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168 Cards in this Set

  • Front
  • Back
sulfydryl groups are a defining feature of:
thiol compounds, R-SH
Hydroxyl groups are a defining feature of:
alcohols
Amino groups are a defining feature of:
Amines. eg: putrecine
Amido groups are a defining feature of:
Amides. eg: pepties
Carbonyl groups are a defining feature of:
a variety of compounds
Acyl groups are a defining feature of:
a variety of compounds
What are the four major classes of biomolecules?
amino acids, carbohydrates, lipids, and nucleotides
Characteristics of amino acids?
amphoteric, exist as zwitterions (at neutral pH), and polymerize to form polypeptides
amphoteric
has both acidic and basic groups
zwitterions
have both positive and negative charges
Characteristics of carbohydrates:
1. are polyhydroxylated aldehydes or ketones (or derived thereof)
2. may be simple or polymeric
glycosidic bond
bond connecting 2 saccharides into a disaccharide
oxidation
loss of electrons
reduction
gain of electrons
Order of electronegativity most to least
O-N-S-C-H
log10 x =
10^? = x

the power to which 10 is raised to get x
antilog10 y =
10^y

10 raised to the yth power
pH =
-log[H+]
What is an acid by the bronsted definition?
H+ donor
Bronsted base?
H+ acceptor
A reaction is at equilibrium when...
...the rate of the forward reaction equals the rate of the reverse reaction. NO net change in product or reactant concentration.
how would you deteremine the equilibrium constant?
concentration of the products at eq. divided by the concentration of the reactants at eq.
What does Keq tell you?
how likely the reaction is to proceed in the forward or reverse direction
Keq>1 will proceed in which direction
foreward
Keq less than 1 will proceed in which direciton?
reverse
Dissociation constant of an acid Ka=?
[A-][H+]/[HA]
pka=?
-logKa
smaller ka = ?
weaker acid
smaller pka=?
stronger acid
henderson hasselach equation?
ph = pka + log([A-]/[HA])
the pKa of most alpha amino acids is about?
9.3
pKa of alpha-carboxylic acid group of most amino acids is about?
2.2
What is a buffer?
a solution that resits changes in pH when either acid or base is added

