Brainscape's Knowledge GenomeTM

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


See full index

MBB 222 > Midterm 2 (Lect 8-13) > Flashcards

Midterm 2 (Lect 8-13) Flashcards

1
Q

What is the function of the B-clamp on DNA polymerase?

A

The clamp holds the DNA on the core polymerase of DNA pol III, increasing the processivity of
this enzyme.

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

What are transitions and transversions?

A

Transitions are mutations that result in a purine-to-purine or pyrimidine-to-pyrimidine change
(eg. C:G to C:A or A:T to A:C) whereas transversions result in a purine-to-pyrimidine or
pyrimidine-to-purine change (eg. C:G to C:T or A:T to A:G)

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

Why do you think transitions are more common than

transversions?

A

Transversions are more dramatic
structural changes and are thus more likely to be recognized and corrected by DNA repair enzymes and by DNA polymerases during replication

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

List 2 mechanisms for (a) direct DNA repair, and (b) indirect DNA repair.

A

(a) DNA repair enzymes O6
- alkylguanine alkyltransferase and photolyase
(b) Base excision repair, nucleotide excision repair, mismatch repair

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

List the 3 steps that are common to every type of indirect repair: base excision repair, nucleotide excision repair and mismatch repair.

A

They all use (1) nucleases (exo, endo) to excise the damaged base or nucleotide (usually excise a segment of nucleotides around the damaged site), (2) polymerases to fill in the missing nucleotides using the undamaged complementary DNA strand as a template, and (3) a DNA ligase to ligate the final newly added nucleotide to the remaining DNA strand.

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

List 3 cellular processes that utilize DNA recombination.

A
  • repair of double strand breaks
  • repair of replication forks stalled at the site of DNA damage (to one strand)
  • recombination of antibody H and L genes to produce a diverse immune repertoire with more than a million distinct antibodies with unique antigen specificities (by VJD recombination)
  • integration/excision of viral genomes.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Name 3 enzymes we have encountered that utilize an active site tyrosine. What do all these enzyme mechanisms have in common?

A

DNA ligase, Topo I, Topo II, Cre recombinase – tyrosine performs a nucleophilic attack on a phosphate in the DNA backbone, forms a covalent intermediate

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

Briefly describe 2 mechanisms that insure that correct nucleotides are added during DNA replication.

A

(i) complementarity between the bases on the template strand and the incoming nucleotide bases
(ii) shape/H-bonding complementarity between the DNA polymerase active site and the bases (in
the minor groove)

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

What is the process call whereby DNA polymerases identify a mismatched base and excise the offending nucleotide? Which of the DNA polymerases has this function? What is the direction of nuclease activity related to this function?

A

Missmatched nucleotides are recognized and excised - this is called proof-reading and is done by both DNA pol I and III – proof-reading/exonuclease activity is in the 3’-5’ direction

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

Comment on the processivity of DNA pol I vs. DNA pol III. What do you think causes DNA pol I to terminate polymerization?

A

DNA pol III is highly processive, polymerizing ~500,000 nt before it falls off. DNA pol I is much less processive, polymerizing <200 nt at a time. It likely falls off when it reaches the 5’ end of the last Okazaki fragment synthesized (i.e. the RNA primer end).

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

How does ultraviolet light damage DNA and how is this repaired in E. coli?

A

UV light induces covalent bond formation between adjacent thymines, which will stall DNA replication and transcription. In bacteria, thymine dimers (pyrimidine dimers) are repaired by a photolyase, which uses visible light energy to hydrolyzes the bonds between the thymines. This is a form of direct repair

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

What is direct repair?

A

When damaged bases are not removed but repaired “on-site” eg. 06-alkylguanine alkyltransferase, photolyase for thymine dimers

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

What is base excision repair?

A

When offending base is removed and replaced, eg bases modified spontaneously or by chemical mutagens

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

What is nucleotide excision repair?

A

when offending nucleotide is removed and replaced, eg thymine dimers in eukaryotes

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

What is mismatch repair?

