ
enthalpy = heat
entropy
measure of disorder
units of entropy
J/K
Gibbs free energy
ΔG = ΔH - TΔS
standard free energy
ΔG = ΔGo + RTln(Q)
ΔGo’ means
it has been adjusted for pH = 7
ATP hydrolysis
breaking down ATP
ATP cleavage
transfer of P from ATP to something else
spontaneous redox reactions have ΔG ___ and E ___
- and +
flavoproteins
contain riboflavin, B2
postprandial state
after eating
more anabolism and fuel storage
lasts 3-5 hours
what cells are insensitive to insulin
nervous and RBC
how dose nervous tissue derive energy
breaking glucose into CO2 and H2O
how do RBC derive energy
glycolysis
what levels are elevated during starvation
glucagon and epinephrine
insulin increase (3)
- glucose and triacylglycerol uptake by fat cells
- lipoprotein lipase activity, clears VLDL and chylomicrons from blood
- lipogenesis in fat tissue
insulin increase (3)
- glucose and triacylglycerol uptake by fat cells
- lipoprotein lipase activity, clears VLDL and chylomicrons from blood
- lipogenesis in fat tissue
insulin decreases (2)
- lipolysis
2. formation of ketone bodies
glucagon increases (4)
- glycogenolysis
- gluconeogenesis
- ketogenesis, less lipogenesis
- lipolysis
glucagon is activated by
low glucose levels and high protein levels
cortisol functions (3)
- inhibits glucose uptake by cells
- increases liver output of glucose by gluconeogenesis
- enhances glucagon, epinephrine, and catecholamines
catecholamines promote
glycogenolysis and lipolysis
T4 effect on metabolic rate
latent over several hours, last days
T3 effects on metabolic rate
rapid increase, shorter duration
Respiratory quotient =
CO2 produced / O2 consumed
BMI =
mass / height ^2
