Brainscape's Knowledge GenomeTM

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


See full index

4th Year Fall > Hubi 2001 Midterm 2 > Flashcards

Hubi 2001 Midterm 2 Flashcards

1
Q

Nucleoside

A

nucleobase bound to pentose (without phosphate)

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

why do enzymes not impact equilibria?

A

they impact fwd and rev rxns equally, and are not used in the process

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

Glycan abbreviations

A

Trioses
Tetroses
Pentoses
Hexoses
Heptoses

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

What is the codon table?

A

3 nucleic acid bases make up a codon

each codon encodes an amino acid (more than one codon for some amino acids)

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

What is the V label in IgG represent?

A

Variable regions

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

What does higher G:C content correlate with in DNA?

A

More stability

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

What Ig class(es) activates complement, i.e. destroy invaders

A

G, M

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

Helicase

A

separates 2 strands of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the two faces representing orientation about the glycosidic bond?

A

1) Watson-Crick Face (anti, normal)
2) Hoogsteen Face (syn, after rotation)

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

Another term for immunoglobulins

A

Antibodies

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

True or False: RNA structure may use Watson-Crick base pairing depending on how they’re sterically positioned.

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the symbol for pentoses?

A

Star

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Is DNA parallel or antiparallel?

A

Antiparallel

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

What are the 4 types of catalysis

A

1) catalysis by approximation
2) general acid-base catalysis
3) covalent catalysis
4) metal ion catalysis

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

How do enzymes overcome the solvation shell of the substrate?

A

solvation shells impede rxns; desolvation replaces solvation shell with weak bonds btwn substrate and enzyme (replace by bonds w enzyme)

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

What factors do mixed inhibitors affect?

A

Usually both apparent Km and Vmax

Vmax decreases when the effective [E] decreases

Km may increase or decrease, depending on enzyme form

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

Does blood type depend on glycans or nucleic acids?

A

glycans

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

Activation energy

A

Difference btwn ground state and transition state energy levels

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

True or False: IgG can activate other parts of the immune response, in example the complement system that pokes holes in the pathogen.

A

T

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

Ig Classes (5): include the letter, heavy chain, nickname, and % in blood

A

1) G: gamma, IgG, 75%
2) M: mu, IgM, 10%
3) A, aloha, IgA, 15%
4) E, epsilon, IgE, 0.002
5) D, delta, IgD, 0.2%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is rRNA

A

makes up ribsome; responsible for synthesis of proetins

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

Which of [ES], V0, vmax, [S], and kM cannot be measured experimentally easily?

A

[ES]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

People with pollen allergy start out with hay fever, but then develop oral allergies to a defined group of foods. This tells us that these foods and pollen all share a common what?

A

Epitope

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

What happens in induced fit when the antigen is bound?

A

The antibody’s binding cavity is enlarged and several sidechains shift in position

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

How to do ELISA plate for the antigen (do not describe fully, just difference from the antibody)

A

Antigens from patient coat the surface of plate, and a specific antibody to HIV is added

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

What would the GalB1-4 Glc glycosidic linkage look like

A

gal on left, glc on right
connected through O between 1 C of Gal and 4 C of Glc

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

Review structures of nitrogenous bases

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

What is the most common DNA modification?

A

Methylation

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

What are the structural requirements for a protein with recognition and/or effector functions?

A

They must have domains for recognition and effectance

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

Guanine Quadraplex

A

forms at the end of chromosomes, regulates transcription

4 guanines H bond w both their Watson-Crick and Hoogsteen faces

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

Regulation of Chymotrypsin

A

Dependent on pH; optimal pH 8
Regulated by proteolytic cleavage (chymotrysinogen: inactive, stored in secretory vesicles, released following nerve stimulation)

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

What do catalysts do? (simple)

A

lower the activation energy

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

How does the induced fit mechanism of enzyme catalysis work?

a) the enzyme assumes a conformation identical to substrate
b) the enzyme undergoes a conformational change to maximize weak interactions to substrate
c) the substrate binds to the active site of the enzyme
d) the enzyme undergoes entropy reduction to accommodate substrate

A

B

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

Who predicted double helix structure and what technique did they use?

A

Rosalind Franklin and Maurice Wilkins, XRD

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is the glucose modification to make N-acetyl-glucosamine?

A

C2 N-acetyl

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

Check L20 slide 10

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

How to prepare monoclonal antibodies and who did this first

A

Cesar Milstein and Georges Kohler

Isolate a clone of B cells to produce a single, identical antibody. Issue: these cells isolated from an animal die quickly, however, there are immortal cell lines that do this derived from a type of cncer (multiple myeloma).

To get antibodies that bind a target protein, fuse short-lived antibody producing cell with a myeloma cell.

Hybridoma cells screened to find one that targets the protein of interest. A clone can be grown in a large scale culture to produce lots of monoclonal antibodies of itnerest.

