Biochem Exam 1
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Covalent- peptide bonds
What are the types of covalent and
noncovalent bonds that stabilize protein Noncovalent- hydrogen bonds, ionic instructure?
teractions, hydrophobic interactions, van
der waals
What are some functions of proteins?
act as enzymes, transport and storage,
cell shape, transmission of signals
General structure and structural features
for amino acids
R group that varies in size, charge,
shape
Amino group NH2
Carboxyl group COOH
Hydrogen attached
Alpha carbon that is chiral
What is the only amino acid where the
carbon is not chiral?
Glycine
What isomer is the major constituent of
amino acids?
L isomer
covalent bond between carboxyl group
of one AA and amino group of another
What are the characteristics of the pepAA; the bond is rigid and planar due to
tide bond and the direction of protein
partial double bond of C-N bond
synthesis?
synthesis happens from amino terminus
(N) to carboxyl terminus (C)
secondary- a helix, b pleated sheet
tertiary- h bond, hydrophobic interactions, etc.
quarternary- two hemoglobin polypeptides interacting with each other
Examples of secondary, tertiary, quarternary structure
the center of the protein will have amino
How are proteins folded with respect to acids that have nonpolar R groups bc
the type of amino acid that is found in the they are hydrophobic and the outside will
center of the protein vs on the exterior? have the charged and uncharged polar
groups as they interact better with water
K= 1 means that it is in perfect equilibrium and the concentration on both sides
is equal at equilibrium
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K<1 means that concentration of left side
What do certain of the equilibrium values is greater than right at equilibrium
for enzymes mean? K values
K>1 means that concentration of right
side is greater than left at equilibrium
What part of the reaction graph do enzymes change and what parts do they
not change?
They change delta G hash and lower
it which is the difference in energy between substrate and transition state
They do not affect delta G 0 which is
the energy between the substrate and
product
What are reaction rates and reaction
equilibria linked to?
rates are linked to activation energy and
equilibria are linked to standard free energy change
The lower the K value is, the less favorable the reaction and the higher the delta
What is the relationship between K value G value
and delta G value?
The higher the K value is, the more favorable the reaction and the lower the delta
G value
Lock and key model is that substrate fits
perfectly into active site; wrong because
this model actually increases activation
What are the two hypothesis for how enenergy
zymes bind to their substrates and which
Induced fit model is that enzymes asone is right?
sumes complimentary shape to substrate only after substrate binds to enzyme, it shifts to fit the enzyme
as the [S] substrate concentration increases the V reaction velocity steadily
increases until all the enzymes active
What are these concepts associated
sites are occupied by substrate at which
with Michaelis-Menten kinetics? V vs in- point the Vmax maximal velocity of reaccreasing [S], Km, and Vmax
tion is achieved
Km is the substrate concentration at
which half the enzyme's active sites are
occupied by substrate
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Why are enzymes so big compared to its allows it to have sites to create regulatocatalytic site?
ry sites to control activity of the enzyme
Properties of enzyme active sites
overall nonpolar character and water is
excluded; some polar residues are there;
it involves amino acids far apart in the
primary sequence
What is proteolytic modification and an when a protein is cleaved by an enzyme,
example?
ex. digestive enzymes
Catabolism- releases energy from large
molecules and reduces the electron carriers and ADP to ATP through doing this
(oxidative process)
Anabolism- uses smaller molecules to
build up to larger ones and uses electron
Define autotroph, heterotroph, catabocarriers and ATP to do this (reductive
lism, anabolism
process)
Autotroph- use carbon and sunlight to
make their own food
Heterotroph- use carbon from food to
get energy and makes H2O and CO2 as
byproducts
They convert atmospheric N2 to ammoWhy do nitrogen fixing bacteria exist and
nia because atmospheric nitrogen canwhat do they do?
not be used by many organisms
nitrifying- convert ammonia to nitrates
What do nitrifying and denitrifying bactedenitrifying- convert nitrates to ammonia
ria do?
or atmospheric nitrogen
Catabolic pathways are convergent as
they all break down materials into one
simple intermediate
What types of pathways are catabolic, Anabolic pathways are divergent as they
anabolic, and cyclic? What is the impor- all start with an intermediate but use diftant intermediate in the middle of these ferent building blocks to build different
pathways that is very versatile in its use? molecules
Cyclic pathways regenerate key intermediates as they cycle through the pathway
The big intermediate is Acetyl-CoA
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What is oxidation and what is reduction?
