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Biochem > Ex 2 > Flashcards

Ex 2 Flashcards

1
Q

What 2 ways can protein interact

A

-act as enzyme to alter chemical configuration or composition of bound molecule
-or interact without changing the chemical configuration or composition of bound molecule

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2
Q

What make up the 6 coordination bonds of iron?

A

-4 bind to nitrogen atoms in the porphyrin ring
-2 bonds perpendicular to the porphyrin ring

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3
Q

Describe the 2 perpendicular coordination bonds

A

-one is occupied by Nitrogen side chain of a conserved proximal His residue
-one is the binding site for O2

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4
Q

Fe2 binds O2 ______
Fe3 binds O2 _______

A

-reversibly
-Fe3 DOESNT

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5
Q

Describe globins

A

-protein family that binds oxygens
-have a highly conserved tertiary structure of 8 alpha helical segments bending into globin fold
-most function in O2 storage or transport

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6
Q

Describe myoglobin

A

-has single binding site for Oxygen
-153 residues, and one molecule of heme
-bends are named after the alpha helical segments that they’re connecting

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7
Q

Describe myoglobin His93 and HisF8

A

-93rd residue from the amino terminal end

F8:
8th residue in a alpha helix F

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8
Q

What does the Equilibrium Expression describe?

A

The reversible binding of a Protein to a Ligand
Forming protein ligand complex

P + L = PL

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9
Q

Hemoglobin transports…

A

Blood oxygen

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10
Q

Describe erythrocytes

A

Red blood cells that transport O2. They’re formed from hemocytoblasts
-main function is to carry hemoglobin

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11
Q

How much of arterial vs peripheral blood is saturated with O2

A

Arterial blood= 96%
Peripheral blood= 64%

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12
Q

What are hemocytoblasts

A

Precursor STEM cells

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13
Q

What is the T to R transition

A

T has low affinity for oxygen
R has high affinity for Oxygen

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14
Q

Hemoglobin undergoes…

A

Structure change on binding oxygen

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15
Q

What are the two conformations of hemoglobin

A

R state; O2 has a higher affinnity for hemoglobin
T state; more stable when O2 is absent, predominant conformation of deoxyhemoglobin

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16
Q

Hemoglobin has a _______ curve for oxygen and binds _____

A

Hybrid sigmoid binding
-cooperatively

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17
Q

Allosteric proteins and what types

A

Means the binding of a ligand to one site, affecting binding properties of another site on the same protein
Example: Hemoglobin

Types:
Modulators, homotropic, heterotropic

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18
Q

Define modulators, homotropic, and hetero tropic

A

Modulators: ligands that bind to an allosteric protein to induce a conformational change
Homotropic- normal ligand and modulators are identical
Heterotropic- modulator is a molecule other than the normal ligand

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19
Q

Describe MWC. Model

A

Concerted model
All subunits in same conformation
Ligand binds more tightly to the R state

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20
Q

Describe sequential model

A

Each subunit can be in either conformation. Equilibrium is altered as additional ligands are bound, progressively favoring the R state

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21
Q

Oxygen binding to hemoglobin is regulated by….

A

2,3. Biphosphoglycerate

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22
Q

Explain 2, 3 BPG

A

Example of heterotropic allosteric modulation
-binds distantly from the O2 binding site
- reduces affinity of hemoglobin for oxygen

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23
Q

Leukocytes

A

White blood cells
-including macrophages and lymphocytes

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24
Q

What are the 2 systems of the immune response

A

-humoral - directed to bacterial infections and viruses
-cellular - destroys infected host cells, parasites, and foreign tissues

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25
Q

Define antigen

A
  • a virus, a bacterial cell wall, or a protein that can elicit an immune response.
    -antibodies or T cell receptors bind to an EPITOPE within the antigen
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26
Q

Define hapten

A

Small molecules that can elicit an immune response when its covalently attached to large proteins

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27
Q

Immunoglobulin G

A
  • heavy and light chains having variable domains.
  • varibale domains associate to create 2 antigen binding sites
  • allows formation of an antigen antibody complex
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28
Q

Phagocytosis of antibody-bound viruses by Macrophages

A

-when Fc receptors bind an antibody pathogen complex, macrophages engulf that complex

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29
Q

Explain Western blots

A
  1. Virus isolation
  2. Protein suspension
  3. SDS page
  4. Electro transfer (membrane)
  5. Antibody probing
  6. Chemical-imaging
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30
Q

What does ELISA stand for?

A

Enzyme linked immunosorbent assay

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31
Q

In 1897 what did Eduard Buchner discover

A

-demonstrated cell-free yeast extracts could ferment SUGAR into ALCOHOL
-showed fermentation was promoted by molecules that could continue to function after being removed from cells
-these were given the name ENZYMES

32
Q

Two most common types of ELISA’s?