A

when the wrong nucleotide is added during DNA replication - system must discriminated between the template (correct) and the newly synthesized strand (incorrect), many enzymes involved

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

What is post-replication repair?

A

Important in bacteria, involves recombination

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

Name and describe the 2 types of mutations

A
  1. Point mutations: substitution of one base pair for another because of base mismatches - usually caused by modification/damage of bases
  2. Insertions/deletions of one of more base (“indels”) - often generated by “DNA intercalating” agent
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the 2 models for DNA replication? Which is correct

A
  1. Semiconservative model (correct)

2. Conservative model (incorrect)

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

What is a nucleotide comprised of?

A

phosphate + sugar + base

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

What are the 2 purines and how do they differ?

A

Adenine - conjugated system, has an amino group at the top

Guanine - has a keto carbonyl at the top

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

What are the 3 pyrimidines and how do they differ?

A

Cytosine - has an amino group
Thymine - has a carbonyl group and methyl group right beside
Uracil - only found in RNA and replaces Thymine, has a carbonyl group but does not have a methyl group beside.

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

What are the base + sugar names?

A
  • Adenosine
  • Guanosine
  • Thymidine
  • Cytidine
  • Uridine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the nucleotide names? (base + sugar + phopshate)

A
  • Adenosine 5’ - monophosphate
  • Guanosine 5’ - monophosphate
  • Thymidine 5’ - monophosphate
  • Cytidine 5’ - monophosphate
  • Uridine 5’ - monophosphate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the difference between ribonucleotides and deoxyribonucleotides?

A
  • Have a hydroxyl at the ribose 2’ carbon

- Have a uracil base instead of thymine (uracil is like thymine but without the methyl group)

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

2 strands of DNA are wound around the same axis to form a ____-______ double helix

A

Right-handed

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

Which base pairs are stronger? Why?

A

G-C bonds are stronger than A-T bonds. This is because guanine forms 3 H-bonds with cytosine, while adenine only forms 2 H-bonds with thymine (uracil in RNA).

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

How many base pairs per turn in DNA?

A

~ 10.5 bp/turn

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

The hydrophilic deoxyribose-phosphate backbones are ______ to the surrounding water, and the hydrophobic bases are ______ __ ___ ______ of the helix nearly perpendicular to the back bone.

A

Exposed/stacked on the inside

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

Which base pairs are more exposed to the solvent?

A

The ones on the major groove side.

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

DNA binding proteins tend to interact with the atoms of the bases on the ____ ____ ____.

A

Major groove side. This is because they are more accessible than those in the minor groove.

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

Are the major and minor grooves equivalent?

A

No, they are non-equivalent.

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

Which type of DNA double helix is normally found in cells?

A

B-form (B-helix, B-DNA) - right handed, most stable form under physiological conditions

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

What form does DNA assume when it is dehydrated (relative humidity is less than ~75%)?

A

A-form

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

A form of DNA is ____ and ____ than the B-helix, and its base pairs are ____.

A

wider/shorter/tilted

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

Where is the A-helix found?

A

in DNA-RNA hybrids and in double stranded RNA (eg tRNA).

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

What is the Z-form of DNA?

A

left-handed and “stretched out” compared to A and B forms.

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

What does UV-light do to DNA?

A

Causes thymine dimers - this blocks replication and transcription because the helix distortion blocks polymerization past this site.

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

What is the primary job of enzymes?

A

By lowering delta G double dagger - the activation energy for the transition state.

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

What is Delta-G‡?

A

The activation energy required to establish the transition state

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

What level of energy does the transition state have?

A

High-energy, unstable

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

What do enzymes not change?

A

Delta G or Keq. Enzymes are also not used up in the process

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

There are 2 main models to explain the exquisite specificity of enzyme active sites for their substrates. Name them and describe why one is better than the other.

