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AP® Biology flashcards Biology 101 flashcards
1
Q

DNA Double Helix

A
  1. Two Polynucleotide Chains
  2. Antiparallel Orientation
  3. Sugar-Phosphate Backbone
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2
Q

Bond between Base Pairs

A

Hydrogen bonds

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3
Q

Bond between Sugar and Base

A

Covalent bond

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4
Q

DNA replication is

A

Semi-conservative

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5
Q

Meselson–Stahl Experiment (1958)

A

• Parental DNA labeled with heavy isotope
• Formation of the Hybrid DNA duplex in Generation 1
confers Semiconservative DNA Replication

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6
Q

Head dsDNA to Tm

A

Denaturation

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7
Q

Polymerase Chain Reaction (PCR) uses

A

Denaturation and renaturation property of the DNA used for experimentation in molecular biology

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8
Q

Renaturation occurs when

A

DNA temperature is reduced to annealing temperature

Annealing = DNA to DNA or RNA to RNA

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9
Q

Point Mutation

A

Loss/gain of a single base pair
Transition (purine to purine or pyrimidine to pyrimidine) or transversion (purine to pyridimidine or pyridimidie to purine)

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10
Q

Insertion

A

Addition of multiple base pairs

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11
Q

Purine

A

A and G

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12
Q

Pyrimidine

A

C and T

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13
Q

Point Mutation reversed by

A

-True reversion or second-site reversion

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14
Q

Insertion mutation reversed by

A

Deletion

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15
Q

Deletion mutation is

A

Irreversible

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16
Q

Null mutation

A

Tests whether a gene is essential

Completely eliminates gene function

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17
Q

Silent mutation

A

Mutations that do not affect protein sequence or function

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18
Q

Centromere

A

“Center” of the chromosome
Highly repetitive DNA called α-satellite DNA
A-T rich

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19
Q

Specific proteins that bind and/or maintain the centromere

A
  1. Nucleosome = incorporation of specific histone (CENP-A)

2. Chromatin-remodeling proteins = cohesions, condensin, topoisomerase II

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20
Q

Acentric fragment:

A

Absence of a centromere = unable to attach to spindle = lost chromosome = lost genetic information

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21
Q

Dicentric/polycentric chromosome:

A

A single chromosome with 2 or more centromeres (commonly due to to fusion of two chromosomes)
Only one centromere is functional (centromere that most
efficiently assembles the kinetochore)
Allows normal cell division

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22
Q

Features of the telomere:

A
  1. G-quartets/G-quadruplex
  2. T-Loop/D-Loop Formation
  3. Binding of the Shelterin Complex
  4. Telomerase Activity
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23
Q

G-quartets/G-quadruplex function

A

Unknown!

Transient DNA structure

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24
Q

What regulates telomere length?

A

Binding of shelterin complex and telomerase activity

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25
Q

Hierarchy of DNA Organization:

A

Ensures that the DNA is packaged in the most compact state.

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26
Q

RNA polymerase I synthesizes

A

5.8S, 18S, and 28S rRNA in the nucleolus.

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27
Q

RNA polymerase III synthesizes

A

tRNA, 5S rRNA genes, small

RNAs in the nucleoplasm.

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28
Q

RNA polymerase II synthesizes

A

hnRNA; all RNA with the exception of those transcribed by RNA polymerase I & III

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29
Q

TFIIH

A
  • Recruited by TFIIE
  • Helicase activity
  • Rapidly repairs damaged DNA to avoid RNAP II stalls.
  • Phosphorylates the C-terminal domain (CTD) of RNAP II (functions in elongation, 5’ capping)
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30
Q

Epigenetics

A

Inheritable changes in a cell’s phenotype

Independent of changes to the DNA sequence or genotype

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31
Q

Mechanism associated with Epigenetics:

A
  1. Histone Post-translational Modifications
  2. DNA Methylation
  3. Regulatory RNA (non-coding RNA)
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32
Q

Histone acetylation

A

Activation of gene expression

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33
Q

Position-effect variegation (PEV)

A

Propagation of the inactive heterochromatin structure is
dictated by:
1. Availability of silencing proteins
2. Activation of promoters
3. Presence of insulator/boundary sequence.
Example: Drosophila eye color

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34
Q

Interrupted gene:

A

A gene in which the coding sequence is not continuous

Therefore expressed via a precursor RNA

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35
Q

Prokaryotes have ___________ genes.

A

Prokaryotes have uninterrupted genes - DNA and mRNA sequences are the same.

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36
Q

Three classes of Introns:

A
  1. Nuclear RNA
  2. Group II
  3. Group I
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37
Q

Similarity among all three classes of intron

A

All require two-step trans-esterification reactions!