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

Apoenzyme

A

protein part of a holoenzyme

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

What are the 7 most common modifications? (and what amino acids)

A

1) Phosphorylation (Y, S, T, H)
2) Adenyylylation (Y)
3) Acetylation (K, N terminus)
4) Myristoylation (N-terminus)
5) Ubiquitination (K)
6) ADP-ribosylation (R, Q, C, H)
7) methylation (E)

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

How does an antibody bind a macromolecular antigen?

A

There are different antibodies which bind to distinct areas on the surface of the macromolecule

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

The conversion of sucrose to CO2 and water has a very large and negative dG, but sugar left out doesn’t spontaneously turn into CO2 and water. Why?

A

There is a large activation energy barrier; kinetically disfavoured

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

True or False: RNA and DNA are polymers of nucleotides

A

True

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

Mixed inhibition (aka non-competitive)

A

binds at a site distinct from active site
binds to either E or ES complex
increasing [S] does not overcome the inhibition

Study diagrams in L18

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

What does the Fab label in IgG correspond to?

A

F for fragment, ab for antigen binding

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

True or False: enzymes bind in a “lock and key” fashion

A

False

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

Binding in the active site

A

major source of free E to lower activation energy through non-covalent interactions which stabilize the interaction

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

What does RNA do?

A

carries genetic info from the nucleus to the cytosol

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

Which part of the immune system is the one that makes vaccines effective?

A

Adaptive

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

What is an example of covalent catalysis?

A

Citrate synthase (review slide)

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

What is the name of Nucleoside and Nucleotide of guanine for RNA and DNA?

A

RNA: guanosine, guanylate

DNA: deoxyguanosine, deoxyguanylate

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

What are a couple examples of non-coding RNAs?

A

tRNA
rRNA
miRNA
siRNA
lncRNA
snRNA
snoRNA

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

Review the process of DNA replication

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

What does the double dagger represent?

A

Transition state

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

What can we use monoclonal antibodies to study?

A

Antibodies themselves. Also used for identification of other molecules

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

Do we prefer polyclonal or monoclonal antibodies?

A

Monoclonal, easier to work with

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

3 General Regulatory Mechanisms

A

1) allosteric control: rev, noncovalent binding (sec to min)
2) reversible covalent modification: min to hrs
3) proteolysis: irreversible, removal of peptide segments

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

How do enzymes lower free E of transition state?

A

It uses binding E from interactions btwn enzyme and transition state, not substrate

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

What is coenzyme A?

A

A nucleoside acting as a cofactor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What bonds link sugars?

A

Glycosidic bonds

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

What is bound to IgG?

A

Carbohydrates, attached to CH2 domain, stabilize structure

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

Where do antibodies bind antigens?

A

Complementary determining regions (CDRs)

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

Humoral Immunity

A

immunity driven by molecules in solution in the body (antibodies); recognize invading pathogens

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

Michaelis-Menten equation

A

rate eqn for one substrate enzyme catalyzed rxns

V0 = vmax[S] / (KM + [S])

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

What are the two ways to test if someone is infected with HIV?

A

1) do they have antibodies against HIV?
2) do they have a particular antigen known to be produced early in infection, the p24 protein?

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

What Ig class(es) causes histamine release

A

E

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

Equilibrium

A

rxn has no net change in conc of reactants or products

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

What Ig class(es) crosses placenta

A

G

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

Antigen

A

any substance capable of eliciting an immune response

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What label do we give regions in IgG that are less variable?

A

C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

How many angstroms between base pairs in DNA

A

3.4

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

tRNA

A

bring amino acids to ribosome for protein synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

Lineweaver-Burk Equation

A

algebraic transformation of Michaelis-Menten equation to convert hyperbolic curve into linear form

1/V0 = Km/Vmax[S] + 1/Vmax

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

How do we detect HIV antibodies using ELISA?

A

HIV antigens coated onto ELISA plate, patient serum added to plate. Non-antigen binding proteins are washed free of plate.

Second antibody added with an enzyme, that will detect the presence of the primary antibody. A substrate for the enzyme is added, and the enzyme acts on it by changing color.

Measure the intensity of the colour; the darker the color, the more antibodies in the origianl sample. No color change - no HIV.

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

Rank the strength of base pair stacking

A

Strongest: G:C - G:C
Middle: A:T - G:C
Weakest: A:T - A:T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

What are the two types of the immune system?

A

1) innate immunity
2) adaptive immunity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

Explain how influenza virus works using glycans

A

Infectious diseases use glycans on outside of cells to choose their host organism; influenza binds to glycans terminated with a2-6-linked sialic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

Review L19 slide 18

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

What technique is best for quantifying the amount of Ag in a sample?

A

ELISA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

What is the triangle symbol used for?

A

Deoxysugar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

Holoenzyme

A

complete catalytically active enzyme with its bound coenzyme and/or metal ions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

What Ig class(es) are in B lymphocyte membrane

A

M, D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

What type of plot has the fastest v_0?