Oxidation is loss of electrons
Reduction is gain of electrons
Functions of NAD, FAD, and FMN
NAD is an electron carrier that can be
reduced to NADH
FAD is an electron carrier that can be
reduced to FADH2
FMN is an electron carrier reduced to
FMNH2
What is NAD derived from, and what disease is caused by this deficiency? What
amino acid is this all derived from?
Niacin
Pellagra
Tryptophan
What is FAD derived from?
Riboflavin
Dehydrogenases that transfer electrons
from one compound to another
Substrate undergoes oxidation and losWhat are redox reactions catalyzed by es 2 hydrogen atoms, which NAD+ then
and what do they do?
accepts (hydride ion)
What happens in a redox reaction?
OR
NADH donates a hydride ion to an oxidized substrate for it to then become
reduced
oxidation of ethanol by NAD+
What are two common redox reactions
reduction of pyruvate to lactate done by
seen in metabolism?
lactate dehydrogenase
Name the oxidations of methane to CO2.
Methane-> alcohol-> aldehyde -> carboxylic acid -> carbon dioxide
Homolytic vs Heterolytic Cleavage
Homo- bond electrons shared equally
(each atom gets 1)
Hetero-Bond electrons shared unequally and forms carbanions, carbocations,
protons, and hydride ions
Redistribution of electrons within a molWhat is isomerization reaction and what ecule
is a common one?
ex. going from glucose 6 phosphate to
fructose 6 phosphate
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removal of water to create a double bond
between carbons
What is an elimination reaction?
transfer of acyl, glycosyl, and phosphoryl
What is a group transfer reaction and an groups from one nucleophile to another
example of it?
ex. glucose to glucose-6-phosphate is a
phosphryl transfer reaction
Homolytic cleavage of covalent bonds to
create free radicals
What is a free radical reaction and an
example, name enzyme and start and
end produce.
methylmalonyl-CoA mutase turns
methylmalonyl CoA to succinyl CoA
Cleavage of triphosphate from ATP is
what produces coenzyme B12 and then
How is coenzyme B12 formed and then attaches the Cobalamin to the 5' carbon
how is it used in the methylmalonyl reaction?
In the reaction, the Cobalt and 5' carbon
bond is weak so it is easily broken to
create the radical to start the reaction
Usually the phosphate from ATP is attached to the substrate to create an intermediate, and then displacement of phosIn reality, how does ATP aid in reactions
phate from substrate gives energy for
for the most part? What are some places
product to be formed
in which ATP simply drives reactions?
ATP simply drives reactions in muscle
contraction and conformational changes
in proteins
PEP, 1,3-BPG, Phosphocreatine, Acetyl
CoA
Name four high energy intermediates
What is delta Gp and why is it important?
It is the oxidation of glucose to pyruvate
For glycolysis, what is it, where does it
it happens in the cytoplasm
happen and what does it create?
it creates ATP, NADH, CO2
Pyruvate oxidized to citrate, happens
For the TCA cycle, what is it, where is it,
in mitochondria, and creates NADH,
and what does it create?
FADH2, and CO2
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It is when electron transfer and proton
For oxidative phosphorylation, what is it, pumps drive ATP synthesis, happens in
where is it, and what does it create?
mitochondria, and creates ATP and water
What makes sucrose and what bonds do glucose and fructose, and connected by
they produce?
a-1,2-glycosidic bonds
What makes lactose and what bonds do glucose and galactose and connected by
they produce?
b-1,4-glycosidic bonds
What makes maltose and what bonds do glucose and glucose and connected by
they produce?
a-1,4-glycosidic bonds
made of glucose connected together and connected by b-1,4-glycosidic
bonds
What is cellulose made of and what
bonds are between it?
cellulose is made up of b-1,4-glycosidic
bonds and we don't have enzymes to
Why can't we digest cellulose and why
digest that
can we then digest lactose?
lactase to digest lactose but cellulose is
too big for lactase active site
Where are the largest stores of glycogen
held?
liver, then muscle
Why can't we store glucose in its
monomeric form?