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38
Q

Autosplicing introns

A

Group I, Group II

NO ATP or GTP HYDROLYSIS for energy

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39
Q

Spliceosomes required for

A

Nuclear introns

NEED ENERGY

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40
Q

Alternative Splicing:

A

A SINGLE GENE gives rise to more than one mRNA sequence due to changes in the splicing pattern of the
pre-mRNA
Contributes to the structural and functional
diversity of the gene product (either mRNA or protein)

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41
Q

E-complex

A

Commitment complex

Requires U1 at 5’ splice site

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42
Q

A-complex

A

Pre-spliceosome = ATP-dependent

U2-snRNP binding to the branch site

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43
Q

B1-complex

A

Spliceosome
Contains all splicing components

Formed with the binding of U5 and U4/U6-snRNPs

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44
Q

B2-complex

A

Release of U1 and U4

Allows association of U6 with 5’ splice site and U2

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45
Q

C1- and C2-complexes

A

Transesterification and lariat structure

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46
Q

tRNA splicing:

A

ENDONUCLEASE cleaves the at 2 sites to dissociate
the intron

ATP-dependent LIGATION of the 2 exons

Forms a mature tRNA

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47
Q

Autosplicing of Group I introns:

A

Requires only guanosine and 2 metal ions.
GTP NOT hydrolyzed; no hydrolysis reaction occurs during self-splicing.

• Two-step transesterification
1. 3’OH of G nucleotide attacks phosphate at 5’-end of intron
2. 3’OH at 5’-exon attacks phosphate at second exon
• No lariat structure; the released intron engages in additional reactions.

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48
Q

Core regions of Group I introns

A

The cores of regions P3, P4, P6, and P7 form the minimal region required for catalytic activity

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49
Q

What mediates enzymatic reaction in a protein?

A

Ionic and hydrogen bonds mediate enzymatic reaction

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50
Q

What mediates enzymatic reaction in a ribozyme?

A

Base pairing with RNA substrate mediate enzymatic reaction

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51
Q

High affinity for substrate of ribozyme

A

= Low KM

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52
Q

Slow catalytic rate of ribozyme

A

= Low Kcat (turnover)

53
Q

Protein Splicing

A

Autocatalytic process that excises an intein (analogous to RNA intron) and forms a peptide bond between the two adjacent exteins (analogous to RNA exons).

54
Q

Does protein auto-splicing require energy?

A

Similar to RNA auto-splicing, protein auto-splicing does not require energy.

55
Q

How do proteins mediate auto-splicing?

A

Similar to RNA, proteins mediate autosplicing via conformational changes through bond rearrangement.
Like mobile RNA intron, some protein inteins code for a homing endonuclease.

56
Q

mRNA induced error

A

Wrong base
= MOST DETRIMENTAL
Not common

57
Q

Ribosome induced error

A

Wrong aa-tRNA
= MOST COMMON
Not very detrimental

58
Q

Termination codons are recognized not by charged-tRNAs but instead by

A

Protein release factors (RF).

59
Q

Prokaryotes have ______ types of class 1 release factors…

A

Prokaryotes have two types of class 1 release factors (RF1 and RF2) and eukaryotes have one class 1 release factor (eRF1).

60
Q

Both prokaryotes and eukaryotes require ________ for release…

A

Both prokaryotes and eukaryotes require the GTP-binding protein class 2 release factors (RF3 or eRF3).

61
Q

The wobble hypothesis

A

Conventional base pairing between codon/anticodon occurs at the first 2 codons, but unconventional base pairing at the 3rd codon.
The unconventional base pairing occurs because ribosomal A site allows greater flexibility at the first anti-codon position.
U-G is a common base pair.
First anticodon may also be modified base.

62
Q

Aminoacyl-tRNA synthetases are a family of enzymes that charge tRNA with an amino acid in a two-stage reaction:

A
  1. ATP hydrolysis to form aminoacyladenylate.

2. A.A. transfer to tRNA and release AMP.

63
Q

Each tRNA synthetase aminoacylates all the tRNAs…

A

In an isoaccepting group with the SAME amino acid.

64
Q

Recognition of tRNA by tRNA synthetases is based on…

A

A particular set of nucleotides that often are concentrated in the acceptor stem and anticodon loop regions of the
molecule.

65
Q

2/3 of RNA Poly II transcripts are cryptic unstable transcripts (CUTs)

A
  • a subset of noncoding RNA (ncRNA)
  • extremely unstable due to rapid degradation
  • 3’ polyadenylation via TRAMP
  • TRAMP recruitment of exosome responsible for rapid CUT
    decay
66
Q

Digestion of poly(A) tail to short oligoA tail

A

Triggers mRNA decay

67
Q

5’-3’ decay

A

Decapping by Dcp
Xrn1 eats fragments
5’ to 3’ exonuclease digestion by Lsm1-7

68
Q

3’-5’ decay

A

Exosome-mediated 3’ to 5’ digestion

69
Q

If cell division

A

A new round of replication must be initiated before
the previous replication round is completed
Daughter cell is produced with replication already occurring with the presence of multi-forked chromosomes.