A

Plot with steepest tangent line at t=0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

What nitrogen base is present in deoxythymidine?

A

Thymine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

What is the specificity constant?

A

ratio of kcat/km

best way to compare turnover of different substrated by same enzyme

lower km = higher affinity the enzyme for S and higher rate of conversion of S to P

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

What does catalytic activity of enzymes depend on?

A

Conformation / strucutre

Activity lost if subunits dissociate or denatured (usually)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

Where are proteins made in the cell?

A

Cytosol

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

Helix rise per base pair in A, B, Z forms

A

2.6, 3.4, 3.7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

Which statement is true bout both mixed inhibitors and uncompetitive inhibitors?

a) both bind to the active site of an enzyme
b) both affect Km, but not Vmax
c) both can bind to ES complex
d) both can bind to either free enzyme or ES complex

A

C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

How do enzymes align catalytic groups in enzyme

A

The enzyme undergoes conformational changes when the substrate binds, induced by multiple weak interactions, known as induced fit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

What factors do competitive inhibitos affect?

A

Apparent Km (increased with [I])
Not Vmax

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

Why would the addition of an enzyme make a rxn faster?

a) active site provides area of increased pH
b) prosthetic groups act as additional substrates
c) cofactors act as additional substrates
d) amino acid residues help bring substrates together

A

D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

Phosphodiester linkages

A

bonds in nucleic acid polymers; can only be added to 3’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

Epitope

A

particular part of antigen bound by the antibody

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

Irreversible inhibitors

A

impact an essential functional group in enzyme

bind covalently, destroys groups, forms stable association

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q
A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

What are the 9 biologically relevant monosaccharides in humans? List their symbols

A

1) Glucose (Glc, blue circle)
2) Galactose (Gal, yellow circle)
3) Mannose (Man, green circle)
4) N-Acetylglucosamine (GlcNAc, blue square)
5) N-Acetylgalactosamine (GalNAc, yellow square)
6) L-Fucose (Fuc, red triangle)
7) Sialic Acid (Sia, purple diamond)
8) Xylose (Xyl, orange star)
9) Glucuronic acid (GlcA, half blue/half white diamond)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

Innate Immunity

A

1st line of defense; foreign particles eliminated (within hours); no memory; detects patterns, not molecular differences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
98
Q

True or False: complementary DNA strands are antiparallel, so we write the DNA label backwards to get the 5’-3’ direction

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
99
Q

Fractional saturation formulas (2)

A

= [ES] / [E_T]

= [S] / (KM + [S])

see derivation slide 26 L17

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
100
Q

What is the name of Nucleoside and Nucleotide of adenine for RNA and DNA?

A

RNA: adenosine, adenylate

DNA: deoxyadenosine, deoxyadenylate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
101
Q

Carbohydrate abbreviations

A

Monosaccharide
Disaccharide
Oligosaccharide (<12 units)
Polysaccharide (>= 12 units)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
102
Q

Primer

A

sets the template for DNA replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
103
Q

Where do small molecules usually bind?

A

In the cleft of the antigen binding region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
104
Q

How many angstroms per turn in DNA

A

36

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
105
Q

How is DNA read vs. synthesized/replicated?

A

read in 3’ to 5’ direction, replicated in 5’ to 3’ direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
106
Q

What are some features of polyclonal antibodies? (4)

A

1) they are heterogeneous
2) they have different amino acid sequences
3) they recognize different regions of the target protein
4) they bind the target protein with different strengths

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
107
Q

Proeoglycan vs. Glycoprotein

A

Proteoglycan: 50-60% carb content; in connective tissues

Glycoprotein: 10-15% carb content; cell surfaces; recognition and signaling

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
108
Q

Most common source of chemical energy (hydrolysis of phosphate bond releases energy in this form)

A

ATP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
109
Q

What form does IgA take

A

monomer, dimer, or trimer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
110
Q

IgG binds to an invading bacterium or virus, and through the Fc region, activates certain white blood cells to engulf and destroy the invader. What function of the immune system is this?

A

Effector

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
111
Q

Two kinds of antigens

A

1) small molecules (contact with around 15 residues of antibody)
2) macromolecules (20 or more residues of the antibody)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
112
Q

What factors do uncompetitive inhibitors affect?

A

Both apparent Km and Vmax
Vmax and Km decrease with increase in [I]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
113
Q

What happens if you add mercaptoethanol and urea to IgG? i.e. how many chains will the protein break into?

A

The protein will break into 4 separate chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
114
Q

Glycobiology

A

study of glycan functions related to their structures, recognition, biosynthesis, and molecular context

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
115
Q

What are the differences in DNA and RNA structure?

A

Only difference is in the sugar, ribose (OH group on 2’ and 3’ C) vs. deoxyribose (no OH group on 2’ C)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
116
Q

Covalent catalysis

A

transient covalent bond btwn enzyme and substrate; enzyme with nucleophilic group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
117
Q

Glycan

A

polysaccharide that does not have nutrient role; carbohydrate portion of glycoconjugate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
118
Q

What Ig class(es) is found in secretions

A

A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
119
Q

For what conditions is the Michaelis-Menten equation valid?

