BMSC 200 Final no pics Flashcards
difference between coenzymes and cofactors
coenzymes = organic (vitamins)
cofactors = inorganic (metalions)
describe the difference between the rate and the equilibrium of a reaction
the equilibrium is determined by the difference in free energy between the substrate and the product
the rate of the reaction is determined by the difference between the energy of the transition state and the substrate, enzymes can lower this influencing the rate of the reaction
however, an enzyme has no effect on the equilibrium of a reaction
what are the binding effects of an enzyme catalyst
substrate binding –> reduces entropy
aligns functional groups
desolves substrate ( removes water)
distorts substrate
induced fit
transition state stabilization
increased interaction between enzyme and substrate during transition state
active site is complimentary to TS
must be similar enough to substrate to ensure specificity but different enough to promote change
enzymes have higher affinities to TS than S
provides microenvironment
what are transition state analogs
stable compound resembling unstable transition state
type of competitive inhibitor
bind to active site w high affinity
Antibodies against transition state analogues may have catalytic activity.
what are the chemical effects of enzyme catalyst
acid base catalysis –>
uses his
catalytic proton transfer
covalent catalysis –>
covalent linkage to substrate
regenerates free enzyme
ex) sucrose phosphorylase
describe Michalis menton kinetics
describe relationship of substrate concentration and initial velocity
allosteric enzymes do not obey this
V0= vmax(S) / km+(S)
km = 1/2vmax
When [S] < Km, enzymes are highly sensitive to changes in substrate
concentration but have very little activity.
When [S] > Km, enzymes have high activity but are insensitive to
changes in substrate concentration.
When [S] = Km, enzyme has significant activity and is responsive to
changes in substrate concentration.
describe lineweaver burke plots
can find vmax and km
Comp –> Y axis same but X axis closer
increase Km
bind only free enzyme E
Vmax is same
Non Comp –> Y axis higher X axis same
decrease Vmax
bind to E and ES
Km same
Uncomp –> y and x both farther
decrease vmax
decrease Km
bind to only ES
discuss serine proteases
cleave polypep chains (peptide bonds)
diff proteases have diff specificity
example of both acid base and covalent catalysis
trypsin –> cleave pos (lys arg)
chymotrypsin –> cleave aromatics (phe met)
elastase –> cleaves small hydrophobic (gly ala)
what is the catalytic triad
His, H, acid base catalysis
aspartate, Asp, D, stabilization
Ser, S covalent catalysis
enzyme regulation
through covalent modification (phosphorylation)
non covalent –> allosteric regulation
uses negative feedback loops
one at end can regulate one at beginning, or first one of branch
if two join to form one, can regulate first of each branch
allosteric enzymes
usually quaternary structure
usually rate limiting step
do not obey Michalis mention kinetics instead have S curve
bind non covalently
have active R and inactive T (R ready to go)
activators bind to R, so can substrates but not T
more sensitive to changes in substrate concentration near Km then MM enzymes
this sensitivity is called the threshold effect (think back to r t states of hemoglobin, once one switches they all do
Describe phosphofructokinase 1
in glycolysis
PEP is heterotropic allosteric inhibitor
ADP is heterotropic allosteric activator
noncovalent modification
describe glycogen metabolism
covalent modification
glucose –> glycogen
glycogen synthase to form glycogen anabolic, when non phosphorylated/ insulin
glycogen phosphorylase to form glucose catabolic when phosphorylated/ hungry
how do you find the number of stereoisomers in a monosaccharide
2^n where n is number of chiral carbons
what are epimers
sugars that differ at only a single chiral center
what are the two ring structures cyclized sugars can form
pyran of pyranose 6 c
furan or furanose 5c (in the ring)
what is the anomeric carbon
carbon that becomes chiral as a result of cyclization
cyclization always involves either 1-5 or 2-5c
on 6c or pyran ring forms the anomeric carbon is C1 (ALDOSES)
on 5c or furan ring forms the anomeric carbon is on c2 (KETOSES)
how can you tell the alpha or beta forms of cyclized carbons
what is switching between the two called
beta on top
alpha on bottom
