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Molecular Cell Biology > Exam 3 material > Flashcards

Exam 3 material Flashcards

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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
Karyotype
an ordered display of chromosomes in the nucleus of a eukaryotic cell
26
what do chromosomes contain?
telomeres, replication origins and centromeres – specialized sites needed for correct replication and segregation of genetic information
27
_______ chromosomes are organized within the nucleus
interphase
28
What enables DNA packaging?
histones
29
Nucleosomes are the basic units of ___________ chromatin structure
eukaryotic
30
Five histones
-H2A, H2B, H3 and H4 (nucleosome core) – H1(required for 30 nm fiber packing level)
31
Bacteria don’t have __________
nucleosomes
32
ATP dependent chromatin remodeling complexes…
utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression.
33
Acetylation (lysine)
removes positive charge, reducing affinity of histone to DNA – makes DNA more accessible for replication
34
Methylation
can either increase or decrease DNA accessibility, depending on the amino acid it is added to
35
Heterochromatin
condensed; – about 10% of interphase chromosome most heterochromatin does not contain genes
36
Euchromatin
more loose structure (different from heterochromatin)
37
_______ chromosomes contain different forms of chromatin
interphase
38
Heterochromatin can be used to silence _______
unwanted gene expression
39
What causes Calico cat coloration?
patterns of X chromosome inactivation
40
DNA replication is
Semiconservative
41
Who did the experiment that proved that DNA is not replicated as a conservative method?
Meselson and Stahl
42
Are replication origins more likely to be A-T rich or G-C rich?
A-T because there are less Hydrogen bonds there
43
Initiator proteins...
allow the separation of the dsDNA
44
Replication machine
group of proteins that are recruited to the site and replicate the DNA after separation of double helix
45
What is DNA synthesis is catalyzed by?
DNA polymerase
46
Nucleotides are added only to the which end of a DNA strand?
3'
47
DNA synthesis is 5’ to 3’
5’ to 3’
48
Proofreading
DNA Polymerase also has an error-correcting activity
49
If DNA is synthesized only in the 5’ to 3’ direction how are both strands replicated?
Leading and lagging strands
50
Is the replication fork symmetrical or asymmetrical?
asymmetrical
51
Primase
synthesize RNA primer to begin replication
52
DNA polymerase extends what until it runs into the next RNA primer?
Okazaki fragment
53
RNA primer will then be degraded by
ribonuclease
54
DNA polymerase called ___________________________ replaces the RNA with DNA
Repair polymerase (DNA polymerase I)
55
DNA Ligase
joins the fragments (5’ P to 3’ OH)
56
Initiator proteins
helix opening at replication origin
57
DNA Polymerase polymerization direction
polymerization (5’-3’)
58
DNA Primase
synthesis of short RNA primer
59
Ribonuclease
degradation of RNA primer
60
Repair polymerase
replace RNA with DNA
61
Ligase
joining of DNA fragments
62
DNA Helicase
unzipping DNA helix prior to replication
63
Single-stranded DNA-binding protein
prevent reanealing
64
Sliding clamp
keeps DNA polymerase attached to template and on lagging strand, releases when Okazaki fragment is completed
65
Telomerase
needed to replicate chromosome ends
66
Depurination
removal of purines (A and G) from the sugar
67
Deamination
removal of NH2 group from cytosine, converting it to uracil
68
Thymine dimerization
covalent link between two adjacent Thymines. Caused by UV radiation
69
Somatic cells
can accumulate mutations over a lifespan that may impact health
70
General mechanism of DNA repair
Excision, Replacement, Ligation
71
Excision
a nuclease will remove the damaged/ wrong region
72
Replacement
DNA polymerase will synthesize new strand
73
Ligation
the enzyme ligase will connect the newly synthesized nucleotide with the next one (nick repair)
74
Transposons
common mobile genetic elements (also called “jumping genes”)
75
transposase
an enzyme necessary for transposon mobility
76
Transposons can make bacteria _______ to antibiotics
resistant
77
Transposons in eukaryotes
move via an RNA intermediate - retrotransposons
78
Retroviruses found only in ______ cells
eukaryotic
79
RNA is synthesized by ________________
RNA polymerase
80
Promoter
DNA sequence that is recognized by RNA polymerase as a start point.
81
Transcription provides _____________ of genetic information
amplification
82
mRNA
codes for proteins
83
rRNA
from the core of the ribosomes and catalyze protein synthesis
84
miRNA
regulate gene expression
85
tRNA
serve as adapters between mRNA and amino acids during protein synthesis
86
other small RNAs
used in RNA splicing, telomere maintenance, and many other processes
87
Sigma factor
subunit of RNA polymerase
88
3 steps of transcription
1) Initiation 2) Elongation 3) Termination
89
RNA polymerase transcribes in only __ direction
one
90
RNA polymerase in prokaryotes
They have a single type
91
RNA polymerase in eukaryotes
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
Initiation in prokaryotes
RNA pol can initiate without helper proteins
93
Initiation in eukaryotes
RNA pols require general transcription factors
94
Transcript processing in prokaryotes
transcripts are generally NOT processed
95
Packing of DNA into nucleosomes in eukaryotes because
Prokaryotes do not have nucleosomes
96
TATA-binding protein (TBP)
is a subunit of TFIID; involved in the recognition of the promoter
97
How is RNA Pol II released from the transcription initiation complex?
Phosphorylation of RNA Pol II by TFIIH, transcription proceeds
98
Key steps in Transcription initiation by RNA polymerase II
* 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
Where does transcription take place?
the nucleus
100
where does translation (protein synthesis) take place?
the cytosol
101
RNA capping
modification of 5’ end, 7-methylG)
102
Polyadenylation
modification of 3’ end, polyA tail
103
Splicing
removal of introns
104
Exons
expressed sequences
105
Introns
intervening sequences
106
What provides a mechanism for functional diversity?
alternative splicing
107
Translation
conversion of the information in RNA to protein Deciphering the genetic code
108
Each trinucleotide is called a ______
Codon
109
true or false: tRNA is charged when linked to an amino acid
true
110
aminoacyl-tRNA synthetase
recognizes nucleotides at the anticodon and the 3’ amino acid-accepting arm to provide specificity
111
Where is the mRNA mesage decoded?
the ribosome
112
Ribozyme
RNA molecule with a catalytic activity
113
There are three bringing sights
A site, P site, E site
114
A site
(aminoacyl-tRNA) charged tRNA binds to its mRNA codon
115
P site
(peptidyl-tRNA) condensation of amino acids
116
E site
(exit): where the “uncharged” tRNA is ejected
117
What codon codes for methionine?
AUG
118
DNA polymerase proofreading direction
proofreading (3’-5’)

Molecular Cell Biology (3 decks)

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