A

[S]&raquo_space; [E], i.e. [ES] is constant, steady state assumption

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
120
Q

List the 7 classes of enzymes and what rxns they catalyze

A

1) oxidoreductases: transfer of e- (hydride ions or H atoms)
2) Transferases: group transfer (adding)
3) Hydrolases: hydrolysis (water)
4) lyases: cleavage of C-C, C-O, C-N, or other bonds by elimination, leaving double bonds or rings, or addition of group to double bond
5) Isomerases: transfer of groups within molecules to yield isomeric forms
6) Ligases: formation of C-C, C-S, C-O, C-N bonds by condensation rxns coupled to cleavage of ATP or similar cofactor
7) Translocases: mvmt of molecules or ions across membranes or their separation within membranes

121
Q

How do pigs transmit viruses from birds to humans?

A

they have glycans making them susceptible to human and avian viruses

122
Q

Competitive Inhibition

A

competes with substrate for active site, depends on [S]:[I] ratio. Can be overcome by increasing [S]

123
Q

HIV Vaccine Development

A

There are a few rare antibodies from asymptomatic, HIV infected people that show a neutralizing responses (b12) —- read rest of HIV slides

124
Q

Enzyme

A

-biomolecule catalyst
-specific chemical rxn
-increases rxn rate
-unchanged
-usually a protein, occassionally RNA
-does not change spontaneity of a process

125
Q

The barrier to rxn may be due to a variety of factors, including: (4)

A

1) the entropy of molecules in soln (low prob of interaction)
2) solvation shell that surrounds and stabilizes biomolecules in soln
3) the distortion of substrates
4) need for proper alignment on enzymes

126
Q

Adaptive immunity

A

Occurs only after exposure; delayed response, but specific; memory is rapid and effective

127
Q

What monosaccharide is made from removing the C6 of glucose?

A

Xylose

128
Q

What is the sugar in DNA?

A

2’ deoxyribose

129
Q

Coenzymes

A

type of cofactor; complex organic or metalloorganic molecules that act as transient carriers. Usually derived from vitamines

130
Q

Which statement is not associated with covalent catalysis by enzymes?

a) when the rxn is complete, the enzyme returns to its original state.
b) it never involves coenzymes.
c) a transient covalent bond is formed btwn enzyme and substrate
d) a new pathway from substrate to product is formed that is faster than the uncatalyzed rxn

A

B

131
Q

What is an advantage of polyclonal over monoclonal?

A

They are easier to make

132
Q

How do initial velocities change with increasing concentration?

A

Increase

133
Q

How many times can inhibitor molecules act, and what are serpins?

A

Only once
Serpins: serine protease inhibitors (use large conformational change to trap protease)

134
Q

Explain how IgE releases histamines and initiatives an allergic response

A

Through Fc region, to special receptors on mast cells, which leads to secretion of histamines. This causes dilation / increased permeability of blood vessels, facilitating movement of immune cells and proteins to site of inflammation

135
Q

Example of small molecule antigen

A

Phosphorylcholine; review how it binds

136
Q

General acid-base catalysis

A

transfer of protons to/from unstable intermediate to stabilize an unfavourable charge.

137
Q

Base tilt normal to the helix axis in A, B, Z forms

A

20deg, 6deg, 7deg

138
Q

What is the diameter of DNA in angstroms

A

20

139
Q

True or False: if [S] is very high, we would expect v0 to approximately be equal to vmax

A

T
See mathematical derivation (L17 slide 14)

140
Q

In samples of DNA isolated from two unidentified species of bacteria, X and Y, adenine makes up 32% and 17%, respectively, of the total bases. One of these species was isolated from a hot spring (64C). Which species is most likely to live in the hot spring?

A

Y

141
Q

How do enzymes work?

A

Active sites

142
Q

How to prepare polyclonal antibodies

A

Inject an antigen into a rabbit twice, 3 weeks apart, which stimulates the reproduction of cells producing antibodies that recognize it. Blood is drawn from rabbit, and the serum of the blood contains antibodies to all antigens the rabbit has been exposed, some of which recognize the injected protein.

143
Q

What factors determine specificity and affinity of antibody for antigen?

A

1) shape of binding site: complementary, often concave
2) amino acid sidechains of binding site - should maximize noncovalent interactions

144
Q

What of the typical role of carbs does not apply to glycans?

A

Acting as an energy source

145
Q

Review structure diagrams of IgG

A
146
Q

Are G:C or A:T base pairs stronger?

A

G:C

147
Q

How do the number of polysaccharides for 3 different monosaccharides compare with the number of polypeptides for 3 amino acids

A

polysaccharides: 1056 possible structures

polypeptides: 6 possible structures

148
Q

How many domains are there in Ig and how many different domain folds are there?