switching between the two is called mutarotation
describe the nomenclature of disaccharides
glycosidic bonds are the structural linkage
0-glycosisic occurs through oxygen
N glycosidic is on nitrogen or amide
monosaccharides involved
ring type
configurations
‘linkages
end chain with free anomeric carbon is reducing end
always name non reducing end first (osyl then ose)
describe the energy storage polysaccharides
in plants
starch (amylose, unbranched; amylopectin, branched)
has a1-6 branch every 25 residues
many non reducing ends
in animals
glycogen
has a a1-6 branch every 9 residues
even more non reducing ends
means animals can mobilize their energy faster than plants bc more branches
all use a1-4 linkages
all homopolysaccharides
describe the structural polysaccharides
cellulose (fiber in plant cells)
chitin
use B1-4 linkages instead
linear
fibrils formed from parallel long linear chains linked through hbonds
means they are rigid and cannot be broken easily by amylase
glycolipids
used in blood group antigens
difference between glycoproteins and proteoglycans
glycoproteins
more protein
variety of roles
either 0 or N linked
ex) EPO
Proteoglycans
more sugar (carb)
structural and lubricating
ex) glycosaminoglycans –> introduces negatively charged fibrous strands
what is a fatty acid, what are the different types of FA
hydrocarbon tail with a carboxylic head group, associate thru hphobic interactions
saturated = no double bonds –> solid, hard to melt
unsaturated = one double bond –> less solid, easier to melt
polyunsaturated = multiple double bonds –> liquid, easiest to melt
when naming carbon of carboxy group is carbon one
what are the main energy storage molecules in the body and why
triacylglycerols which are 3 fatty acids linked thru ester linkages
have glycerol backbone
hydrophobic
works well because it has a low oxidation state and low hydration state
how do you release the fatty acids from the triacylglycerol?
saponification
what are structural lipids in membranes
have two hydrophobic tails and one head group
can be classified based on backbone
either glycerol of sphingosine
glycerophospholipids
most abundant in membranes
glycerol backbone with 2 FA and 1 phosphate
can have diff head groups
ex) phosphatidylinositol –> signal transduction with both head group and backbone, would be inside cell
sphingolipids
single long chain fatty acid linked by an amide bond
sphingosine backbone
can have a variety of polar head groups
sphingomyelins
cerebrosides
gangliosides
what do glycosphingolipids do
determine blood type, reflects sugar patterns in head group
explain steroids
sterols are structural membrane lipids
contain 4 fused ring nucleus (3 6c, 1 5c)
rings are rigid
steroid hormones also exist
sterol derivative
can pass thru plasma membrane and bind receptors in nucleus
alters gene expression and metabolism
explain cholesterol
mediates membrane fluidity
precursor of steroids
what are the three types of eicosanoids
paracrine hormones (act near point of production)
prostaglandins –> constriction of blood vessels
Thromboxanes –> blood clot formation
Leukotrines –> smooth muscle contraction
Lipid vitamins
A eyes, from egg
D bones, from light
E no free radicals
K blood coagulation
explain the membrane lipid bilayer
amphipathic
self assembling through hydrophobic effect
lipids with two hydrocarbon tails form bilayers
one hydrocarbon tail forms micells\
only small or non polar molecules can cross the membrane without help
the more active the membrane the more proteins than lipids it has
follows the fluid mosaic model, meaning that shit moves around in there within the membrane, but movement across the membrane is restricted
explain lipid rafts within a membrane
frosm from spontaneous association of lipids with tails of a similar length
usually sphingolipids cuz they are longer
often serves signalling functions
docking points for lipid anchored proteins
explain peripheral membrane proteins
associated with one side of the membrane
easiest to remove from membrane–> changes in pH
associate through either hydrogen bonding or electrostatic interactions
non covalent
lipid anchored membrane proteins
covalently linked on (harder to remove)
GPI anchored proteins on outside (lipid rafts)
proteins with only one hydrocarbon tail on inside
Integral membrane proteins, 3 broad types
span the membrane
either single pass ahelical, helical bundles or b-barrels