70
Q

ftsZ mutations:

A

Multinucleated, long filaments form when septum formation is inhibited but replication is unaffected.

71
Q

ftsZ overexpression:

A

No chromosome, small cells (called minicells) form when septum formation is either too rapid or not mid-cell.
Minicells different from anucleated mutants

72
Q

Most of eukaryotic cells are in the…

A

Most of eukaryotic cells are not growing or in the G0 stage.

Exception: stem cells, embryonic cells, and cancer cells.

73
Q

Replication and cell division is controlled via:

A

Signal transduction pathway - process by which a stimulus or cellular state is sensed by and transmitted to pathways
within the cell.
Example: From the EGFR Signal Transduction Pathway.

74
Q

Generating and Maintaining ssDNA is important for replication.
Requires two functions:

A
  1. A helicase to separate/unwind the strands of DNA using energy provided by hydrolysis of ATP.
  2. A single-stranded binding protein (SSB) is required to
    maintain the separated strands.
75
Q

A single-stranded binding protein (SSB) is required to:

A

Maintain the separated strands of DNA during replication.

76
Q

There are several methods for providing the free 3’-OH

end that DNA polymerases require to initiate DNA synthesis:

A
  • RNA primer
  • a nick in DNA
  • a priming protein
77
Q

RNA primer used:

A
  • One time in leading strand

- Multiple times in lagging strand

78
Q

Primase

A

SPECIAL RNAP
Synthesizes RNA chain that provides priming end
Different from other RNAP!

79
Q

Most ‘important’ to initiate DNA synthesis is

A

NICK in the DNA

80
Q

DnaB

A

The helicase DnaB is responsible for interacting with the primase DnaG to initiate each Okazaki fragment

DnaB contacts the τ subunits of the clamp loader to connect the helicase-primase complex and the catalytic core.

81
Q

Synthesis of the leading strand creates

A

A loop of ssDNA on the lagging strand
Enzyme complex pulls the lagging strand through the clamp while synthesizing the new strand
“Opposite direction” from leading strand - but still 5’ to 3’ synthesis

82
Q

Bivalent

A

Synapse or chromosome pairing of all 4 chromatids during meiosis; this structure is called a bivalent.
Recombination initiated and strands exchanged.

83
Q

Synaptonemal complex function

A

Stabilizes the synapse

Could present an obstacle to recombination

84
Q

Synaptonemal complex structure

A

Could present an obstacle to recombination.
• Loops of chromatin project from the axis.
• Cohesions connect sister chromatids so that they segregate properly at mitosis or meiosis. Form the lateral elements.
• Zip proteins transverse and link together to form the synaptonemal complex central element.

85
Q

All recombination repair systems

A

REQUIRE LIGASE!

86
Q

Direct Repair

A

Reversal/removal of the damage.

LEAST common

87
Q

Excision Repair

A

One strand of DNA is directly excised and then replaced

by resynthesis using the complementary strand as template.

88
Q

Mismatch Repair

A

Corrects recently inserted bases that do not pair
properly.
MOST common

89
Q

Recombination Repair

A

Fills in a gap in one strand of duplex DNA by retrieving a homologous strand from another complex.
BEST to repair DSB

90
Q

Non-homologous end-joining

A

Rejoins DSB

91
Q

What happens to a replication fork when it encounters a damaged site or nick in DNA?

A

Stalls, then:

1) May reverse by pairing between the two newly synthesized strands
2) May restart after repairing the damage and use a helicase to move the fork forward
3) May initiate translesion/excision repair or recombination repair (also called “post-replication repair”)

92
Q

Activator, when introduced, can…

A

Control kernel color in maize.

93
Q

Activator (Ac) element

A

Autonomous transposable element in maize.

94
Q

Dissociation (Ds) element

A

Non autonomous transposable element in maize, requires Ac.

95
Q

Transcription generates ________ DNA ahead of

RNA polymerase.

A

More tightly wound (positively supercoiled)

96
Q

DNA behind RNAP becomes _________ during transcription.

A

Less tightly wound (negatively coiled)

97
Q

Gyrase

A

Introduces negative supercoils (rectifies in front of RNAP)

98
Q

Topoisomerase

A

Removes negative supercoils (rectifies behind RNAP)

99
Q

Negative inducible

A

Active repressor + inducer => Inactive repressor

100
Q

Negative repressible

A

Inactive repressor + corepressor => Active repressor

101
Q

Positive inducible

A

Inactive activator + inducer => Active activator

102
Q

Positive repressible

A

Active activator + corepressor => Inactive repressor

103
Q

Polycistronic mRNA

A

mRNA that includes coding regions representing more than one gene

104
Q

The cluster of the lac operon containing the 3 lac structural
genes

A

lacZ, lacY, and lacA.