A

12 domains, all the same domain fold

149
Q

Why is it important to control enzymes?

A

Some processes should only occur controllably

150
Q

Rate of rxn

A

speed at which rxn takes place

151
Q

Enzyme Commision

A

number that provides progressively finer classification

152
Q

What does the label Fc correspond to in IgG?

A

F for fragment, c for crystallization, since it crystallizes readily

153
Q

Which technique is best for determining the intracellular location of a protein?

A

Immunofluorescence

154
Q

Why is DNA replication important?

A

To create new genetic info 4 cells to grow and divide

155
Q

What are 2 main types of irreversible inhibitors?

A

1) transition state analogs
2) suicide inhibitors

156
Q

How does a protein recognize another molecule?

A

It binds to it using a number of very specific noncovalent interactions

157
Q

Problems with DNA damage

A

if damage is not repaired, it can lead to permanent changes to DNA, causing diseases such as cancer

158
Q

Glycosyl bond conformation for A, B, Z forms

A

Anti, Anti, Anti for pyrimidines, syn for purines

159
Q

How many polypeptide chains are in IgG? How are these divided?

A

4
2 heavy chains
2 light chains

160
Q

What are the two important terminal sugars for glycans and what functional groups do they have?

A

1) Sialic acid: 6-Glycerol, 1-carboxyl, and 5-acetamido side chains

2) L-Fucose, a 6 - methyl group

161
Q

What enzymes break glycosidic bonds?

A

glycohydrolases

162
Q

Is the symbol for N-acetylhexosamine a square or a circle?

A

Square

163
Q

What happens if DNA is mutated?

a) it can’t be replicated anymore
b) it gets degraded
c) point mutations arise in the protein
d) there are no consequences

A

C

164
Q

What are the 3 parts of RNA and DNA structure?

A

1) pentose sugar
2) nitrogenous base
3) phosphate group

165
Q

How do strands of DNA form double helix?

A

Hydrogen bonds

166
Q

What enzyme helps make glycosidic bonds

A

glycosyltransferases

167
Q

Key features of antibodies

A

Binding and recognition of foreign molecules

168
Q

Do allosteric enzymes display Michaelis-Menten behaviour?

A

No, they diverge

169
Q

Suicide inactivators

A

action requires enzymatic mechanism

reacts like substrate for first few steps, but is then converted into a new compound that binds irreversibly to enzyme

170
Q

Which technique is best for determining the size of a protein?

A

Western blot

171
Q

What is the diamond symbol used for?

A

Acidic Sugars

172
Q

What is the complementary DNA strand of ATG?

A

CAT

173
Q

DNA Melting, tm

A

when DNA is 50% denatured

174
Q

What does an enzyme impact?

A

Reaction rate

175
Q

Types of glycoconjugates (4)

A

1) glycoprotein
2) proteoglycan
3) glycolipids
4) glycoRNA

176
Q

Induced Fit

A

conformational changes can occur upon ligand binding. Allows for tighter binding of the ligand

177
Q

Glycoconjugate

A

covalent modification of another molecule with glycan

178
Q

Transition state

A

highest E state; decay to substrate/product are equally likely

179
Q

Phosphorylation of enzymes:

a) always increases their activity
b) is irreversible
c) is one of only five types of covalent regulation
d) generally occurs on Ser, Thr, Tyr side chains, His happening less frequently

A

D

180
Q

Uncompetitive inhibition

A

Not very common
Binds at a site distinct from active site, and only binds to the ES complex
Increasing [S] does not overcome this

181
Q

What 2 functions must the immune system possess?

A

1) recognition: recognize foreign material
2) defence: initiate a response to protect against foreign material

182
Q

What is the diameter of A, B, Z forms of DNA?

A

A: 26Angstroms
B: 20A
Z: 18A

183
Q

Immunoglobulin Diversity

A

Each Ig needs a unique sequence to allow it to bind a particular antigen; can produce more than 10^8 different antibodies with distinct binding specificities

184
Q

DNA polymerase

A

works in 5’ to 3’ direction to replicate DNA

185
Q

Role of the immune system

A

Defend the body against bacteria, viruses, fungi, and toxic materials

186
Q

What does Km depend on

A

substrate and enzyme

187
Q

T or F: vo is dependent on [S] when [S] is low

A

T
see derivation, L17 slide 15

188
Q

What is different about immunoglobulins compared to other proteins?

a) they are composed of several structure domains
b) they can have different primary sequences
c) they can bind specifically to other proteins
d) they are composed of beta-sandwich type domain folds

A

B

189
Q

IgG has a permanently attached carbohydrate, that means IgG is (choose as many as apply):
a) glycoprotein
b) hemoprotein
c) conjugated protein
d) allosteric protein
e) kinase

A

A and C

190
Q

Immunofluorescence

A

an antibody specific for a specific protein is attached to a molecule that fluoresces.

191
Q

Why is heterogeneity a drawback of polyclonal antibodies?

