Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIO 214 > Midterm #1 > Flashcards

Midterm #1 Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

how many amino acids are found in the genetic code

A

20

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

how many amino acids have ionizable chains

A

7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what is the structure of an amino acid

A

H
|
+NH3-Ca-COOH
|
R

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

which amino acids are exceptions to amino acid structure

A

glycine (R-group is an H)
proline (R group is bound to alpha amino group)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

how do you name the carbon atoms on amino acids

A

alpha, beta, gamma, delta, episilon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

how are amino acids grouped

A

non polar, polar, electrically charged side chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

how does the symmetry of polar vs. non polar molecules differ

A

polar compounds –> asymmetrical
non polar compounds –> symmetrical

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

which amino acids have non polar side chains

A
  • glycine (Gly)
  • alamine (Ala)
  • valine (Val)
  • leucine (Leu)
  • isoleucine (Ile)
  • methionine (Met)
  • phenylalanine (Phe)
  • tryptophan (Trp)
  • proline (Pro)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what do all amino acids with non polar side chains have in common

A

possess hydrocarbons –> CH4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what does aliphatic mean

A

compounds that have open chains (ex. -CH2CH2CH3) that are acyclic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

which amino acids have polar side chains

A
  • serine (Ser)
  • threonine (Thr)
  • cystine (Cys)
  • tyrosine (Tyr)
  • asparagine (Asn)
  • glutamine (Gln)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

which amino acids have electrically charged side chains

A
  • aspartate (Asp)
  • glutamate (Glu)
  • lysine (Lys)
  • arginine (Arg)
  • histidine (His)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

whats the protonated form of aspartate

A

aspartic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

whats the protonated form of glutamate

A

glutamic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what is the structure of amino acid in a vacuum

A

H
|
H2N-C-COOH
|
R

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what is the structure of amino acid in biological conditions (water)

A

H
|
H3N-C-COO
|
R

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

rank the solubility of side chains

A

non polar are least soluble, then polar, and electrically charged are the most soluble

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is a delineation for typical solubility rules

A

molecule factors (ex. size)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

why might one molecule be more soluble in water than another

A

polar molecules make favorable interactions with water - ex. ion dipole and hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

explain an ion-dipole

A
  • ions make ion-dipole interactions in water
  • ion dipole occurs between charged atom / molecule and a polar molecule
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what is a hydration shell

A

water that surrounds a charged atom

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

describe a hydrogen bond

A
  • H atom covalently bonded to N, O, or F (hydrogen donor) attracted to another EN atom (hydrogen acceptor)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what is the hydrophobic effect

A

occurs when non-polar molecules are excluded by water in order to maximize the number of hydrogen bonds it can make with itself

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

what is a diprotic amino acid

A

an amino acid with two places that can donate a proton

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

do notes on other slides

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what is a triprotic amino acid

A

an amino acid with ionizable side chains
three places on the structure where protons can dissociate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

where does alpha carboxylic group deprotonate

A

pKa1 (more acidic)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

where does alpha amino group deprotonate

A

pKa2 (more basic)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

where does the R-group deprotonate

A

pKa3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

why do acidic residues want to deprotonate

A

to donate -OH proton so they exist primarily in their conjugate base form in biological conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

why do basic residues want to deprotonate

A

to accept protons so they exist primarily in their conjugate acid form in biological conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

conjugate acid form of amine

A

|
–N+–
|

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

conjugate base form of amine

A

–N–
|

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

what is a polypeptide

A
  • a chain (polymer) of amino acid residues
    - they are the primary structures of proteins
    - they fold on themselves to make the 3-D shape
    - polypeptides are synthesized during translation, when the ribosome catalyzes the reaction (between two amino acids and synthesizes a new peptide bond). the rxn that takes place is a condensation rxn
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

what does a peptide bond form between

A

carbonyl (left) and amide (right)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

what is the isoelectric points of polypeptides

A

pH at which there is no net charge in the molecule
- protein solubility is at its least when its at its pI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

how is pI calculated

A

(pka2+pka1)/2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

what does it mean for pH if the pI increases

A

increasing pI means you have a more basic solution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

what is the bond angle between an amino acid (tetrahedral stereochemistry)

A

109.5 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

define chirality

A

non superimposable mirror images

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

define a stereoisomer

A

a molecule with the same chemical bonds, but different arrangements of them in space

