PHRD 5025 - Applied Biochem > Lecture 2 - Protein Function > Flashcards

Lecture 2 - Protein Function Flashcards

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1
Q

ligand

A

a molecule bound reversibly by a protein

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2
Q

a ligand binds to a protein at the ____ ____ which is _____ in size, shape, charge, and hydrophobic/phillic character

A

binding site, complementary

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3
Q

induced fit

A

The structural adaptation (conformational change) that occurs between a protein and a ligand that makes the binding site more complementary to the ligand (tighter binding)

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4
Q

three examples of protein function

A
  • O2 transport by hemoglobin
  • immune function and immunoglobulins
  • muscle contractions by myosin/actin interactions
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5
Q

what does hemoglobin do?

A

transport O2 from the lungs to other parts of the body

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6
Q

oxygen is ______ soluble in water

A

poorly

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7
Q

T/F Amino acids are capable of binding to oxygen reversibly.

A

FALSE

No amino acid can bind to O2 reversibly

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8
Q

What does hemoglobin use to bind to oxygen so it is reversible?

A

the prosthetic group heme

aka iron

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9
Q

How many heme are in one hemoglobin molecule?

A

FOUR

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10
Q

Hb contains four polypeptide chains, what are they?

A
  • 2 identical alpha chains
  • 2 identical beta chains
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11
Q

Wyman Linkage relationship

A

If the ligand specifically binds to one of the two states of Hb, then equilibrium between those states will be shifted in favor of the state with bound ligand with the
increase of ligand concentration

Hb and O2 or CO2

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12
Q

Which conformation of Hb has high affinity towards O2?

A

R conformation

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13
Q

Which conformation of Hb has low affinity towards O2?

A

T conformation

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14
Q

What conformation does Hb exist in when no O2 is bound to it?

A

T

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15
Q

What happens when O2 binds to the T state of Hb?

A

Induces a conformational change from T to R

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16
Q

What is the conformational change from T to R in Hb? (3)

A
  • individual subunits change a little
  • alpha and beta subunit pairs slide past each other and rotate
  • narrows the pocket between beta subunits
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17
Q

Hb/O2 cooperative binding equation

A
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18
Q

allosteric protein

A

one in which the binding of a ligand to one site affects the binding properties of another site in the same protein (hemoglobin is an example)

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19
Q

The slope of the curve is known as what?

A

the Hill coefficient nH

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20
Q

Hill coefficient nH > 1 means…

A

the ligand binding at one site promotes ligand binding at another

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21
Q

Hills coefficient nH = 1

A

no cooperativity is experienced

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22
Q

Hills coefficient nH <1

A

indicated negative cooperativity, in which binding of one ligand impedes binding of others

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23
Q

T/F CO has a 250-fold greater affinity for Hb than O2 does

A

TRUE

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24
Q

What happens when CO binds to hemoglobin?

A

it gets trapped in the high affinity state, unable to release bound O2 in the tissues

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25
What does Hb transport from the TISSUES to the LUNGS? (2)
- 40% of total H+ - 15-20% of CO2
26
the binding of H+ and Co2 to Hb is _____ related to the binding of oxygen
inversely
27
Bohr effect
the effect of pH and CO2 concentrations on binding and release of O2 by Hb
28
T/F Oxygen and H+ are not bound at the same sites in hemoglobin
TRUE
29
Where do H+ ions bind on hemoglobin?
several amino acid residues
30
antibodies are also called
immunoglobulins (Ig)
31
what do immunoglobulins do?
bind to bacteria, viruses, foreign molecules (antigens) and target them for destruction
32
antigen
any molecule or pathogen capable of eliciting an immune response
33
what percent of blood do antibodies make up?
20%
34
five classes of antibodies
- IgG - IgA - IgD - IgE - IgM
35
Where is IgA found? (3)
saliva, tears, breast milk
36
what is the most common antibody in serum?
IgG
37
most newly approved innovator drugs are _____
mAbs
38
mAbs
monoclonal antibodies
39
Why are mAbs generally very safe?
their target selectivity is high, thus avoiding unnecessary exposure to and consequently activity in nontarget organs
40
reduction of what portion of the mAb structure decreases the immunologic potential of the murine mAbs allowing their wider application?
xenogenic
41
murine mAbs
derived from mice
42
chimeric Ab
The human Fc region renders a longer in vivo half-life than the parent murine mAb
43
humanized AB
human mAbs except the CDRs in the variable domain
44
four peptide chains of IgG
- two large heavy chains - two smaller light chains
45
what are the chains in immunoglobulins linked by?
disulfide bonds
46
each branch of an immunoglobulin had a single....
antigen binding site
47
Fab immunoglobulin fragments...
contain the antigen-binding site and top portion of the heavy chains
48
Fc portion of immunoglobulins contains
lower portion of both heavy chains
49
constant dominant domains
sequence and structure constant between IgG's
50
variable domains
varying amino acid structure in immunoglobulins
51
IgG has all of what secondary structure?
beta sheets
52
_____ do not affect the IgG structure and function but stabilize it
carbohydrates
53
each antigen-binding site can bind to how many antigens?
ONE
54
epitope
part of an antigen molecule to which an antibody attaches itself
55
Upon binding, the binding site undergoes....
a conformational change
56
What happens when IgG binds to an antigen?
activates macrophages to engulf and destroy an invader
57
Receptors on the macrophage surface recognize and bind to what region of IgG?
the Fc region
58
myosin has six subunits, what are they?
- two heavy chains - four light chains
59
the globular domain of myosin is also known as...
the myosin head
60
myosin aggregates to form structures called ____ ____
thick filaments
61
myosin thick filaments form what kind of structure?
bipolar globular domains project from either end of the structure
62
each actin monomer in the thin filament can bind to how many myosin heads?
one
63
motor proteins convert chemical energy into...
kinetic energy
64
A band in muscle cells
dark band of myosin molecules
65
I band in muscle cells
light band of actin molecules
66
Z disk in sarcomeres
The structure serves as an anchor to which thin filaments are attached
67
how does muscle contraction occur?
the sliding of thick and thin filaments past each other so that the neighboring I bands draw closer together
68
B
69
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PHRD 5025 - Applied Biochem
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