A

Makes them unnecessarily complicated

192
Q

What Ig class(es) activates phagocytosis

A

G, M

193
Q

What is the role of Fab vs. Fc in IgG?

A

Fab = recognition
Fc = effector

194
Q

The best antibody raised against the peptide KRVLFK would have what mix of residues?

A

A mix of negatively charges and hydrophobic residues

195
Q

Rate limiting step

A

highest activation energy step of a multistep rxn

196
Q

What are active sites?

A

specific area in enzyme where reaction happens. Bind to specific substrates with specific amino acid residues

197
Q

Nucleic acids

A

DNA and RNA
central dogma of biology
source of E (ATP)
cofactors (NADPH)

198
Q

What is vmax in Lineweaver-Burk plot?

A

y-intercept = 1/vmax

199
Q

2 types of general acid-base catalysis

A

1) specific: uses only H+ or OH- from water
2) general: mediated by weak acids or bases other than water, usually in the enzyme

200
Q

Enzyme inhibitors and the 2 classes

A

Molecules that interfere with catalysis, slowing or halting rxns

1) reversible
2) irreversible

201
Q

Practice Math examples: L17 slide 16,17,24, and 27

A
202
Q

Cofactors

A

inorganic ions that binds to enzyme to assist in binding

203
Q

Ground state

A

starting point for forward or reverse reaction

204
Q

What are the 3 factors of complementary DNA strands?

A

1) antiparallel
2) complementary
3) major and minor groves (see diagrams on L20 slide 23)

205
Q

Describe ELISA

A

Enzyme-Linked immunosorbent assay

used to measure if or how much of an antigen/antibody is in a sample.

Ex) HIV

206
Q

Western Blotting

A

aka immunoblotting

for proteins that have been separated by gel electrophoresis

similar strategy to ELISA:
primary antibody, selective for protein of interest. Secondary antibody, binds primary antibody and catalyzes a reaction to produce a color change

207
Q

True or False: tighter binding is achieved by less interactions that are more complementary

A

False; we want more interactions to have more complementary binding surface

208
Q

Immunoglobulins

A

Proteins produced by the immune system

209
Q

How do enzymes overcome the barrier of rxn due to entropy?

A

Productive collisions are rare; enzymes increase collisions by restricting relative motion of substrates and holding in proper orientation for rxn

210
Q

Immunoglobulin G

A

the major class of antibody molecules; one of the most abundant proteins in blood

211
Q

Which of the following statements is true?

a) glycoproteins have a higher % of carb than proetoglycans
b) glycolipids are inside the cell
c) synthesis of glycans controlled by enzyme regulation
d) glycans do not form glycoconjugates with RNA

A

C

212
Q

What would we call a nucleoside with 1/2/3 phosphates?

A

1-Nucleotide
2- nucleoside diphosphate
3-nucleoside triphosphate

213
Q

How many base pairs per turn in DNA

A

10.5

214
Q

DNA ligase

A

fill in breaks where primers were used in DNA replication

215
Q

Metal Ion Catalysis

A

1/3 of enzymes need metal ions for catalytic activity, can be prosthetic groups or cofactors. They help orient the substrate and stabilize transition states.

Metal ions mediate oxidation-reduction rxns via reversible changes in their oxidation state (LEO says GER)

216
Q

Reactive amino acids

A

Found in active sites of enzymes
used in general acid-base and covalent catalysis

Glu, Asp, His
Lys, Arg, Cys, Ser, Tyr (less common)

217
Q

How do allosteric enzymes work to regulate?

A

Undergo conformational changes in response to modulator binding; can be positive (activators) or negative (inhibitors)

218
Q

Chargaff Rule

A

in DNA (not RNA), #A=#T, #G=#C

219
Q

What is the symbol for hexoses?

A

Circle

220
Q

Proteolytic Cleavage (zymogens and proenzymes)

A

Some enzymes exist as inactive precursors called zymogens; cleavage forms an active protease enzyme, often used to amplify a signal

Precursors where cleavage forms other proteins are called proenzymes

221
Q

What is a coenzyme that is very tightly bound to the enzyme?

A

Prosthetic group

222
Q

Allosteric enzymes:

a) are never regulated by substrate binding
b) have their activity changed by changes in intersubunit interactions
c) exhibit Michaelis-Menten kinetics
d) always have both inhibitory and activating modulators

A

B

223
Q

What is the domain fold of Ig called?

A

B-sandwich/immunoglobulin fold
Two sheets of antiparallel B-sheets

224
Q

What type of bonds link light and heavy chains of Fab fragment, and chains of Fc?

A

The disulfide bonds that link the light and heavy chains

225
Q

What are the stop (3) and start (1) codons?

A

Start: AUG (Met)

Stop: UAA, UAG, UGA

226
Q

What is an example of a macromolecule?

A

Lysozyme; read through lysozyme example

227
Q

what is kcat and the formula?