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

what form are amino acids naturally found in

A

L form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

what is the only achiral amino acid

A

glycine because one of its R-groups is another hydrogen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

how do you discern L vs. D amino acid isomers

A

if H faces you and spells CORN clockwise then it is in the L form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

which amino acid is most commonly found in the cis formation (despite favoring trans)

A

proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

psi bond

A

SEA TO SEA
alpha carbon to carboxyl
trident

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

phi bond

A

amine to alpha carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

what is conformational flexibility

A

the ability of the side chains and fragments of the polypeptide backbone to adopt different conformations –> facilitated by phi / psi movement

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

which bond in an AA is rigid (planar) and why

A

polypeptide due to its partial double bond character (resonance - stabilizes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

how do secondary structures form

A

as a result of a polypeptide maximizing the number of H-bonds it can make between its carbonyls and amides from its backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

what are the most common types of secondary structures found in proteins

A

alpha helices and beta sheets

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

alpha helix

A

coiling pattern resulting from the carbonyl of an EARLIER residue hydrogen bonding with an amide of a LATER residue 4 (3.6) residues away. They are right handed and positioned 100 degrees apart

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

what secondary structure is myoglobin entirely composed of

A

alpha helices

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

beta sheets

A

results when hydrogen bonding is maximized and two or more strands of a polypeptide make hydrogen bonds with each other. H-bonds stabilize the sheet. pleats are a result of the polypeptide between the alpha carbons being fully extended.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

what is porin

A

an example of a protein almost entirely composed of beta sheets

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

what effects protein function

A

protein structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

why dont alpha helices have prolines

A

its amide cannot hydrogen bond (no hydrogen) and its presence creates a destabilizing KINK

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

what are the three factors (overall) that contribute to alpha helix stability

A
  1. they don’t contain prolines
  2. opposite charges are found 3-4 residues away
  3. bulky R-groups enhances steric hinderence
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

how far away are the charges on amino acid residues

A

3-4 residues away to stabilize (favorable electrostatic interactions. amino acids with the same charge found 3-4 residues away can be destabilizing due to unfavorable electrostatic repulsion

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

how do bulky r-groups affect AA stability

A

AA residues with bulky r-groups found 3-4 residues away can be destabilizing due to steric hinderance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

how to determine if something is parallel vs. antiparallel

A

identify c-term and n-term of each strand. if both go from c-n in the same direction = parallel

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

based on the bumps on a beta sheet, which r-groups would have the same polarity

A

r-groups facing up are the same polarity; r-groups facing down are the same polarity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

what are beta turns

A

connect two antiparallel strands together (180 degrees) (tight turns ~4 AAs). proline and glycine are often found here (ex. the amino nitrogen of proline can take on the cis form which makes for a right turn)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

tertiary structure

A

refers to the 3-D arrangement of all atoms in the folded polypeptide. the tertiary structure may be the final protein (monomers) or it may be a subunit of the complete final protein.
- results from folding
- unfolded or “denature” state (no activity nor function)
- folded or “native conformation” (functional form)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

what is anfinsens dogma

A

3-D structure determined by the sequence of amino acids

found that denaturation is when a protein can unfold / lose its native conformation when…
- temperature is raised
- pH is increased / decreased
- salt concentration changes
- solvent changes
** denaturation is not when the covalent bonds break, instead the IMFs are interfered with

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

is protein folding spontaneous or non-sponatenous

A

spontaneous - protein folding is energetically favored

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

what is the gibbs free energy equation

A

dekta G = delta H * T * delta S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

delta G

A

gibbs free energy - whether the reaction is spontaneous (exergonic) or non-spontaneous (endergonic)

  • delta G = exergonic
    + delta G = endergonic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

delta H

A

enthalpy - total kinetic and potential energy of the system –> energy transferred in or out of the system

  • delta H = exothermic
    + delta H = endothermic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

T

A

temperature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

delta S

A

entropy

  • delta S = lost entropy (ordered)
    + delta S = gained entropy (disordered)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

what factors allow protein folding to be endergonic

A
  • the hydrophobic effect (MOST EFFECTIVE)
  • formation of IMFs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

what is the hydrophobic effect - in reference to protein folding

A

UNFOLDED
- entropically favorable for polypeptide
- allows R-groups to be very ordered (polar sides vs. non polar R-group facing sides)
- creates a very ordered structure
- enthropically unfavorable for H2O surrounding it
- on non-polar groups, a cathrate forms (water H-bonds occur with itself to make a cage-like structure)