105
Q

lac repressor

A 
Maintains the lac operon in the inactive condition by binding to the operator.
The repressor has 3 binding sites: 
1) Operator DNA binding site
2) Inducer site
3) Multimerization site
106
Q

Inducer for the lac repressor (negative inducible)

A

By-product of β-galactosidase, allolactose

107
Q

cAMP is controlled by:

A

Level of glucose in the cell

Low glucose = High cAMP

High glucose = Low cAMP.

Glucose high = reducing the level of cyclic AMP = high glucose inhibits the transcription of operon

108
Q

The trp operon is

A

The trp operon is negatively controlled by the level of its product (negative repressible), the amino acid tryptophan (autoregulation).

109
Q

The amino acid tryptophan…

A

Activates an inactive repressor encoded by trpR gene.

110
Q

The trp repressor recognizes operators at…

A

Three dispersed gene loci.

111
Q

Lytic and lysogenic pathways both require…

A

Expression of the immediate early and delayed early genes.

112
Q

Lytic development follows if…

A

The late genes are expressed.

The lytic cycle requires the delayed early gene Q.

113
Q

Lysogeny ensues if…

A

cI gene is expressed.

Lysogeny requires the delayed early genes cII-cIII.

114
Q

Lambda has 2 immediate early genes:

A
  1. N gene codes for an antitermination factor.
  2. Cro gene codes for a repressor that prevents the
    expression of the cI gene.
115
Q

The critical stage in deciding between lysogeny and lysis is…

A

WHEN delayed early genes are being expressed.

116
Q

If cII causes sufficient synthesis of repressor…

A

Lysogeny will result because repressor occupies the
operators.

(Otherwise Cro occupies the operators, resulting in a lytic
cycle.)

117
Q

Class II TE

A

= DNA elements
• Class I à Retroelements or RNA intermediates.
• LTR retrotransposon – A transposon that
mobilizes via an RNA form
- Similarity with a retrovirus à a virus with RNA
as its genetic material.
- like retrovirus, it expresses long-terminal repeats
(LTR) which are repetitive sequences analogous
to that of the provirus for integration into the
genome.
- like retrovirus, it’s RNA codes for and is subject
to an active reverse transcriptase.
- unlike retrovirus, it does not have a infective,
viral form.
• non-LTR retrotransposon (retroposon) – A
transposon that mobilizes via an RNA
intermediate, similar to an LTR retrotransposon,
but that lacks LTRs and uses a distinct
transposition mechanism.

118
Q

Class I TE

A

Retroelements of RNA intermediates

119
Q

LTR retrotransposon

A

A transposon that mobilizes via an RNA form
Similar to a RETROVIRUS!
Like retrovirus, expresses long-terminal repeats (LTR) = repetitive sequences analogous to a provirus = for integration into the genome.
RNA codes for and is subject to an active reverse transcriptase.

120
Q

non-LTR retrotransposon (retroposon)

A

Mobilizes via an RNA intermediate
Lacks LTRs
Uses a distinct transposition mechanism

121
Q

Transduction

A

Viral vector to release DNA into target cells

122
Q

Transfection

A

Liposome bound, microinjection, nanospheres to release DNA into target cells

123
Q

Sanger method

A

Chain termination sequencing
Uses dideoxynucleotides to terminate DNA synthesis at
particular nucleotides.
ddNTP = modified nucleotides that can be incorporated into a growing DNA strand, but lack the 3’-hydroxyl group needed to attach the next nucleotide.

124
Q

Sequencing by synthesis (SS-sequencing)

A

Relies on the detection of each nucleotide as it is added to a growing strand.
Example #1: Tethered primer and fluorescent-dNTP
Example #2: Pyrosequencing is a process to detect
the release of the pyrophosphate (diphosphate) with the addition of the nucleotide to a growing strand; detection via
bioluminescence.

125
Q

Real-time PCR

A

Real-time, or quantitative, PCR detects the products

of PCR amplification during their synthesis, and is more sensitive and quantitative than conventional PCR.

126
Q

Ct

A

Threshold cycle = when the amplicon/product can be detected

127
Q

MCS

A

MCS (multiple cloning site) = A sequence of DNA containing a series of tandem restriction endonuclease sites, used in
cloning vectors for creating recombinant molecules.
Insert between two MCS sites.

128
Q

Staggered cuts

A

Requires SAME restriction enzyme for Vector and Insert.

129
Q

Blunt cuts

A

Do NOT require the same restriction enzyme for Vector and Insert

Molecular Biology Final (1 decks)

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