A

kcat=vmax/[Etot]

turnover number; limiting rate of rxn at saturation

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

228
Q

What monosaccharide is modified to make N-acetyl-galactosamine and what is the modification?

A

Galactose; C2 N-acetyl

229
Q

Km

A

Michaelis constant; [S] at 1/2 vmax

Approximates cellular substrate concentration

230
Q

Topoisomerase

A

prevents supertwisting

231
Q

Review free E diagrams for enzymes

A
232
Q

Which type of inhibitor binds to the active site of an enzyme and undergoes the initial steps of rxn before combining irreversibly with the enzyme?

A

Suicide inactivators

233
Q

What is the primary source of the energy enzymes used to reduce activation energies?

A

Noncovalent enzyme-substrate interactions

234
Q

What is the most common secondary structure in RNA?

A

Hairpins

235
Q

Consequences of DNA Damage

A

Damaged DNA leads to C*:G and C:G daughter strands

Damaged mutagenic DNA C:T base pair leads to CT and A:T daughter strands

No way to differentiate A:T from damage and natural A:T

236
Q

Enzymes:

a) are always proteins
b) can be denatures and retain activity
c) may require multiple subunits for full activity
d) are also referred to as coenzymes

A

C

237
Q

Is the interaction surface larger and/or flatter for small molecules or macromolecules?

A

Macromolecules

238
Q

Stereochemistry of Carbs

A

carbs are chiral, with D form being biologically relevant (opp of proteins). Chair conformation; less hindered in equatorial positions

239
Q

3 biochemical methods that make use of monoclonal antibodies

A

1) ELISA
2) Western Blotting
3) Immunofluorescence

240
Q

Initial Velocity

A

Tangent to each curve at time t=0 (mM/min)

241
Q

Why do C and A/T not form H bonds?

A

see L20 slide 18 for diagrams

242
Q

What is a protein made by B lymphocytes?

A

Immunoglobulins, also called antibody or gamma globulin

243
Q

True or False? DNA structure is more complex than RNA structure

A

False

244
Q

How does induced fit in antibodies lead to tighter binding?

A

Allows complementary groups to interact fully

245
Q

Pyrimidines

A

Pyrimidine, Cytosine, Thymine, Uracil

246
Q

How would we identify a nucleic acid using a code for a phosphate group followed by NA with adenine, cytosine, guanine, thymine, and then adenine again?

A

pACGTA

247
Q

Different classes of antibody

A

multiple effector regions to bind to antigens; each class has its own unique heavy chain, giving it a different and characteristic effector function

248
Q

What are alpha and beta conformations of carbs?

A

beta on top (equatorial)
alpha on bottom (axial)

249
Q

How do we name glycosidic bonds? (5 steps)

A

1) Name non-reducing left-most sugar
2) name anomeric configuration (alpha or beta)
3) name anomeric carbon number (i.e. where is the glycosidic bond)
4) name substituted carbon number
5) name substituted sugar

250
Q

What is a problem with basing HIV tests on detecting anti-HIV antibodies?

A

Some people don’t have anti-HIV antibodies, if they are early in the infection

251
Q

Purines

A

Purine, Adenine, Guanine

252
Q

Types of DNA damage (not rxns, 6) and examples

A

1) SIngle base damage (oxidative stress, alkylation, hydrolysis)
2) mismatches (replication errors and stress)
3) pyrimidine dimers (T or C bases) (UV light)
4) Interstrand and intrasand cross-links, bulky adducts (environmental mutagens, chemotherapy)
5) single strand breaks (reactive oxygen species)
6) double strand breaks (ionizing radiation, endogeneous endonucleases)

253
Q

What is Km in Lineweaver-Burk plot (2 eqns)

A

slope = km/vmax
x-intercept = -1/km

254
Q

What do higher tm values mean

A

strands are held together more strongly, i.e. higher G:C content

255
Q

Nucleophile vs. electrophile

A

Nucleophile: e- rich, donates e-, attacks bonds
Electrophile: e- deficient, accepts e-, pulls e- toward their side of the bond

256
Q

How do some nucleotides act as signalling molecules?

A

Second messengers inside the cell; commonly the cyclic form is used

257
Q

Hybridoma cells

A

a mixture of cells from the spleen fused with myeloma cells.

258
Q

What two classes of Igs have similar structure to IgG?

A

IgD and IgE

259
Q

What do the variable amino acid regions of IgG represent?

A

The regions that bind to the antigen; they are so variable because of the specificity

260
Q

Many people with mild egg allergies are okay eating egg as long as its well cooked. Why?

a) cooking gets rid of the protein (lysozyme) that people are allergic to.
b) cooking disrupts the primary structure of lysozyme, so it cannot bind to the antibody.
c) cooking disrupts the tertiary structure of lysozyme, preventing the antibody from recognizing it.

A

C

261
Q

In early studies of IgG, it was found that IgG was cleaved into how many fragments of what mass by papain?