FOLDED
- hydrophobic side groups are excluded to a hydrophobic core
- allows water to be disordered and make favorable interaction with polar and electrically charged R-groups on the exterior of the protein
**THIS IS THE MAIN FORCE THAT DRIVES PROTEIN FOLDING

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

IMFs - in reference to protein folding

A
  • IMFs (van der waals, ionic attractions, H-bonds)
    • between two groups and can occur at the c or n terminus
  • disulfide bonds between cysteins (covalent bonds between R-groups of two cysteins)
75
Q

quaternary structure

A

the final protein composed of 2 or more subunits
- each subunit is its own polypeptide that folds onto its own tertiary structure
- subunits may be identical or may be different
- hydrophobic effect and IMFs keep the subunits together

76
Q

primary vs. secondary vs. tertiary vs. quaternary

A

primary = amino acid
secondary = alpha helices and beta sheets
tertiary = folded
quaternary = two identical subunits - each subunit had tertiary structure

77
Q

function of hemoglobin

A
  • delivers oxygen to the tissues
78
Q

what type of solvent is blood

A

its an aqueous solvent that the polar oxygen is non-soluble in

79
Q

what is a heterotetramer

A
  • TETRA = 4 subunits
  • HETERO = not all subunits are identical

ex. hemoglobin

80
Q

what is the structure of hemoglobin

A

has two alpha subunits and two beta subunits
- less than half of AA sequence is identical yet overall tertiary structure is similar between the two subunits
- subunits are almost entirely comprised alpha helices

81
Q

what subunits compose hemoglobin

A
  • alpha subunit –> 7 helices labeled A-H (missing D)
  • beta subunit –> 8 helices (A-H)
82
Q

what is a heme

A

a heme is a prosthetic group (non-protenatious part of the protein)
- responsible for binding oxygen since hemoglobin has four hemes, it can bind oxygen in four places

83
Q

myoglobin

A
  • 8 helices (A-H)
  • does not have quaternary structure in the same way that hemoglobin has
  • suitable for oxygen storage
  • stored in muscles, has high affinity for oxygen
  • important when the body is starved for oxygen
    - as O2 decreases in muscles (ex. during anaerobic exercise), myoglobin releases its oxygen, which diffuses through muscle cells so the mitochondrion can pick it up to be used in generating ATP
84
Q

explain the bonding affinity between protein and ligand

A

protein (ex. hemoglobin or myoglobin) needs a ligand (ex. oxygen)

85
Q

ligand

A

any sort of small molecule that binds to a binding site of a protein
- must be complimentary in shape, size, and hydrophobicity for the protein to discriminate the molecule amongst thousands of others

86
Q

explain the fraction of proteins bound to a ligand vs. concentration of a ligand

A

binding sites become occupied as the concentration of the ligand increases –> initially, the jump is rapid because there are many proteins with a free binding site

87
Q

hyperbolic curve

A

one high line
- one ligand binding site
- or multiple negatively cooperative binding sites
ex. myoglobin

88
Q

sigmoidal curve

A

protein has both high and low affinity forms
- multiple binding sites
- cooperative (binding sites work together)
ex. hemoglobin

89
Q

what are the p50s for myoglobin and hemoglobin

A

myoglobin: p50 = 3 torr (mmHg)
hemoglobin: p50 = 28 torr (mmHg)

90
Q

why does hemoglobin adopt a sigmoidal shape, but myoglobin does not?

A

hemoglobin regularly binds and drops off O2, so it has to have properties with high O2 and low O2 affinity (its ligand)

91
Q

what is pO2 like in the lungs vs. the tissues

A

lungs –> pO2 is high
tissues –> pO2 is low

92
Q

explain how hemoglobin behaves cooperatively

A
  • binding one ligand affects the remaining sites
  • initially difficult to bind ligand, but once bound then more can bind (one binding increases the propensity for more to bind)
93
Q

describe the two conformations that hemoglobin adopts

A

a low and a high affinity for oxygen
- T state (Tense) –> deoxyhemoglobin –> low O2 binding affinity (low pO2 –> tense formed)
- R state (Relaxed) –> oxyhemoglobin –> high O2 binding affinity
(high pO2 –> relaxed formed)d

94
Q

describe a porphyrin ring (heme)