residues with non polar side chains dominate middle
usually can tell if there’s 24 hydrophobic residues in a row
simple diffusion
small nonpolar molecules dont need no man
determined by concentration gradient
can only move down gradient
no carrier
not saturable
down gradient
no energy
Facilitated diffusion
removes hydration shell
lower activation energy
no energy
channels
fast, do not saturate
carriers
slow, do saturate
ex) uptake of glucose into RBC/ erythrocytes
Primary active transport
driven by atp
can move against gradient
ptype –> phosphorylated intermediate –> NaKATPase
3 Na out/ 2 K in
vtype –> pumps protons in Vesicles
ABC type–> removes toxins from cells
Secondary active transport
uses concentration gradient as a source of energy
couples the movement of one molecule down its concentration gradient with another against
ex) glucose uptake into epithelial cells
uses Na and glucose , Na down, glucose up
ion channels
enable rapid movement of ions across the membrane
very selective and regulated
faster and no saturation limits
K+ channel
even though Na is smaller than K it still cannot get through based on ability to shed water molecules
structural features of nucleotides
building blocks for nucleic acids
all have ribose sugar ( ribose or deoxyribose)
nitrogenous bases ( purine or pyrimidine)
phosphate(s)
which has ribose DNA or RNA
DNA has deoxyribose, RNA has ribose
Nitrogenous bases
either purine (A,G) or pyrimidine (C,T,U)
planar and non polar
link to ribose through N-glycosidic bonds
all nitrogenous bases link to C1 of sugar
In purines, N-glycosidic bond is to N9 of nitrogenous base
in pyrimidines N-glycosidic bond is to N1 of nitrogenous base
difference between nucleotides and nucleosides
differ in wether they are phosphorylated at the C5 position
Nucleotides have 1 to 3 phosphates on the 5’ position\
Nucleotides are phosphorylated nucleosides
forming and compostion of nucleic acids
nucleotides form linear strands through 3’-5’ phosphodiester linkages
identical in DNA and RNA, independent of the nucleotides that are being joined
strand of sugars linked by phosphodiester bonds is the backbone of nucleic acids
how is RNA different from DNA
rna contains ribose instead of deoxyribose
contains uracil rather than thymine
is single stranded but can adopt complex 3d structures (don’t care lol)
less stable because of 2’ hydroxyl group, intentional ad DNA is needed for long term information storage not RNA
explain the structure and formation of the double helix of DNa
`right handed helix
complimentary and antiparallel
sugars outside, n bases inside
purine matched with pyrimidine
A-T
G-C
(determined by hydrogen bonding)
chargaffs rule implies that A+G= T+C in DNA
what are the four weak forces that stabilize a double helix
hydrophobic effects –> burying n bases in center
stacking interactions –> stacked base pairs form VDW interactions
hydrogen bonds –> hydrogen bonding between base pairs
Charge-charge interactions –> electrostatic repulsion of neg charged phosphate groups
restriction endonucleases
cleave specific DNA sequences
bacterial defense mechanism against viral invasion
restriction enzymes cut at palindrome sequences (flipped below not across)
restriction enzymes used as molecular scissors
DNA as a carrier of genetic information
complimentary nature is important for replication and repair
since one sequence determines the other, each strand can be used as a template
the resulting DNA duplexes will be identical
Information about destroying and rebuilding DNA`
can be denatured and separate the strands via heat
will reform –> annealing
Melting point Tm is when half the DNA has become single stranded
reflects composition –> more GC = harder to melt
Packaging of eukaryotic DNA
involves formation of nucleosomes –> DNA histone complexes
5 Histone proteins –> H1, H2A, H2B, H3, H4
nucleosome has 8 histone proteins –> 2 of H2A, H2B, H3, H4
H1 binds the region of linker DNA
histones can be reversibly modified
Bacterial Genome
closed and circular
no introns
may have additional info in the form of plasmids
Eukaryotic genome
have multiple chromosomes
chromosomes are linear –> some gets lost each replication –> telomeres help this
have introns
some may contain extra DNA in mitochondria and chloroplasts
introns are removed from mRNA prior to translation
introns mean multiple mRNas of diff sequences can be generated from single gene
