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Molecular Cell Biology > Exam 3 material > Flashcards

Exam 3 material Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Freidrich Miescher identified

A

Nuclein

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2
Q

What was nuclein later renamed?

A

Nucleic Acid

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3
Q

What did Kossel and Levene show that DNA consisted of?

A

sugar, nitrogenous bases, and phosphate

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4
Q

what was the conundrum of the time of discovering DNA?

A

Proteins are more complex than DNA (20 amino acids vs. 4 nitrogenous bases), therefore it was thought that proteins Must be the genetic material

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5
Q

What was the first key experiment that lead to the identification of DNA as a genetic material?

A

Frederick Griffith’s Streptococcus pneumococcus experiment

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6
Q

Describe the Streptococcus pneumococcus experiment

A

bacteria from the S strain were killed by heat, and their remains were added to R strain bacteria. While neither alone harmed the mice, the combination was able to kill its host. Griffith was also able to isolate both live R and live S strains of pneumococcus from the blood of these dead mice.

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7
Q

what was the process called that happened in the Streptococcus pneumococcus experiment

A

transformation

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8
Q

what is key idea #1 that Avery, MacLeod and
McCarty demonstrated that
DNA is the transforming
principle

A

A mixture of things
has an effect on something.
Separate the components,
see which one has the effect.

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9
Q

what is key idea #2 that Avery, MacLeod and
McCarty demonstrated that
DNA is the transforming
principle

A

A mixture of
things has an effect on
something. Delete
components one by one, see
which deletion cause the
effect to disappear.

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10
Q

Hershey-Chase experiment

A

Label phage DNA with 32P and phage proteins with 35S, then infect bacteria, let the
‘injection’ occur, then tear off the virus and see what got injected into the bacteria

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11
Q

Structure of DNA

A

Nucleotide = base + pentose + phosphate

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12
Q

Chargaff’s Rule

A

Most importantly, A=T and G=C, that is A and T were
present in equimolar amounts as were G and C, and A+T does not equal G+C

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13
Q

Three rules to the structure of DNA

A

5’ to 3’; anti-parallel; complementary base pairing

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14
Q

What do the 5’ end have that the 3’ end doesn’t?

A

phosphate

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15
Q

What does the 3’ end have that the 5’ end doesn’t?

A

OH group

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16
Q

How many Hydrogen bonds does A-
T have?

A

two

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17
Q

How many hydrogen bonds does G-C have?

A

three

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18
Q

Which are more stable, A-T or G-C base pairs?

A

G-C

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19
Q

Properties of the DNA Double Helix

A

-Two DNA strands
wrapped in a right-
handed helix
-The bases are stacked
one on top of the other
(hydrophobic
interactions and van der
Waals forces stabilize
the helix)
-10 bases per helical turn
-Spaces between the turns of the
helix forms major and minor
grooves - important sites for
DNA/protein interactions

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20
Q

Central dogma

A

DNA -> RNA -> Protein

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21
Q

Chromosomes

A

very long, single DNA
molecules associated with proteins that
fold and pack the DNA into a compact
structure
(10,000-fold compaction)

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22
Q

Chromatin

A

the complex of DNA and
associated proteins is called

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23
Q

Gene

A

a segment of DNA that
contains the instructions for making a
particular protein or RNA

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24
Q

Genome

A

the total DNA complement
of an organism

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25
Q

Karyotype

A

an ordered display of
chromosomes in the nucleus of a
eukaryotic cell

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26
Q

what do chromosomes contain?

A

telomeres, replication origins and
centromeres – specialized sites needed for correct replication and segregation of genetic information

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27
Q

_______ chromosomes are organized within the nucleus

A

interphase

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28
Q

What enables
DNA packaging?

A

histones

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29
Q

Nucleosomes are the basic units of
___________ chromatin structure

A

eukaryotic

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30
Q

Five histones

A

-H2A, H2B, H3 and H4 (nucleosome core)
– H1(required for 30 nm fiber packing level)

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31
Q

Bacteria don’t have __________

A

nucleosomes

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32
Q

ATP dependent chromatin remodeling complexes…

A

utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression.

