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z F1: Phys Chem > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

Rotations around bond axis is possible around ______ bonds but not _______ bonds

A

single, double

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2
Q

All single bonds for C, N, O are in _______ manner but if there is a double bond then the configuration is _______

A

tetrahedral
trigonal planar

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3
Q

Coordination bonds

A

-both electrons are donated by the same atom
-coordination bonds with transition metals are weaker than regular covalent bonds

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4
Q

Configuration

A

chiral centers are not possible to use rotation to superimpose one form or another

can be cis or trans (can’t transition between the two)

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5
Q

Conformations

A

geometric arrangements around single bond
proteins can accomplish this

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6
Q

Commonly used categories of non-colvalent bonds are

A

electrostatic
hydrogen bonds
van der waals
interactions of aromatic systems
hydrophobic interactions

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7
Q

How many coordination bonds does iron have

A

6, formed in octahedral manner

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8
Q

Charge-charge
charge-dipole
dipole-dipole
charge-induced dipole
dipole-induced dipole
dispersion
van der waals

A

Charge-charge: longest-range force
charge-dipole: depends on orientation
dipole-dipole: mutual orientation
charge-induced dipole: polarizability of molecule which dipole is induced
dipole-induced dipole: polarizability of molecule which dipole is induced
dispersion: mutual synchronization of fluctuating charges
van der waals: outer electron orbitals overlap

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9
Q

What is a H-bond donor

A

Strongly electronegative and can pull electrons

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10
Q

What is a H-bond acceptor

A

can be either a full or a partial charge

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11
Q

What is van der waals distance fall off and repulsive fall off

A

distance: 1/r^6
repulsion: 1/r^12

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12
Q

Why are the properties of water important

A

Its a universal solvent
They fold biological macromolecules
Core of compartmentalization of rxns by membranes
Bodies consist of about 60% water

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13
Q

What are the properties of water

A

liquid at room temp
high melt pt, boil pt, heat capacity, surface tension
it has a high dielectric constant (shielding)
higher density than ice

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14
Q

Why is a tetrahedral geometry important for water

A

it has a lot of empty space

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15
Q

What are the favorable conditions of delta G,H and S

A

delta G = (-)
delta H = (+)
delta S = (+)

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16
Q

Molecules that have both polar and non-polar groups are

A

Amphipathic

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17
Q

When non-polar groups move together there is less contact with water. Water molecules surrounding the hydrophobic surface are released into bulk-phase, increasing their disorder. What is this term

A

hydrophobic interactions

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18
Q

What is the dissociation constant of water and molarity of water

A

1.8*10^-16 M
55.5 M

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19
Q

What is the formula for pH and poH

A

pH= -log10[H+]
poH= -log[OH-]

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20
Q

What is the henderson-hasselbalch equation

A

pH=pKa+log(acid/base)

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21
Q

Ka
1/Ka

A

Ka: acid proton dissociation constant, tendency to release a proton
1/Ka: proton affinity, tendency to bind a proton

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22
Q

pKa>pH

A

protonated form predominates

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23
Q

What buffer system is used in physiological range of intracellular pH

A

H2PO4- / HPO4 2-

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24
Q

Breathing out CO2 causes what to happen to pH in your body

A

increase pH making your body more basic

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25
Q

Importance of amino acids

A

building blocks of proteins
biologically active or precursors for biologically active molecules

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26
Q

L and D amino acids are ________. Only ______ are commonly found in proteins

A

enantiomers
L-amino acids

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27
Q

What ion contains both a positive and negative charge

A

Zwilter ion

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28
Q

What kind of acid is proline

A

imino acid
it produces kinks in the polypeptide

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29
Q

Cystines have sulfhydryl groups that form what kind of bonds

A

disulfide bonds

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30
Q

What is the only amino acid that is not chiral

A

glycine

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31
Q

What amino acids need to be obtained through diet

A

Phenylalanine, Valine, Theonine, Tryptophan, Methionine, Histidine, Isoleucine, Leucine, Lysine (PriVaTe TiM HILL)

