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z F1: Phys Chem > Exam 1 > Flashcards

Exam 1 Flashcards

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
Importance of amino acids
building blocks of proteins biologically active or precursors for biologically active molecules
26
L and D amino acids are ________. Only ______ are commonly found in proteins
enantiomers L-amino acids
27
What ion contains both a positive and negative charge
Zwilter ion
28
What kind of acid is proline
imino acid it produces kinks in the polypeptide
29
Cystines have sulfhydryl groups that form what kind of bonds
disulfide bonds
30
What is the only amino acid that is not chiral
glycine
31
What amino acids need to be obtained through diet
Phenylalanine, Valine, Theonine, Tryptophan, Methionine, Histidine, Isoleucine, Leucine, Lysine (PriVaTe TiM HILL)
32
What is the pKa of carboxylic acid and amino groups
carboxylic acid: 2 amino: 9-11
33
What is hydropathy index
when there is a higher number then its more hydrophobic
34
What are ionizable groups
Amino acids with positively or negatively charged side chains can act as proton donors and acceptors respectively (acids or bases)
35
Once formed the peptide bond is very stable due to its ____ _________ energy of cleavage. A peptide bonds is _________ stable
high activation, kinetically
36
When does an amino acid name get switched from being called oligopeptide to peptide
When there are more than 50 amino acids
37
What is the only way amino acids are written
animo (n terminal) to carboxyl (c terminal)
38
Peptide bond are stabilized by resonance, its resonance gives it ______ _____ character
double bond, no rotation
39
Adjacent planes containing adjacent peptide bonds can be rotated around ___ and ___ angles
phi and psy
40
How are phi and psy angles created
phi-characterize the bond at the amino-terminal side of alpha carbon psy- carboxy-terminal side
41
Due to steric hinderance the phi and psy angles are _______. How are the angles predicted
restricted ramachandran plot
42
Secondary structure of a protein
structure features generated by hydrogen bonds between amide groups and carbonyl groups of polypeptide backbone
43
What are the three common local structure elements of secondary structure
alpha helix beta conformation loops and turns (can contain irregulatory coiled or extended regions)
44
Linus pauling and robert corey proposal of alpha helix
spiral backbone and side chains pointing outward stabilized by H-bond between carbonyl and amide groups
45
R-groups are ____ residues apart in a primary sequence
3-4
46
What helices are more stable right or left
right
47
Two or more alpha helices can intertwine and form a ________
superhelix (not all helices are alpha helices)
48
Beta conformation
zig zag conformation beta pleated sheet H-bonds in between strands
49
What are silk, fatty acid binding proteins, alpha-hemolysin, and porin
Beta sheets
50
How are beta sheets typically depicted
as broad arrows pointing in the same direction or opposite directions
51
What two amino acids are found in turns
prolines and glycines
52
What are alpha, and gamma turns
alpha: 5 residues gamma: 3 residues, H-bond btw 1st and 3rd residue
53
What are beta turns
4 residues found in antiparallel beta sheets proline type one and glycine type two H-bond between 1st and 4th residue
54
What are loops
They contain more residues and there is a more gentle turn in direction
55
Tertiary structure
Not just hydrogen bonds but have side chain interactions along with backbone interactions
56
Chaperones and heat shock proteins can facilitate ________ in tertiary structure
folding
57
Both folding and _______ are highly cooperative
denaturation
58
What are protein domains
distinct structural units that fold independently they are sections of a single polypeptide chain
59
What are motifs
recognizable folding pattern involving two or more elements of secondary structure and connections between them
60
A fold can contain several ______
motifs (polypeptide chains contains domains, domains contain motifs, motifs contain secondary structural elements)
61
an oligomeric protein can be made of identical of different subunits, what are they called
identical: homodimer different: heterodimer
62
What are the 5 covalent modifications of proteins
glycosylation phosphorylation acetylation hydroxylation upiquitination
63
What are the 4 unwanted reactions of proteins
oxidation deamidation nitration glycation
64
What is a schiff base
presence of a double bond linking carbon and nitrogen atoms
65
__________ is an indicator of glucose control
HbA1c *glycation end products play a role in diabetes
66
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
Alzheimers
67
What part of intrinsically disordered proteins are structurally incorrect
lacking a hydrophobic core rich in AA with charged side chains
68
What are these characteristics of: spacers, insulators, linkers in larfer structures, scavengers, interaction patners, core forming of a protein
Intrinsically disordered proteins
69
X-ray crystallography
scattering of x-rays by electrons
70
Advantages and disadvantages of x-ray crystallography
Ad: larger proteins, high resolution Dis: crystallization is necessary, static picture of protein, can't see hydrogens
71
NMR
nuclei have magnetic moment "spin" with C and N isotopes
72
NMR advantages and disadvantages
ad: determines solution structures, reveals info about protein dynamics, can see hydrogens dis: not possible for large proteins, large amount of material needed
73
Cryo-Electron Miscroscopy
compounded from transmission electron micrographs of single protein molecules each viewed from a different angle
74
Cryo-Electron Miscroscopy advantages and disadvantages
ad: large proteins, high-resolution, crystals not necessary dis: protein not in solution, static structures are produced
75
proteins with similar sequence + fold + function are called, proteins with similar fold + function are called
protein families superfamilies
76
what is Kd and Ka
Kd = 1/Ka Ka = acid dissociation constant
77
when the ligand concentration is equal to Kd saturation ___% and binding is ____ max
50% 1/2
78
molecules that are permanently bound to proteins suck as the heme group are called ______ _______
prosthetic groups
79
Protein without its prosthetic group = Protein with its prosthetic group =
apoprotein holoprotein
80
Iron has 6 coordination bonds four taken by ____, one by ___, and one for ____
heme his O2
81
Binding of O2 to one site causes a transition from the low affinity state to the high affinity state this is called?
cooperatively
82
What does a high affinity state for O2 represent
too little oxygen is released in the tissues
83
Myosin and hemoglobin both bind _____, belong to the same ______ family
oxygen protein
84
Is O2 cooperative in hemoglobin or myoglobin and where is the oxygen stored in both
cooperative in hemoglobin myo: stored in muscle hemo: transports between lungs and tissues
85
What are the two states for hemoglobin
T state: low affinity R state: high affinity transition leads to sigmoid binding curve
86
O2 regulating its own binding is called what and what is it called when it does not bind its own
own: homotropic regulator other: heterotropic
87
Actin motors and Microtubule motors
Actin motors: myosin Microtubule motors: kinesin, dynein
88
H+ ions in O2 hemoglobin
tissues with active metabolism are more acidic increase in acidity favors the low affinity state of Hb -> release of O2
89
CO2 in O2 hemoglobin
CO2 is higher in metabolically active tissues, increase in CO2 causes release of O2 from Hb
90
2,3-biphosphoglycerate
small molecule that binds in the cavity between subunits of Hb
91
Difference between fetal hemoglobin and adult hemoglobin
fetal hemoglobin has 2 gamma chains instead of beta chains
92
Myosin contains how many subunits
6 2 heavy 4 light thick filaments
93
F-actin is called
thin filaments
94
What does the Z-disk do
thin filaments held here by alpha actin, desmin, vimentin
95
What does the A-band do
spans the length of thick filaments
96
What does the M line do
Adjacent to thick filament are joined tail to tail extending structure is called sacromere
97
Myofibils are what
multiple actin-myosin filaments form muscle fiber
98
What is the calcium sensory info
Troponic C
99
How is force generated in muscle contraction
concerted series of actin and myosin binding dissociation steps, conformaiton changes and ATP hydrolysis
100
4 steps of muscle contraction
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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