A
  • Lock and key model: the substrate forms a perfect fit w/ the enzyme active site. But, do not fully describe enzyme action - how do the products fit in active site?
  • Induced fit model: this is the better theory. Says that the substrate and active site are complementary in shape and chemical properties, but do not have an exact fit. Upon binding, both active site & substrate undergo conformational change
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Catalytic activity depends on ___ _____ ______ ___ __ ______.

A

the folded conformation of the enzyme

44
Q

Where do substrates bind?

A

The active site; also called the substrate binding pocket.

45
Q

What is the enzyme active site?

A

The region of an enzyme that binds and catalyzes the substrate. The bonds formed between enzyme and substrate lower delta-G double dagger.

46
Q

Which feature of chymotrypsin is responsible for its substrate specificity?

A

the hydrophobic pocket

47
Q

BPG binds to and stabilizes the R or T state of hemoglobin?

A

T - tense

48
Q

What are cofactors?

A

ions that are essential for catalysis (Fe2+, Mg2+, Mn2+…)

49
Q

What is a coenzyme?

A

complex organic compounds that cannot be synthesized by the cell - must be taken up in the diet eg vitamins.

50
Q

What is V? What does it depend on?

A

the rate of velocity (V) of a reaction is measured as the change in reactant or substrate conc [S] or product conc [P] over time. V depends on [S] and the rate constant, k, for the rxn.

51
Q

V_0 ____ with increasing initial [S]

A

increases

52
Q

E + S > ES > E + P. Which is the rate-limiting step?

A

ES > E + P is slower, and the rate limiting step.

53
Q

What type of enzymes do not obey Michaelis-Mentin kinetics?

A

Allosteric enzymes

54
Q

What are allosteric enzymes?

A

They are enzymes that have more than one active site. Binding of substrate to one active site can positively influence binding to another active site.

55
Q

What is allosteric control?

A

When an allosteric enzyme is bound at one site and a conformational change is induced in the protein that alters its substrate binding/processing.

56
Q

Explain the 2 types of reversible inhibitors.

A

Competitive inhibition: an inhibitor resembles the substrate and binds to the enzyme active site & blocks substrate binding. Competitive inhibitor can be displaced by increasing [S].
Non-competitive inhibition: an inhibitor binds to a site on the enzymes that is distinct from the active site,, exterting negative allosteric effect on the substrate binding. Substrate can still bind but the enzyme cannot convert to its transition state as efficiently, slowing or preventing catalysis. Cannot be overcome by increasing [S].

57
Q

What are irreversible inhibitors?

A

Inhibitors that bind very tightly to an enzyme, either covalently or non-covalently and inactivate them. Almost all irreversible inhibitors are toxic.

58
Q

Hemoglobin is used for _____ ______ while myoglobin is used for _____ ______.

A

oxygen transport/oxygen storage

59
Q

What is P50?

A

P50 is the partial pressure at which 50% of the iron-binding sites (hemes) have O2 bound.

60
Q

Where do you find myoglobin?

A

In tissues (muscles)

61
Q

Where do you find hemoglobin?

A

In blood

62
Q

Compare and contrast myoglobin and hemoglobin

A

myoglobin:
- monomer
- high affinity for O2
- unaffected by pH, [CO2] or [BPG]
- binds to 1 O2 molecule
- doesnt bind to BPG
hemoglobin:
- tetramer: 2 alpha, 2 beta subunits
- moderate affinity for O2
- sensitive to pH [CO2], and [BPG]
- binds to 4 O2 molecules

63
Q

In myoglobin the interior residues are non-polar except 2. Which 2?

A

Residue 7 of helix E (His E7) and His F8, which bind to the heme group.

64
Q

Iron is chealated by a tetrapyrrole ring system. What is it called?

A

protoporphyrin IX

65
Q

For human myoglobin, what is P50? Why is it so low?

A

P50 = 2.8 torr. Myoglobin binds to O2 with high affinity.

66
Q

At 20-30 torr, in tissues, virtually all the myoglobin molecules are?