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32
Q

What is the pKa of carboxylic acid and amino groups

A

carboxylic acid: 2
amino: 9-11

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33
Q

What is hydropathy index

A

when there is a higher number then its more hydrophobic

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34
Q

What are ionizable groups

A

Amino acids with positively or negatively charged side chains can act as proton donors and acceptors respectively (acids or bases)

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35
Q

Once formed the peptide bond is very stable due to its ____ _________ energy of cleavage. A peptide bonds is _________ stable

A

high activation, kinetically

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36
Q

When does an amino acid name get switched from being called oligopeptide to peptide

A

When there are more than 50 amino acids

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37
Q

What is the only way amino acids are written

A

animo (n terminal) to carboxyl (c terminal)

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38
Q

Peptide bond are stabilized by resonance, its resonance gives it ______ _____ character

A

double bond, no rotation

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39
Q

Adjacent planes containing adjacent peptide bonds can be rotated around ___ and ___ angles

A

phi and psy

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40
Q

How are phi and psy angles created

A

phi-characterize the bond at the amino-terminal side of alpha carbon
psy- carboxy-terminal side

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41
Q

Due to steric hinderance the phi and psy angles are _______. How are the angles predicted

A

restricted
ramachandran plot

42
Q

Secondary structure of a protein

A

structure features generated by hydrogen bonds between amide groups and carbonyl groups of polypeptide backbone

43
Q

What are the three common local structure elements of secondary structure

A

alpha helix
beta conformation
loops and turns
(can contain irregulatory coiled or extended regions)

44
Q

Linus pauling and robert corey proposal of alpha helix

A

spiral backbone and side chains pointing outward
stabilized by H-bond between carbonyl and amide groups

45
Q

R-groups are ____ residues apart in a primary sequence

A

3-4

46
Q

What helices are more stable right or left

A

right

47
Q

Two or more alpha helices can intertwine and form a ________

A

superhelix
(not all helices are alpha helices)

48
Q

Beta conformation

A

zig zag conformation
beta pleated sheet
H-bonds in between strands

49
Q

What are silk, fatty acid binding proteins, alpha-hemolysin, and porin

A

Beta sheets

50
Q

How are beta sheets typically depicted

A

as broad arrows pointing in the same direction or opposite directions

51
Q

What two amino acids are found in turns

A

prolines and glycines

52
Q

What are alpha, and gamma turns

A

alpha: 5 residues
gamma: 3 residues, H-bond btw 1st and 3rd residue

53
Q

What are beta turns

A

4 residues
found in antiparallel beta sheets
proline type one and glycine type two
H-bond between 1st and 4th residue

54
Q

What are loops

A

They contain more residues and there is a more gentle turn in direction

55
Q

Tertiary structure

A

Not just hydrogen bonds but have side chain interactions along with backbone interactions

56
Q

Chaperones and heat shock proteins can facilitate ________ in tertiary structure

A

folding

57
Q

Both folding and _______ are highly cooperative

A

denaturation

58
Q

What are protein domains

A

distinct structural units that fold independently
they are sections of a single polypeptide chain

59
Q

What are motifs

A

recognizable folding pattern involving two or more elements of secondary structure and connections between them

60
Q

A fold can contain several ______

A

motifs
(polypeptide chains contains domains, domains contain motifs, motifs contain secondary structural elements)

61
Q

an oligomeric protein can be made of identical of different subunits, what are they called

A

identical: homodimer
different: heterodimer

62
Q

What are the 5 covalent modifications of proteins

A

glycosylation
phosphorylation
acetylation
hydroxylation
upiquitination

63
Q

What are the 4 unwanted reactions of proteins

A

oxidation
deamidation
nitration
glycation

64
Q

What is a schiff base

A

presence of a double bond linking carbon and nitrogen atoms

65
Q

__________ is an indicator of glucose control

A

HbA1c
*glycation end products play a role in diabetes

66
Q

What disease is associated with two alpha helix part of larger protein, proteolytic cleavage creates amyloid beta peptide, and then beta loses its alpha helix and creates amyloid fibrils

A

Alzheimers

67
Q

What part of intrinsically disordered proteins are structurally incorrect

A

lacking a hydrophobic core
rich in AA with charged side chains

68
Q

What are these characteristics of: spacers, insulators, linkers in larfer structures, scavengers, interaction patners, core forming of a protein