A

Fe in the center engages in coordinate covalent bonding –> a type of covalent bond where one atom donates both electrons; these are bonds that occur between metal ions and ligands
- EWD that helps helps keep Fe in its ferrous state (Fe2+) –> Fe2+ helps oxygen bind reversibly
- when oxygenated, iron (ii) in heme participates in 6 different bonds (oxygen binds to heme at an angle which places oxygen next to another histadine called the distal His)

95
Q

describe the oxygenation change of hemoglobin

A

oxygenation induces a conformational change of hemoglobin
- F alpha helix is flat and heme is planar

96
Q

describe the deoxygenation change of hemoglobin

A

deoxygenation induces a conformational change of hemoglobin
- F alpha helix is angled (changes positions) and its heme is domed (non planar) which expels oxygen toward the proximal histadine

97
Q

what is a dimer in terms of hemoglobin

A

a dimer refers to a complex formed by two subunits of hemoglobin coming together. Each hemoglobin molecule consists of four subunits: two alpha globin chains and two beta globin chains

98
Q

describe the alpha an beta subunits from dimers with each other

A

horizontally, the subunits of the dimer are held together by 30+ residues. these subunits have stronger interactions than the ones that hold these subunits together

vertically, the subunits are held together by 19 residues

99
Q

how does the central channel change from the T deoxy state to the R oxy state

A

narrowing of central channel in the R (oxy) state – narrows upon oxygenation

100
Q

where is iron in the t state

A

outside of the dome (domed shape)

101
Q

what drives the F alpha helix to stand straight for oxygenation

A

steric hinderence

102
Q

what happens to the histidine as it transitions from T to R state

A

small movement of the proximal histadine upon oxygen binding relays a conformational shift to the rest of the subunit

103
Q

which states are most energetically favored at different O2 concentrations

A

at a low concentration of O2, the T-state is favored. The t-state is stabilized by a larger number of ion pairs when oxygen is absent, which can be found connecting the two diners

at a high concentration of O2, the R-state is favored. not as much energy is necessary to get to this conformation

104
Q

define allostery

A

the binding of a ligand at one site affects the binding of a ligand at another

105
Q

what is positive allostery

A

stabilizes ligand-binding conformation
ex. O2 is positive homortrophic
(positive homotrophic affectors

106
Q

what is negative allostery

A

destabilizes ligand-binding conformation (destabilizes the R-state)
ex. CO2, H+, BPG
(negative heterotrophic affectors) - molecules are different from the ligands

107
Q

how is CO2 transferred back

A
  1. 7%-10% of CO2 can dissolve in plasma of blood (this is so low because CO2 is nonpolar and has low solubility in blood)
  2. 70% of CO2 dissolves in the blood as HCO3- (this rxn generates negative allosteric effector protons)
  3. 20% of CO2 is carried away by hemoglobin –> this formof hemoglobin is called carbaminohemoglobin (another negative allosteric effector)
108
Q

describe H+ as a negative allosteric affector

A
  • red blood cells contain carbonic anhydrase enzyme that catalyzes the folowing rxn:
    CO2 + H2O <–> H+ + HCO3-

protons generated are negative allosteric effectors –> hemoglobin transports ~40% of the protons produced when CO2 is hydrated
- when pCO2 increases, the rxn is driven right increasing protons released

109
Q

if an increase in protons decrease hemoglobin’s affinity for O2, how will that affect its hemoglobin’s p50?

A

it raises its p50

110
Q

describe the Bohr effect

A

effects the pH on the oxygen binding curve
- protons are a negative allosteric effector
- as pH descreases, p50 increases

111
Q

explain how bohr protons help facilitate electrostatic attractions

A
  • R-groups on histidine can only interact if protonated
  • when proton concentration is high in the capillaries we can see its more likely that histadine acquired a proton and is able to make these salt bridges that stabilize the t-state
112
Q

does myoglobin exhibit the bohr effect

A
  • myoglobin lacks allostery (hyperbolic curve that exists in high affinity state exclusively)
113
Q

describe the negative allosteric effector CO2

A
114
Q

what percent of histidine is in its protonated form at a pKa of 6 vs. 7

A

pKa of 6 –> ~10% is in its protonated form
pKa of 7 –> ~50% is in its protonated form