A

Saturated, or bound to O2

67
Q

The differences between myoglobin and hemoglobin are all due to?

A

The quaternary structure of hemoglobin

68
Q

What initiates structural changes in hemoglobin?

A

Oxygen

69
Q

Which state of hemoglobin has an increased affinity for O2?

A

The R state (oxy)

70
Q

What are the 2 states of hemoglobin? What are it’s intermediate states?

A

2 States: deoxyhemoglobin (0 O2 bound) and oxyhemoglobin (4 O2 bound).
- There are no intermediate states. It is either one or the other

71
Q

How does hemoglobin bind O2 cooperatively?

A
  • Due to the existence of cooperative or allosteric interaction among O2 binding sites. Initial binding acts like a switch
  • This phenomenon requires “communication” b/w different hemoglobin subunits. This is only possible due to the quaternary structure of the protein.
72
Q

What does the difference in O2- binding affinity between Hb and Mb ensure?

A

it ensures that O2 bound to hemoglobin in the lungs is relased to myoglobin in the muscles (tissues).

73
Q

What does BPG do to hemoglobin?

A

It lowers the O2 affinity. It does not do anything to myoglobin though.

74
Q

What happens when you reduce the pH in hemoglobin.

A

It also lowers O2 affinity.

75
Q

What happens tp hemoglobin when CO2 is accumulated in respiring tissues?

A

It again, lowers O2 affinity.

76
Q

What do higher concentrations of H+ and CO2 in respiring tissue do?

A

They help to stabilize the deoxygenated T state of Hb, which promotes the release of O2 and works against rebinding of O2.

77
Q

How does BPG affect hemoglobin oxygen affinity?

A

A single molecule of BPG binds to the central pocket in the hemoglobin tetramer. BPG prefers to bind to deoxy-Hb (T form), b/c the oxy-Hb (R form) pocket is too small for this molecule.

78
Q

During pregnancy, what happens to BPG levels?

A

They are elevated. BPG allows fetal hemoglobin to compete with maternal hemoglobin for O2 since fetal Hb has a lower affinity for BPG.

79
Q

What is the Bohr effect?

A

The decrease of O2 affinity of Hb in the tissues due to high concentrations of H+ and CO2, and the increase in O2 affinity in the lungs due to low concentrations of H+ and CO2.

80
Q

How do you get sickle-cell anemia?

A

Results from autosomal recessive mutation. There is a single amino acid change from Glu6 to Val.

81
Q

What is an exonuclease?

A

An enzyme that catalysesthe hydrolysis of phosphodiester bonds at the end of nucleic acid molecules?

82
Q

How is diversity maintained?

A

By both mutation, which alters a single gene, and recombination, which distributed the contents of the genome among various individuals during reproduction

83
Q

What is recombination?

A

any process by which DNA strands are broken and recombined to produce new combinations of alleles

84
Q

What does recombination usually involve?

A

Strand breakage and rejoining of DNA (crossing over), usually for homologous duplexes

85
Q

What is homologous recombination?

A

Crossing over between sister chromosomes in meiosis

86
Q

What is another term for the crossover point?

A

Chiasma

87
Q

What are some recombination examples?

A
  • Repair of double strand breaks
  • Formation of 2 Holliday junctions
  • Repair of the replication forks stalled at the site of DNA damage
  • Integration of viral genomes into host cell chromosomes
88
Q

How does the RecA protein recombinase play a key role in recombination in E. coli?

A

The RecA protein promotes all the central steps in the homo recombination process:

  • pairing of 2 homologous DNAs
  • strand invasion
  • formation of Holliday intermediates
  • branch migration
89
Q

How does RecA mediate strand exchange between single stranded DNA (ssDNA) and double stranded DNA (dsDNA)?

A
  • RecA protein polymerizes on ssDNA to form a nucleoprotein filament
  • the RecA-coated ssDNA then invades the homologous duplex
90
Q

How does RecA mediate strand invasion and branch migration?