A

Intrinsically disordered proteins

69
Q

X-ray crystallography

A

scattering of x-rays by electrons

70
Q

Advantages and disadvantages of x-ray crystallography

A

Ad: larger proteins, high resolution
Dis: crystallization is necessary, static picture of protein, can’t see hydrogens

71
Q

NMR

A

nuclei have magnetic moment “spin” with C and N isotopes

72
Q

NMR advantages and disadvantages

A

ad: determines solution structures, reveals info about protein dynamics, can see hydrogens
dis: not possible for large proteins, large amount of material needed

73
Q

Cryo-Electron Miscroscopy

A

compounded from transmission electron micrographs of single protein molecules each viewed from a different angle

74
Q

Cryo-Electron Miscroscopy advantages and disadvantages

A

ad: large proteins, high-resolution, crystals not necessary
dis: protein not in solution, static structures are produced

75
Q

proteins with similar sequence + fold + function are called, proteins with similar fold + function are called

A

protein families
superfamilies

76
Q

what is Kd and Ka

A

Kd = 1/Ka
Ka = acid dissociation constant

77
Q

when the ligand concentration is equal to Kd saturation ___% and binding is ____ max

A

50%
1/2

78
Q

molecules that are permanently bound to proteins suck as the heme group are called ______ _______

A

prosthetic groups

79
Q

Protein without its prosthetic group =
Protein with its prosthetic group =

A

apoprotein
holoprotein

80
Q

Iron has 6 coordination bonds four taken by ____, one by ___, and one for ____

A

heme
his
O2

81
Q

Binding of O2 to one site causes a transition from the low affinity state to the high affinity state this is called?

A

cooperatively

82
Q

What does a high affinity state for O2 represent

A

too little oxygen is released in the tissues

83
Q

Myosin and hemoglobin both bind _____, belong to the same ______ family

A

oxygen
protein

84
Q

Is O2 cooperative in hemoglobin or myoglobin and where is the oxygen stored in both

A

cooperative in hemoglobin
myo: stored in muscle
hemo: transports between lungs and tissues

85
Q

What are the two states for hemoglobin

A

T state: low affinity
R state: high affinity
transition leads to sigmoid binding curve

86
Q

O2 regulating its own binding is called what and what is it called when it does not bind its own

A

own: homotropic regulator
other: heterotropic

87
Q

Actin motors and Microtubule motors

A

Actin motors: myosin
Microtubule motors: kinesin, dynein

88
Q

H+ ions in O2 hemoglobin

A

tissues with active metabolism are more acidic
increase in acidity favors the low affinity state of Hb -> release of O2

89
Q

CO2 in O2 hemoglobin

A

CO2 is higher in metabolically active tissues, increase in CO2 causes release of O2 from Hb

90
Q

2,3-biphosphoglycerate

A

small molecule that binds in the cavity between subunits of Hb

91
Q

Difference between fetal hemoglobin and adult hemoglobin

A

fetal hemoglobin has 2 gamma chains instead of beta chains

92
Q

Myosin contains how many subunits

A

6
2 heavy
4 light
thick filaments

93
Q

F-actin is called

A

thin filaments

94
Q

What does the Z-disk do

A

thin filaments held here by alpha actin, desmin, vimentin

95
Q

What does the A-band do

A

spans the length of thick filaments

96
Q

What does the M line do

A

Adjacent to thick filament are joined tail to tail
extending structure is called sacromere

97
Q

Myofibils are what

A

multiple actin-myosin filaments
form muscle fiber

98
Q

What is the calcium sensory info

A

Troponic C

99
Q

How is force generated in muscle contraction

A

concerted series of actin and myosin binding dissociation steps, conformaiton changes and ATP hydrolysis

100
Q

4 steps of muscle contraction

A

1: ATP binds to myosin head, causing dissociation from actin
2: as tightly bound ATP is hydrolyzed conformational change occurs. ADP and Pi remain associated with myosin head
3: Myosin head attaches to actin filament, cause release of Pi
4: Pi release triggers power stroke, conformation change in myosin head that moves actin and myosin filaments, ADP released

z F1: Phys Chem (4 decks)

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