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33
Q

Acetylation (lysine)

A

removes positive charge, reducing affinity of histone to DNA – makes DNA more accessible for replication

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34
Q

Methylation

A

can either increase or decrease DNA accessibility, depending on the amino acid it is added to

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35
Q

Heterochromatin

A

condensed; – about 10% of interphase chromosome
most heterochromatin does not contain genes

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36
Q

Euchromatin

A

more loose structure (different from heterochromatin)

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37
Q

_______ chromosomes contain different forms of chromatin

A

interphase

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38
Q

Heterochromatin can be used to silence _______

A

unwanted gene expression

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39
Q

What causes Calico cat coloration?

A

patterns of X chromosome inactivation

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40
Q

DNA replication is

A

Semiconservative

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41
Q

Who did the experiment that proved that DNA is not replicated as a conservative method?

A

Meselson and Stahl

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42
Q

Are replication origins more likely to be A-T rich or G-C rich?

A

A-T because there are less Hydrogen bonds there

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43
Q

Initiator proteins…

A

allow the separation of the dsDNA

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44
Q

Replication machine

A

group of proteins that are recruited to the site and
replicate the DNA after separation of double helix

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45
Q

What is DNA synthesis is catalyzed by?

A

DNA polymerase

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46
Q

Nucleotides are added only to the which end of a DNA strand?

A

3’

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47
Q

DNA synthesis is 5’ to 3’

A

5’ to 3’

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48
Q

Proofreading

A

DNA Polymerase also has
an error-correcting activity

49
Q

If DNA is synthesized only in the 5’ to 3’ direction
how are both strands replicated?

A

Leading and lagging strands

50
Q

Is the replication fork symmetrical or asymmetrical?

A

asymmetrical

51
Q

Primase

A

synthesize RNA
primer to begin replication

52
Q

DNA polymerase extends what until it runs into the next RNA primer?

A

Okazaki fragment

53
Q

RNA primer will then be
degraded by

A

ribonuclease

54
Q

DNA polymerase called ___________________________ replaces the RNA with DNA

A

Repair
polymerase (DNA polymerase
I)

55
Q

DNA Ligase

A

joins the fragments
(5’ P to 3’ OH)

56
Q

Initiator proteins

A

helix opening at replication origin

57
Q

DNA Polymerase polymerization direction

A

polymerization (5’-3’)

58
Q

DNA Primase

A

synthesis of short RNA primer

59
Q

Ribonuclease

A

degradation of RNA primer

60
Q

Repair polymerase

A

replace RNA with DNA

61
Q

Ligase

A

joining of DNA fragments

62
Q

DNA Helicase

A

unzipping DNA helix prior to replication

63
Q

Single-stranded DNA-binding protein

A

prevent reanealing

64
Q

Sliding clamp

A

keeps DNA polymerase attached to template
and on lagging strand, releases when Okazaki fragment is completed

65
Q

Telomerase

A

needed to replicate chromosome ends

66
Q

Depurination

A

removal of purines (A and G) from the
sugar

67
Q

Deamination

A

removal of NH2 group from cytosine,
converting it to uracil

68
Q

Thymine dimerization

A

covalent link between two
adjacent Thymines. Caused
by UV radiation

69
Q

Somatic cells

A

can accumulate mutations over
a lifespan that may impact
health

70
Q

General mechanism
of DNA repair

A

Excision, Replacement, Ligation

71
Q

Excision

A

a nuclease will remove the
damaged/ wrong region

72
Q

Replacement

A

DNA polymerase will
synthesize new strand

73
Q

Ligation

A

the enzyme ligase will
connect the newly synthesized
nucleotide with the next one (nick
repair)

74
Q

Transposons

A

common mobile genetic elements (also called “jumping genes”)

75
Q

transposase

A

an enzyme necessary for
transposon mobility

76
Q

Transposons can make bacteria _______ to antibiotics

A

resistant

77
Q

Transposons in eukaryotes

A

move via an RNA intermediate - retrotransposons

78
Q

Retroviruses found
only in ______ cells

A

eukaryotic

79
Q

RNA is synthesized by ________________

A

RNA polymerase

80
Q

Promoter

A

DNA sequence that is recognized by RNA polymerase as a start point.