A
  • when the RexA/ssDNA nucleoprotein filament contacts a duplex DNA w/ a strand complementary tothe bound ssDNA, RecA partially unwinds the duplex and, in an ATP-driven rxn, exchanges the ssDNa w/ the corresponding strand on the dsDNA
  • as the RecA filament rotates about its axis, the duplex DNA is spooled in
  • 2 such strand exchange processes occur simultaneously in a Holliday junction, both mediated by RecA in E. coli
91
Q

How do double-strand breaks in DNA present both a problem and an opportunity?

A
  • ds breaks occur from ionizing radiation (x-rays. gamma rays, UV light), oxidative damage and other environmental factors
  • ds breaks can also occur as a natural consequence of DNA replication at the site of a “lesion” - will result in collapse of the replication fork
  • ds breaks are lethal to cells and must be repaired
  • ds breaks are initiation sites for homologous recombination - can result in diversity/adaptation, especially in bacteria, when recombination occurs with homologous segments of DNA taken up from other bacteria
92
Q

What do ds breaks produces?

A

“blunt ends” - the RecBCD protein complex then processes these ends to produce ssDNA w/ a 3’-OH

93
Q

What is RecBCD?

A

it is both a helicase and an exonuclease

94
Q

What does RecBCD do?

A

It binds linear DNA at a free (broken) end and moves inward along the duplex, unwinding the duplex w/ its helicase activity, and degrading both strands

95
Q

How can double-strand breaks (DSB) in a eukaryotic chromosome be repaired?

A

By homologous recombination using the sequence information of the homologous chromosome to reconstruct the original DNA

96
Q

What are types of mobile genetic elements?

A

Plasmids, viruses, transposable elements (transposons)

97
Q

What are plasmids?

A

self-replicating (using host proteins), extra-chromosomal ds DNA circles found in bacteria, yeast, and fungi. Plasmids lack a protein coast and generally cannot move independently from cell to cell

98
Q

What are viruses?

A

self-replicating (using host proteins), infectious DNA - or RNA - containing elements that possess a protein coat an can move from cell to cell

99
Q

What are transposons?

A

Transposable elements: mobile DNA elements that lack a coat an can insert into and move around the host genome via recombination.

100
Q

Explain branch migration

A
  • a branch forms when a template strand pairs with 2 different complimentary DNA single strands (ssDNA)
  • the branch “migrates” when base pairing to one strand is broken and replaced by base pairing to the other
101
Q

What happens when RecBCD encounters a Chi sequence?

A

its 3’ to 5’ exonuclease activity slows and its 5’ > 3’ exonuclease activity increases, resulting in ssDNA with a 3’-OH end

102
Q

What is the Chi sequence?

A

5’ -GCTGGTCC

  • named for Crossover Hotspot Instigator
  • Chi sequences occur ~ every 5kb in E. coli
103
Q

What is the term where plasmids are transferred from one bacterium to another?

A

Conjugation

104
Q

Which cell properties can be conferred by plasmid genes?

A
  • Drug (antibiotic) resistance
  • virulence factors
  • metabolic activities
  • chromosome transfer
105
Q

How do viruses vary?

A
  • type of nucleic acid in genome, structure of viral chromosome
  • structure of coat
  • presence of membrane “envelope”
  • mode of entry into or exit from the host cell
  • site and mechanism of replication
106
Q

How do virus STRUCTURES vary?

A
  • nucleic acid: either RNA or DNA genome
  • coat protein: surrounds and protects the nucleic acid
  • nucleoprotein: packages the viral genome (not on all viruses)
  • envelope: some viral coats are surrounded by a lipid bilayer (envelope)
107
Q

What is the main difference between the lytic and lysogenic virus life cycle?

A
  • Lytic phage genome: does not integrate into the host chromosome. it is replicated extra-chromosomally. Phage often kills host cell.
  • Lysogenic phage genome: becomes integrated into the host cell chromosome + replicated long w/ the bacterial chromosome + passed onto daughter cells.

MBB 222 (3 decks)

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