A

Direct and sandwich

33
Q

Catalytic/enzyme activity depends on…

A

Integrity of the native protein conformation

34
Q

Range for enzyme mw

A

12000 to >1 million

35
Q

Enzyme cofactors

A

1+ inorganic ions like Fe2+ , Mg2+ , Mn2+ , Zn2+

36
Q

Enzyme coenzymes

A

Organic or metallorganic molecule that acts as transient carriers of functional groups

37
Q

What are the seven enzyme classes

A

Oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase, translocase

38
Q

What is enzyme class: oxidoreductase

A

Transfer of e- (hydride or H atoms)

39
Q

What is enzyme class: transferase

A

Group transfer

40
Q

What is enzyme class: hydrolase

A

Hydrolysis (transfer of functional groups to water)

41
Q

What is enzyme class: lyase

A

Cleavage of C-C, C-O, C-N , or other bonds by elimination, leaving double bonds or rings or addition of groups to double bonds

42
Q

What is enzyme class: isomerase

A

Transfer of groups within molecules to yield isomeric forms

43
Q

What is enzyme class: ligase

A

Formation of C-C, C-S, C-O, and C-N bonds by condensation rxn, coupled to cleavage of ATP or similar cofactor

44
Q

What is enzyme class: translocase

A

Movement of molecules or ions across membranes or their separation within membranes

45
Q

An enzyme that catalyzes the reaction S — > P also catalyzes ….

A

The reaction P ——> S

-enzymes are NOT used up in the process
-the equilibrium point is UNAFFECTED

46
Q

Describe induced fit

A

Enzyme undergoes a conformational change when the substrate binds . This is induced by multiple weak reactions with the substrate to enhance catalytic properties

47
Q

Enzymes must be complementary to the…

A

Reaction transition state

48
Q

The full interactions between substrate and enzyme is formed only when…

A

Substrate reaches transition state

49
Q

What is enzyme kinetics

A

Determining rate of reaction and how it changes in response to changes in experiments

50
Q

When is Vmax observed

A

All the enzyme is present as the ES complex
-further increases in [S] have no effect on rate

51
Q

Michaelis Menten Equation

A

Rate equation for a one substrate catalyzed reaction

52
Q

Michealis menten kinetics. (Hyperbolic dependence of V0 on S)

A

Km= [S] when V0= 1/2Vmax

53
Q

General rate constant kcat

A

Kcat=Vmax/[Et]

54
Q

Kcat=turnover number

A

Number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated

55
Q

Specificity constant

A

Rate constant for the conversion of E+S to E+P

56
Q

Enzyme inhibitors

A

Molecules that interfere with catalysis, slowing or halting enzymatic reactions

57
Q

2 classes of enzyme inhibitors

A

Reversible: competitive, uncompetitive, mixed, noncompetitive
Irreversible

58
Q

Competitive inhibitor

A

Competes with the substrate for the active site. (reversible)

59
Q

Uncompetitive inhibitors

A

Bind at a site distinct from the substrate active site. Unlike a competitive inhibitor, it binds only to the ES complex.
(Reversible)

60
Q

Line weaver Burke plot uncompetitive inhibition

A

Parallel lines
Vmax decreases, Km decreases.

61
Q

Line weaver Burke plot competitive inhibition

A

Lines intersect at the y axis. No change in Vmax, increase in Km.

62
Q

Mixed inhibition

A

Binds at a site different from the substrate active site. Binds to either the E or ES complex. Type of reversible inhibition

63
Q

Line weaver Burke plot mixed inhibition

A

Lines intersect to the left of the Y axis. V max decreases and the Km will increase

64
Q

Noncompetitive inhibition

A

Mixed inhibition , a = a’
Affects Vmax NOT. Km
Lines intersect at the X axis, dec V max, no Change in Km.

65
Q

Irreversible inhibition

A

Can bind covalently with or destroy a functional Group on an enzyme that’s essential to enzyme activity. Or form a highly stable noncovalent association
(Suicide inhibitors)

66
Q

Induced fit in HEXOKINASE

A

When glucose and Mg ATP bind, the binding energy derived induces a conformational change in hexokinase to its active form

67
Q

regulatory enzymes

A

They catalytically increase or decrease in response to certain signals, allowing the cell to meet changing needs for energy/biomolecules.

68
Q

Types of regulatory enzyme modulation

A

Allosteric enzymes- function through reversible, noncovalent binding of allosteric modulators OR allosteric effectors (cofactors)

Reversible covalent modification

Binding of separate regulatory proteins

Removal of peptide segments by proteolytic cleavage

69
Q

The two types of conformational change of allosteric enzymes in response to modulator binding

A

Homotrophic- regulation where the substrate and modulator are identical

Heterotrophic- regulation where the modulator is a molecule other than the substrate

70
Q

Protein kinase

A

Catalyze attachment of phosphoryl groups to specific AA residues

71
Q

Phosphoprotein phosphotase

A

Remove phosphoryl groups from the same target proteins

72
Q

Zymogen

A

Inactive precursor that’s cleaved to form an active protease enzyme

73
Q

Proprotein / proenzyme

A

Precursors that are cleaved to form other proteins

74
Q

Carbohydrates

A

Aldehydes or ketones with at least 2 hydroxyl groups

75
Q

Types of carbohydrates

A

Monosachharides- simple sugars with a single polyhydroxy aldehyde or ketone unit

Oligosaccharides- short chains of monosaccharide joined by glycosidic bonds

Disaccharides- oligosaccharides with 2 monosaccharide units

Polysaccharides- sugar polymers with 10+ monosaccharide units

76
Q

Epitope AKA

A

Antigenic determinant

77
Q

define the FC and Fab regions.

A

N terminal fragments.

Fab= antigen binding (recognizes antigen)
Fc= crystallizable, well conserved AA seq. (Interacts with immune system)

Biochem (8 decks)

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