composed of a weak acid and its conjugate salt
What are the most important intracellular buffers?
phosphate and proteins
for every mmHg the partial pressure of CO2 increases, the mM dissolved CO2 increases by how much?
.0301 mM dissolved CO2
The pKa of blood is?
6.1
hydroxyl suffix
-ol
carboxyl ending
acid
amino suffix
-ine
amido suffix
-ide
acid anhydride ending
anyhydride
ketone suffix
-one
aldehyde suffix
-al
Characteristics of Lipids:
1. Diverse
2. poorly soluble in water
3. composed primerily but not exclusively, of C and H
4. Often amphipathic
Characteristics of Nucleotides:
1. compsed of at least on phospate, a sugar(ribose/deoxyribose) and a nitrogenous ring
2. polymerize to form biologically essential molecules (RNA/DNA)
3. in monomeric form are often important as energy currency and components of coenzymes
avagodro's number
6.02x10^23, #C's in 12 grams of carbon
amphipathic
both hydrophyllic and hydrophobic components
salt of organic acid suffix:
-ate
normal blood plasma pH=
7.4
normal blood plasma pH above what? and below what? will cause death?
7.6 and 7.2
Functions of Protiens:
enzymatic catalysis (hexokinase)
mechanical support (collagen)
transport and storage (hemoglobin)
movement (actin)
transmission of never impulses (opsin)
regulation (insulin)
protection (immunoglobulins)
-ase often indicates?
catalytic function
-in often indicates?
non-enzymatic function
only achiral aa at alpha carbon?
glycine
normal aa's are L or D?
L
Abbreviations of glycine
Gly, G
Abbreviations of alanine
Ala, A
Abbreviations of valine
Val, V
Abbreviations of leucine
Leu, L
Abbreviations of isoleucine
Ile, I
Abbreviations of phenylalanine
Phe, F
Abbreviations tryptophan
Trp, W
Abbreviations methionine
Met, M
Abbreviations proline
Pro, P
Abbreviations serine
Ser, S
Abbreviations cysteine
Cys, C
Abbreviations threonine
Thr, T
Abbreviations tyrosine
Tyr, Y
Abbreviations asparagine
Asn, N
Abbreviations glutamine
Gln, Q
Abbreviations Aspartate
Asp D
Abbreviations glutamate
Glu, E
Abbreviations Lysine
Lys, K
Abbreviations arginine
Arg, R
Abbreviations histidine
His, H
Does the pKa of an aa change or remain the same when an aa is incorporated into a protein? Why?
pka changes because interactions between nearby amino acid side chains can affect the ability of a given side chain to donate or accept H+s.
pka aspartate
3.9
pka glutamate
4.3
pka lysine
10.5
pka arginine
12.5
pka histidine
6.0
the peptide bond has ______-_______-_______ character
partial double bond
Does the C and N of a peptide bond rotate with respect to one another?
no
the N terminus of a peptide is always depicted on the________ side?
left
Common modifications to to aa's of polypeptide chains
phosphorylation
gylcosylation
hydroxylation
carboxylation
others
phosphorlyation
occurs on aa side chains with free hydroxyl groups
done to many proteins
can increase or decrease activity
glycosylation
carbohydrate groups may be added to protein via N or O linkages
done to many proteins
carbohydrate groups often act as destination tags
hydroxylation
of prolyl or lysyl residues
done to a few proteins
carboxylation
of glutamyl groups
done to a few proteins
especially ones for blood clotting
aa's that undergo o-linked glycosylation:
ser, tyr, thr
aa's that undergo n-linked glycosylation
asn
lysyl residues are hydroxylated at which carbon
delta
lysyl residue reacts with ________ and _____ via the enzyme __________ to form _____ and ____.
alpha ketoglutarate, oxygen, lysyl hydroxylase, hydroxylysyl residue and succinate
What role does vitamin C play in hydroxylation?
reduces the enzyme if it becomes inappropriately oxidized
prolyl residue reacts with ____ and____ in hydroxylation via enzyme ____ to form _____ and _____
alpha ketoglutarate, oxygen, prolyl hydroxylase, hydroxylprolyl residue, and succinate
What is oxidized in hydroxylation?
lysyl residue and alpha ketoglutarate
What is reduced in hydroxylation?
oxygen
What is oxidized in carboxylation? what is reduced?
oxidized; glutamyl and vitamin K dihydroquinone
reduced: CO2 and O2
Which carbon in glutamyl undergoes carboxylation?
gamma
What types of bonds/interactions orchestrate folding or proteins into 3D shape?
disulfide bonds
ionic interactions
hydrogen bonds
hydrophobic interactions
What energy investment is required to disrupt disulfide bonds?
100 kcal/mol
What energy investment is required to disrupt ionic interactions
10 kcal/mol
What energy investment is required to disrupt hydrogen bonding
5 kcal/mol
What energy investment is required to disrupt hydrophobic interactions?
3kcal/mol
which bonds/interactions are most important in protien 3D shape?
hydrogen bonding and hydrophobic interactions
Describe disulfide bridges
covalent bonds
formed by oxidation of cysteinyl residues
intra or inter chain
What's a hydrogen bond?
bond between O,N,S and hydrogen covalently bonded to another electronegative atom
What's hydrophobic interaction?
occurs between nonpolar R groups
primary structure of a protein is maintained by...
covalent peptide bonds
secondary structure is maintained by...
hydrogen bonds
What's tertiary structure of a proteins? maintained by?
overall 3D shape
h bonds, hydrophobic interactions, ion interactions, disulfide bridges
Quaternary protein structure?
more than one polypeptide and their spatial arrangement
alpha helix is stabalized from h bonds how many residues apart
4
alpha helix is destabled by...
large numbers of charged R groups
bulky R groups
prolyl residues
parallel beta sheet
run in same direction
anti parallel beta sheets
run in opposite directions
Same chain vs. independents chain...
involve segments of same protein/different porteins
Tertiary structure is maintained by which structure?
secondary
Gross classification of tertiary structure...
Fibrous or Gobular
Fibrous
(rod like)
keretin
silk
collagen
Globular
(spherical)
hemoglobin
immunoglobulins
alcohol dehydrogenase
keratin's secondary structure
alpha helical
silk's (fibroin) secondary structure
beta sheet
collagen's secondary structure
neither alpha helix or beta sheet, unique
hemoglobulin
mostly alpha helical
immunoglobuin secondary structure
mostly beta sheet
alcohol dehydrogenase's secondary structure
both aphla helix and beta sheet
oligomeric protein
more than one protein
dimer
2 polypeptide chains
homodimer
both chains are identical
heterodimer
the 2 chains are different
trimer
3 protein subunits
tetramer
4 protein subunits
Changes in what environmental factors cause a protein to lose activity? why?
pH, salt concentration, temperature
destroys weak interactions that maintain protein's shape
Denaturations?
loss of primary structure?
reversible?
breaking of weak bonds maintaining protein's conformation
no
usually not
endothermic
heat is consumed
exothermic
heat is released
endergonic
useful energy is consumed
exergonic
useful energy is released
Gibbs free energy (G)
the amount of energy available to do useful work
change in G measures
how endergonic or exergonic a reaction is
exergonic reactions spontaneous or non spontaneous?
spontaneous
Can you determine if a reaction is endo/exothermic from knowing exer/endergonic?
no
enthalpy
heat content
enzymes
catalysts, undergo no net change
Do enzymes change the keq of a rxn?
no
Can enzymes alter the ability of a reaction to proceed spontaneously?
no
Do enzymes increase the rate of reaction equally in the forward and reverse direction?
Yes, as to not change keq
cofactor
non protein molecule required for enzyme activity
examples of cofactors
metal ions (Fe++, Mg++, Zn++, Ca++)
organic molecules (called coenzymes)
apoenzyme
enzyme without cofactor, usually inactive
holoenzyme
apoenzyme and cofactor together
How are cofactors bound to enzymes?
covalently or non covalently
Enzymes stabilize what?
transition states
induced fit model
substrate binding cuases conformational change in the enzymes that make sit easier to attain the transition state
classifications of enzymes
oxidoreductases
transferases
hydrolases
lyases
ligases
isomerases
oxidoreductases
catalyze oxidation-reduction reactions
transferases
catalyze transfer of groups such as amino, carboxyl, methyl, carbonyl, tec.
hydrolases
catalyze hydrolytic cleavages
lyases
catalyze cleaveage of c-c, c-n, c-o, or c-s bonds without hydrolysis or redox
ligases
catalyze the formation of new c-c, c-n,c-s or c-o bonds, in a reaction coupled to hydrolysis of ATP or other high energy compound
isomerase
catalyze intra molecular rearrangements
enzymes increase rxn rate ____ fold
10^5 to 10^11 times
allosteric effectors
bind to enzyme noncovalently
reversible
sometimes substrate, often not
often products of metabolic pathway
product inhibition
at high product concentration, may compete with substrate for binding in the active
inducible enzymes
rate of enzymes sythesis increases in response to increased substrate concentration or related metabolite
repressible enzymes
rate of enzyme synthesis decreases in response to increased [product] or related metabolite
constitutive enzyme
rate of enzyme synthesis remains virtually constant for the life of the cell