81
Q

Transcription provides _____________ of genetic information

A

amplification

82
Q

mRNA

A

codes for proteins

83
Q

rRNA

A

from the core of the ribosomes and catalyze protein synthesis

84
Q

miRNA

A

regulate gene expression

85
Q

tRNA

A

serve as adapters between mRNA and amino acids during protein synthesis

86
Q

other small RNAs

A

used in RNA splicing, telomere maintenance, and many other processes

87
Q

Sigma factor

A

subunit of RNA polymerase

88
Q

3 steps of transcription

A

1) Initiation
2) Elongation
3) Termination

89
Q

RNA polymerase
transcribes in only __ direction

A

one

90
Q

RNA polymerase in prokaryotes

A

They have a single type

91
Q

RNA polymerase in eukaryotes

A

RNA pol I: most rRNA genes
RNA pol II: protein-encoding genes (makes mRNA)
RNA pol III: tRNA, 5S rRNA, small structural RNA genes

92
Q

Initiation in prokaryotes

A

RNA pol can initiate without helper proteins

93
Q

Initiation in eukaryotes

A

RNA pols require general transcription factors

94
Q

Transcript processing in prokaryotes

A

transcripts are generally NOT processed

95
Q

Packing of DNA into nucleosomes in eukaryotes because

A

Prokaryotes do not have nucleosomes

96
Q

TATA-binding protein (TBP)

A

is a subunit of TFIID; involved in the
recognition of the promoter

97
Q

How is RNA Pol II released from the
transcription initiation complex?

A

Phosphorylation of RNA Pol II by
TFIIH, transcription proceeds

98
Q

Key steps in Transcription initiation by RNA polymerase II

A
  • General transcription factor TFIID binds to TATA box
    TATA box is a conserved sequence found in nearly all
    RNA pol II-transcribed promoters and is located ~25
    base pairs upstream of transcription start sites
  • Assembly of transcription initiation complex on promoter
    Includes other general factors and RNA Pol II
  • Disengage RNA pol II from complex to begin transcription
    Phosphorylation of RNA pol II tail by TFIIH (kinase)
  • General transcription factors release from DNA once
    transcription begins
99
Q

Where does transcription take place?

A

the nucleus

100
Q

where does translation (protein synthesis) take place?

A

the cytosol

101
Q

RNA capping

A

modification of 5’ end, 7-methylG)

102
Q

Polyadenylation

A

modification of 3’ end, polyA tail

103
Q

Splicing

A

removal of introns

104
Q

Exons

A

expressed sequences

105
Q

Introns

A

intervening sequences

106
Q

What provides a mechanism for functional diversity?

A

alternative splicing

107
Q

Translation

A

conversion of the information in RNA to protein
Deciphering the genetic code

108
Q

Each trinucleotide is called a ______

A

Codon

109
Q

true or false: tRNA is charged when linked to an amino acid

A

true

110
Q

aminoacyl-tRNA synthetase

A

recognizes nucleotides at the anticodon
and the 3’ amino acid-accepting arm to provide specificity

111
Q

Where is the mRNA mesage decoded?

A

the ribosome

112
Q

Ribozyme

A

RNA molecule with a catalytic activity

113
Q

There are three bringing sights

A

A site, P site, E site

114
Q

A site

A

(aminoacyl-tRNA) charged tRNA binds to its mRNA codon

115
Q

P site

A

(peptidyl-tRNA) condensation of amino acids

116
Q

E site

A

(exit): where the “uncharged” tRNA is ejected

117
Q

What codon codes for methionine?

A

AUG

118
Q

DNA polymerase proofreading direction

A

proofreading (3’-5’)

Molecular Cell Biology (3 decks)

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