A

3 50kD fragments

262
Q

Roles of Carbohydrates (6)

A

1) Structural
2) Energy source
3) nucleic acid structure
4) lubricants (joints)
5) cell recognition
6) disease states

263
Q

What statement about Ig effector functions is false?

a) Fc fragments that have been cleaves off of their Fab fragments can not interact with the molecules that are part of the effector systems
b) Fc fragments from different classes of antibodies often interact with different components of the immune system
c) Fab fragments bind to antigens but can’t mount an immune response alone

A

A

264
Q

Where is DNA in the cell?

A

Nucleus

265
Q

What form does IgM take?

A

membrane-bound, or a cross-linked pentamer

266
Q

Ribozymes

A

RNA that catalyzes rxns

Roles in cleaving phosphodiester bonds and formation of bonds

found in ribosome; joins amino acids together

267
Q

What monosaccharide is made from C6 acid of glucose?

A

Glucoronic acid

268
Q

How do enzymes overcome the distortion of the substrate

A

Weak interactions with enzyme can compensate thermodynamically for the unfavourable energy from distortions. They can also induce strain from their active sites within a bound substrate to increase reactivity and favor formation of transition state

269
Q

Catalysis by approximation

A

binding with multiple substrates and positioning them favorably for reaction, reduced rotational entropy and improves catalytic rate

100x faster

carbonic anhydrase

270
Q

How many base pairs per helical turn in A, B and Z forms?

A

11, 10.5, 12

271
Q

What is the coding RNA?

A

mRNA

272
Q

Transition state analogs

A

mimic substrate transition state, and can bind very tightly to enzyme

ex) inhibitors to HIV protease (slide 17 L18)

273
Q

True or False: sequences are written from 3’ to 5’, left to right

A

False

274
Q

Reversible covalent modification

A

Add on a modifying group (enzyme catalyzed, conformational changes to alter amino acid interaction)
Second enzyme removes group

275
Q

Carbohydrates

A

most abundant and diverse biopolymer in nature
heterogeneous in size and composition
hydrophilic
carbon hydrate
general formula Cx(H2O)y

276
Q

What 2 forms of DNA are right handed and what form is left handed?

A

Right: A and B
Left: Z

277
Q

Glycolipids

A

membrane components; found on the outside of the cell membrane; antigenic; 2% of membrane lipids

278
Q

What does binding energy provide?

A

Specificity: specific matching between enzyme and substrate

279
Q

What N base is present in uridylate?

A

uracil

280
Q

What are 6 classes of DNA damage reactions?

A

1) oxidation
2) deamination
3) alkylation (can be natural)
4) cross-linking (UV)
5) minor groove adduction
6) major groove adduction

281
Q

What is saturation in v0?

A

When further increases in [S] have no effect on the rate

282
Q

Of A, B, and Z, what is most common DNA type?

A

B

283
Q

What is DNA modification used for?

A

Plays a role in regulating and protecting genetic information

284
Q

Which statement is False about the saturation effect?

a) the maximum initial rate of the catalyzed rxn is observed
b) virtually all of the enzyme is present as the ES complex
c) it is responsible for the linear increase of V0 with an increase in [S]
d) further increases in [S] have no effect on rate

A

C

285
Q

General structure of purines

A

5 membered ring linked to 6 membered ring

286
Q

Okazaki fragment

A

how DNA is replicated in the lagging strand

287
Q

What is the glucose modification to make Galactose?

A

C4 Epimer

288
Q

What are the 4 ways binding energy overcomes the initial barrier

A

reduces entropy
substrate desolvation
substrate distortion
aligns substrate with active site

289
Q

Heterotopic allosteric enzymes

A

activators may cause curve to become more hyperbolic
inhibitor may cause curve to become more sigmoidal

290
Q

True or False: IgG is a conjugated protein

A

True

291
Q

Competitive inhibitors:

a) compete with other inhibitors for the active site
b) occupy the active site to exclude the substrate
c) are rarely similar in structure to the substrate
d) often combine with the enzyme to form a reactive EI complex

A

B

292
Q

What sugars equilibrate between open chain and ring forms?

A

Free sugars / monosaccharides

293
Q

T or F: determining Vmax is always easy.

A

F

294
Q

Reversible inhibition and 3 types

A

rapid dissociation from enzyme

1) competitive
2) uncompetitive
3) mixed

295
Q

What is the name of Nucleoside and Nucleotide of cytosine for RNA and DNA?

A

RNA: cytidine, cytidylate

DNA: deoxycytidine, deoxycytidylate

296
Q

General structure of pyrimidines

A

6 membered rings with substituents

297
Q

Enzyme classification / nomenclature

A

suffix -ase
7 classes based on type of rxn
systematic name describes function
trivial name based on function, location, rxn, etc

298
Q

What are two types of immune system cells?

A

1) T Lymphocytes (cellular immunity)
2) B lymphocytes (humoral immunity, white blood cell)

4th Year Fall (2 decks)

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