Glycogen is insoluble so it won't contribute to increasing osmolarity of the
cell, so cell won't have water increase
and won't burst
Attachment of UDP glucose to glycoWhat two reactions does glycogenin cat- genin protein
alyze?
Transfer for a glycosyl residue to existing
glycogen chain
Primer: 8 glucosyl residues linked via
a-1,4 bonds
Rest: 12 tiers
12-14 residues in each tier
Inner tiers have 2 a-1,6-glycosidic
branches on each residue
Outer tiers are unbranched
What are properties of the glycogen
primer? And the rest of the particle
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Biochem Exam 1
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Glycogen phosphorylase first removes a
glycosyl residue and adds a phosphate
to it to create G1P
Then phosphoglucomutase turns G1P
into G6P (G6P can feed into glycolysis
for muscles)
In only liver, glucose 6 phosphatase reGive the steps of glycogen breakdown
moves the phosphate from G6P so that
from glycogen to unbranched glucose.
it can move into the bloodstream
Debranching enzyme first removes 3 of
the last 4 glucosyl residues and connects them to the straight chain; then
a-1,6-glucosidase activity removes the
last residue off of the 1,6-branched point
and releases it as free glucose
What are reducing sugars?
sugars that can reduce mild oxidizing
agents like Fe2+ and the glucose itself
gets oxidized
What is the main donator of glucose in
glycogen synthesis?
UDP glucose
Hexokinase turns glucose into G6P
through use of ATP
Phosphoglucomutase turns G6P into
G1P
UDP glucose pyrophosphorylase turns
Give the steps of glycogen synthesis
starting with glucose and ending with a G1P into UDP glucose and then uses it
to add to a growing glycogen chain (also
branched chain.
helped by glycogen synthase)
Branching enzyme then introduces a
branch into a chain by forming the
a-1,6-glycosidic bond
Insulin- lower blood glucose by inhibiting
glycogen breakdown and gluconeogenesis and promoting glycolysis and glycoWhat does insulin do, and what do epi
genesis
and glucagon do?
Epi/Glucagon- raises blood glucose by
stimulating glycogen breakdown and
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gluconeogenesis and inhibiting glycolysis; for epi, glucose is mainly used in the
fight or flight mode in muscles and for
glucagon it is from the liver
When there is high blood glucose, give
a breakdown of what happens to insulin, insulin sensitive protein kinase,
PKB, GSK3, PP1, Glycogen synthase,
phosphorylase kinase, glycogen phosphorylase. And what this results in for
glycogen breakdown, glycogen synthesis, and glycolysis.
When there is low blood glucose,
give a breakdown of what happens to
glucagon, cAMP, PKA, phosphorylase
kinase, glycogen phosphorylase, glycogen synthase, and what this results in for
glycogen breakdown, glycogen synthesis, and glycolysis.
If there is high ATP or G6P, it means that
there is no need for glycogen breakdown
How do the concentration of ATP, glu- so it will inhibit glycogen phosphorylase
cose 6 phosphate, and AMP affect
If there is high AMP, indicates that there
glycogen phosphorylase?
is low ATP and more glycogen needs to
be broken down so it stimulates phosphorylase
How do the two GM sites play a role
in the hormonal control of insulin and
epi/glucagon?
Insulin stimulates phosphorylation of
GM site 1 which activates PP1 and all its
effects
Epi/glucagon stimulates phosphorylation of GM site 2 which dissociates PP1
by activating PKA which phosphorylates
an inhibitor protein of PP1 so that it can
bind to it
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