115
Q

describe the negative allosteric effector BPG

A

2,3-BPG is a negative allosteric effector that stabilizes the T-state
BPG allows the significant release of O2 (without BPG not much oxygen is iven up so BPG plays a big role in giving up oxygen)
- takes on a negative five charge to bind in the central cavity
- since BPG has a negative charge, the residues in the cavity would have a positive charge (conjugate acid forms of the basic side chains and n terminal amino groups)

116
Q

describe fetal hemoglobin and BPG

A

alpha and gamma hemoglobin subunits (not beta)
- p50 for fetal hemoglobin has a lower p50 than adult hemoglobin. this is critical to the transport of oxygen to the fetus. fetal hemoglobin needs to have lower p50 (stronger affinity for oxygen) for it to steal oxygen from adult hemoglobin)
- instead of histadine, fetal hemoglobin has a serine

117
Q

what is the difference in the number of charges to stabilize BPG for adult vs. fetal

A

8+ charges to stabilize BPG for adult
6+ charges to stabilize fetal –> so BPG cant bind as tightly (lower p50)

118
Q

what is a zwitterion

A

a molecule / ion having separate positive and negative charged groups

119
Q

conjugate acid of H2O

A

H3O+

120
Q

conjugate base of C6H5COOH

A

C6H5COO-

121
Q

which compound in the forward direction is the B-L acid: H2O + C6H5COOH <–> C6H5COO- + H3O+

A

C6H5COOH

122
Q

where is the equivalence point on a graph

A

where pH = pKa

123
Q

for a polypeptide as it moves from an unfolded to folded state, what is the change in entropy

A

negative delta S

124
Q

for water as it moves from an unfolded to folded state, what is the change in entropy

A

negative delta S

125
Q

for a lysine side group as it moves from an unfolded to folded state, what is the change in enthalpy? what interaction is it participating in?

A

negative delta H; electrostatic interaction

126
Q

for a valine side group as it moves from an unfolded to folded state, what is the change in enthalpy? what interaction is it participating in?

A

negative delta H; van der waals

127
Q

for an amide backbone as it moves from an unfolded to folded state, what is the change in enthalpy? what interaction is it participating in?

A

negative delta H; hydrogen bond

128
Q

describe the properties of myoglobin (p50, bonding curve, heme?, role, and cooperative bonding?

A
  • p50 = 0.2 pKa
  • bonding curve is hyperbolic
  • has one heme prosthetic group
  • best suited for oxygen storage
  • does not cooperate in cooperative binding
129
Q

describe the properties of hemoglobin (p50, bonding curve, heme?, role, and cooperative bonding?

A
  • p50 = 4 pKa
  • bonding curve is sigmoidal
  • has four heme prosthetic groups
  • best suited for oxygen transport
  • does cooperate in cooperative binding
130
Q

what are the characteristics at a high O2…
- what is the conformational state?
- is hemoglobin in a high or low oxygen affinity state?
- what is the shape of the heme prosthetic group?
- each subunit’s heme is more likely to be oxygenated or deoxygenated?
- the proximal histidine is or is not perpendicular in this state?
- this state is favored in the lungs or tissues?

A
  • R state favored
  • high oxygen affinity state
  • heme prosthetic group is planar
  • each subunit is more likely to by oxygenated
  • proximal histidine is perpendicular
  • this state is favored in the lungs
131
Q

what are the characteristics at a low O2…
- what is the conformational state?
- is hemoglobin in a high or low oxygen affinity state?
- what is the shape of the heme prosthetic group?
- each subunit’s heme is more likely to be oxygenated or deoxygenated?
- the proximal histidine is or is not perpendicular in this state?
- this state is favored in the lungs or tissues?

A
  • T state favored
  • low oxygen affinity state
  • heme prosthetic group is domed
  • each subunit is more likely to by deoxygenated
  • proximal histidine is not perpendicular
  • this state is favored in the tissues
132
Q

how does CO2 INDIRECTLY act as a negative heterotrophic allosteric effector of hemogrobin

A

by reacting to generate protons with another allosteric effector that stabilizes the T state

133
Q

how does CO2 DIRECTLY act as a negative heterotrophic allosteric effector of hemogrobin

A

by reacting with the N termini of the hemoglobin’s subunits to form a negatively charged carbamate that participates in salt bridges that stabilize the T state

134
Q

effect of BPG on oxygen affinity

A

higher BPG = lower afinity for oxygen

135
Q

how do protons (pH) affect oxygen affinity

A

less protons (higher pHs - more basic) = higher oxygen affinity

136
Q

how does CO2 effect oxygen affinity

A

higher CO2 = lower oxygen affinity

137
Q

what happens to the curve when the hemoglobin is denatured

A

its curve and binding affinity looks more like myoglobin - lower p50

138
Q

glycine R-group and is it polar / non-polar / electrically charged?

A

-H

nonpolar

139
Q

alanine R-group and is it polar / non-polar / electrically charged?

A

-CH3

nonpolar

140
Q

valine R-group and is it polar / non-polar / electrically charged?

A

-CH(CH3)2

nonpolar

141
Q

leucine R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH(CH3)2

nonpolar

142
Q

isoleucine R-group and is it polar / non-polar / electrically charged?

A

-CH(CH3)-CH2-CH3

nonpolar

143
Q

methionine R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH2-S-CH3

nonpolar

144
Q

phenylalanine R-group and is it polar / non-polar / electrically charged?

A

-CH2-benzene

nonpolar

145
Q

tryptophan R-group and is it polar / non-polar / electrically charged?

A

-CH2-pyrrole-benzene

nonpolar

146
Q

proline R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH2-CH3-attached back to amine

nonpolar

147
Q

serine R-group and is it polar / non-polar / electrically charged?

A

-CH2-OH

polar

148
Q

threonine R-group and is it polar / non-polar / electrically charged?

A

-CH-CH3
|
OH

polar

149
Q

cysteine R-group and is it polar / non-polar / electrically charged?

A

-CH2-SH

polar

150
Q

tyrosine R-group and is it polar / non-polar / electrically charged?

A

-CH2-benzene-OH

polar

151
Q

asparagine R-group and is it polar / non-polar / electrically charged?

A

-CH2=O
|
NH2

polar

152
Q

glutamine R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH2-C=O
|
NH2

polar

153
Q

aspartate R-group and is it polar / non-polar / electrically charged?

A

-CH2-C=O
|
O-

ACIDIC electrically charged

154
Q

glutamate R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH2-C=O
|
O-

ACIDIC electrically charged

155
Q

lysine R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH2-CH2-CH2-NH3+

BASIC electrically charged

156
Q

arginine R-group and is it polar / non-polar / electrically charged?

A

-CH2-CH2-CH2-NH-C=NH2+
|
NH2

BASIC electrically charged

157
Q

histadine R-group and is it polar / non-polar / electrically charged?

A

-CH2-imidazole

158
Q

on histidine, where does the imidazole protonate

A

the amine attached to the double bond

159
Q

which amino acids are non polar

A
  • glycine
  • alanine
  • valine
  • leucine
  • isoleucine
  • methionine
  • phenylalanine
  • tryptophan
  • proline
160
Q

which amino acids are polar

A
  • serine
  • threonine
  • cysteine
  • tyrosine
  • asparagine
  • glutamine
161
Q

which amino acids are electrically charged (BASIC)

A
  • lysine
  • arginine
  • histidine
162
Q

which amino acids are non polar (ACIDIC)

A
  • aspartate
  • glutamate
163
Q

abbreviation for glycine

A

G, Gly

164
Q

abbreviation for alanine

A

A, Ala

165
Q

abbreviation for valine

A

V, Val

166
Q

abbreviation for leucine

A

L, Leu

167
Q

abbreviation for isoleucine

A

I, Ile

168
Q

abbreviation for methionine

A

M, Met

169
Q

abbreviation for phenylalanine

A

F, Phe

170
Q

abbreviation for tryptophan

A

W, Trp

171
Q

abbreviation for proline

A

P, Pro

172
Q

abbreviation for serine

A

S, Ser

173
Q

abbreviation for threonine

A

T, Thr

174
Q

abbreviation for cysteine

A

C, Cys

175
Q

abbreviation for tyrosine

A

Y, Tyr

176
Q

abbreviation for asparagine

A

N, Asn

177
Q

abbreviation for glutamine

A

Q, Gln

178
Q

abbreviation for aspartate

A

D, Asp

179
Q

abbreviation for glutamate

A

E, Glu

180
Q

abbreviation for lysine

A

K, Lys

181
Q

abbreviation for arginine

A

R, Arg

182
Q

abbreviation for histidine

A

H, His

183
Q

define amphipathic

A

a protein having both hydrophilic and hydrophobic parts.

BIO 214 (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions