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BIOL 190 > After Exam 3 > Flashcards

After Exam 3 Flashcards

1
Q

Watson and Crick noted that the specific base pairing suggested

A

A possibly copying mechanism for genetic materiaal

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2
Q

Since the two strands of DNA are complementary each strand acts as

A

a template for building a new strand in replication

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3
Q

In DNA replication the parent molecule unwinds and ____ are built based on base-pairing rules

A

2 new daughter strands

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4
Q

Watson and Crick came up with the ____ model

A

semiconservative

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5
Q

What is the semiconservative model?

A

When a double helix replicates, each daughter nuclei will have one old strand and one new strand

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6
Q

What were the competing models of the semiconservative one?

A

Conservative and dispersive

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7
Q

What did Meselson and Stahl accomplish?

A

They tested the 3 models by interacting old strands with a heavy isotope of nitrogen and new strands were labeled with a lighter isotope.

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8
Q

What did the first replication from meselson and stahl produce?

A

A band of hybrid DNA eliminating the conservative model.

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9
Q

What did the second replication produce?

A

Both light and hybrid DNA, eliminating the dispersive model.

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10
Q

Where does DNA Replication begin?

A

Special sites called origins of replication.

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11
Q

Describe DNA replication

A

2 strands are separated opening up a replication bubble.

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12
Q

What does the replication bubble consist of?

A

A replication fork

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13
Q

What is a replication fork?

A

A y shaped region where new DNA strands are elongating at each end

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14
Q

What is helicase?

A

Untwists the double helix and separates the template DNA strands at the replication fork

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15
Q

What is the single strand binding protein

A

Binds to and stabilizes signle stranded DNA until it can be used as a template

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16
Q

What is topoisomerase

A

corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

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17
Q

What is rate of elongation in bacteria?

A

~500 nucleotides/sec

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18
Q

What is the rate of elongationi in human cells?

A

~50 nucleotides/sec

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19
Q

What is the nucleotide that is added to a growing dna strand?

A

A nucleoside triphosphate

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20
Q

True or false: the antiparallel structure of the double helix affects replication

A

True

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21
Q

What end to DNA polymerases add nucleotides to?

A

free 3’ end of a growing strand

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22
Q

What direction can DNA ONLY elongate in?

A

5’ to 3’ direction

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23
Q

Along what strand of DNA can DNA polymerase synthesize a complementary strand continuously moving toward the replication fork

A

The leading strand

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24
Q

How does DNA polymerase elongate the lagging strand?

A

DNA polymerase must work in the direction away from the replication fork

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25
Q

The lagging strand is synthesized as a series of segments called _____ which are joined together by ______

A

Okazaki fragments,

DNA ligase

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26
Q

True or false: The DNA replication machine is probably not stationary during the replication process

A

false

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27
Q

How do DNA polymerases look for and fix mistakes?

A

They proofread and replace any incorrect nucleotides

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28
Q

What can DNA be damaged by?

A

chemicals, x-rays, UV light, cigarettes

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29
Q

What is the mismatch repair of DNA

A

Repair enzymes correct errors in base pairing

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30
Q

What is the nucleotide excision repair?

A

Enzymes cut out and replace damaged stretches of DNA

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31
Q

What creates problems for the linear DNA of eukaryotic chromosomes?

A

Limitations of DNA polymerase

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32
Q

What do repeated rounds of replication produce and why?

A

Shorter DNA molecules with uneven ends, because the machinery provides no way to complete the 5’ ends

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33
Q

What are telomeres?

A

End nucleotide sequences in eukaryotic chromosomal DNA molecules

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34
Q

What is the function of telomeres?

A

They pospone erosion of genes near the ends of DNA molecules

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35
Q

True or false: Telomeres prevent the shortening of DNA molecules

A

False

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36
Q

What would happen if chromosomes of germ cells became shorter in every cell cycle?

A

Essential genes would eventually be missing from gametes they produce

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37
Q

What is the function of telomerase?

A

Catalyzes the lengthening of telomeres in germ cells

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38
Q

True or false: There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist

A

True

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39
Q

The shortening of telomeres is proposed to be connected to

A

Aging

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40
Q

What is the shortening of telomeres proposed to do?

A

Protect cells from cancerous growth by limiting the number of cell divisions

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41
Q

The _____is a double stranded, circular DNA molecule associated with a ____ amount of protein

A

bacterial chromosome, small

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42
Q

_____ have linear DNA molecules associated with a ____ amount of proteins

A

Eukaryotic chromosomes, large

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43
Q

____ is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells

A

Chromatin

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44
Q

____ are proteins responsible for the first level of DNA packing in chromatin

A

Histones

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45
Q

DNA winds around histones to form nucleosome “beads” called

A

Nucleosomes

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46
Q

Interactions between nucleosomes cause the thin fiber to coil or fold into this

A

thicker fiber, 30nm fiber

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47
Q

The 30 nm forms looped domains that

A

attach to proteins (300 nm fiber)

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48
Q

Arrange in size from smallest to largest:

scaffolded domains, double helix, metaphase chromosome, nucleosome, 30nm fiber

A 
double helix
nucleosome
30 nm fiber
scaffolded domains
metaphase chromosome
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49
Q

Most chromatin is loosely packed in the nucleus during interphase and condenses prior to

A

mitosis

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50
Q

what is euchromatin

A

loosely packed chromatin

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51
Q

What is heterochromatin

A

highly condensed chromatin

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52
Q

Dense packing of the heterochromatin makes it difficult for the cell to express ____ coded in regions of ___ and ____

A

genetic information
centromeres
telomeres

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53
Q

____ are not highly condensed by still occupy specific ____ regions in nucleus

A

interphase chromosomes

restricted

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54
Q

What is gel electrophoresis

A

Indirect method of rapidly analyzing and comparing genomes

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55
Q

What is the function and name of the PCR

A

Polymerase chain reaction

can produce many copies of a specific target segment of DNA

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56
Q

What are the three steps that bring about a chain reaction and what does it produce?

A

Heating, cooling, replication

produces exponentially growing population of identifcal DNA molecules

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57
Q

Taq DNA polymerase do not have to add

A

fresh DNA polymerase

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58
Q

The PCR can amplify DNA from

A

all organisms, fetal cells, and fossils

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59
Q

Once a gene is cloned, complementary base pairing can be exploited to determine

A

The gene’s complete nucleotide sequence called DNA Sequencing

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60
Q

Define gene expression

A

Process by which DNA directs protein synthesis

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61
Q

Define transciption

A

The synthesis of RNA under the direction of DNA

Produces messenger RNA (mRNA)

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62
Q

Define Translation

A

actual synthesis of a polypeptide which occurs under the direction of mRNA
Occurs in ribosomes

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63
Q

How many nucleotide bases and amino acids are there in DNA

A

20 amino acids

4 nucleotide bases

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64
Q

What is a triplet code?

A

A series of nonoverlapping, 3 nucleotide words

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65
Q

The genetic code consists of __ codons and ___ stop codons

A

64

3

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66
Q

What are the 3 stop codons?

A

UAA
UGA
UAG

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67
Q

RNA synthesis is catalyzed by

A

RNA Polymerase

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68
Q

RNA polymerase pries ____ apart and hooks ____ together

A

DNA strands

RNA nucleotides

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69
Q

RNA synthesis follows the same base pairing rules as DNA except

A

uracil substitutes for thymine

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70
Q

What is the promoter

A

The DNA sequence where RNA polymerase attaches

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71
Q

What is the transcription Unit

A

The stretch of DNA that is transcribed

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72
Q

What happens during initiation

A

After RNA polymerase binds to the promoter, the DNA strands unwind and the polymerase initiates RNA synthesis at the start point on the template strand

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73
Q

What happens during elongation

A

Polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5’—>3’. During transcription, the DNA strands reform a double helix

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74
Q

What happens during termination

A

Eventuall the RNA transcript is released and the polymerase detaches from the DNA

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75
Q

During initiation, ___ signal the initiation of RNA synthesis

A

promoters

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76
Q

What is the function of the TA TA box

A

A promoter crucial in forming the initiation comples in eukaryotes

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77
Q

What is the function of transcription factors

A

To mediate the binding of RNA polymerase and initiation of transcription

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78
Q

What is the transcription initiation complex

A

Completed assembly of TF’s and RNA polymerase II bound to a promoter

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79
Q

Describe elongation of the RNA strand

A

As RNA polymerase moves along the DNA, it untwists the double helix 10-20 bases at a time

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80
Q

What end does RNA polymerase add nucleotides to?

A

The 3’ end as it continues along the double helix

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81
Q

Transcription progresses at a rate of ___ in eukaryotes

A

40 nucleotides/sec

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82
Q

True or false: A gene can be transcribed simultaneously by several RNA polymerases

A

True

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83
Q

True or false: The mechanisms of termination are not different in prokaryotes and eukaryotes

A

False

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84
Q

Describe termination in bacteria

A

The polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification

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85
Q

Describe termination in eukaryotes

A

RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10-35 nucleotides past this polyadenylation sequence

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86
Q

Enzymes in the eukaryotic nucleus modify____ before the genetic messages are dispatched to the cytoplasm

A

Pre-mRNA

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87
Q

During RNA processing:

A
  • both ends of primary RNA transcript are usually altered

- usually some interior parts of the molecule are cut out and the other parts spliced together

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88
Q

Describe the modification of the 5’ end of the pre-mRNA molecule

A

It receives a modified nucleotide cap

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89
Q

Describe the modified 3’ end

A

It gets a poly A tail

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90
Q

What are the functions of the modifications to the pre-mRNA molecule

A
  • Facilitate export of mRNA
  • Protect mRNA from hydrolytic enzymes
  • Help ribosomes attach to the 5’ end
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91
Q

True or false: Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions

A

True

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92
Q

What are introns

A

non coding regions, intervening sequences

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93
Q

What are exons

A

expressed, usually translated into amino acid sequences

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94
Q

RNA splicing removes ____ and joins ____ creating an mRNA molecule with a continuous coding sequence

A

introns, exons

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95
Q

What is the structure and function of spliceosomes

A

To recognize the splice states

consist of nuclear snRNPs and a variety of proteins

96
Q

What are ribozymes

A

catalytic RNA molecules that function as enzymes and can splice RNA

97
Q

The discovery of ribozymes rendered what belief obsolete

A

the belief that all biological catalysts were proteins

98
Q

Some genes encode more than one kind of ____ depending on which segments are treated as exons during RNA splicing

A

polypeptide

99
Q

What are the variations in polypeptide codings called

A

alternative RNA splicing

100
Q

Because of alternative splicing, the number of different proteins an organism can produce is much ____ than its number of genes

A

Greater

101
Q

Proteins have a modular architecture consisting of

A

discrete structural and functional regions called domains

102
Q

In many cases ___ code for the ___ in a protein

A

different exons

different domains

103
Q

A cell translates a ____ into the protein with the help of tRNA

A

mRNA message

104
Q

tRNA carry what two things, one on each end

A

specific amino acid, an anticodon

105
Q

The anticodon base pairs with a

A

complementary codon on mRNA

106
Q

A tRNA molecule consists of a single RNA strand that is only about ___ nucleotides long

A

8-

107
Q

A tRNA is ___ into one plane to reveal its base pairing

A

flattened

108
Q

Because of ____ tRNA twists and folds into a 3-D l shaped structure

A

Hydrogen bonds

109
Q

What two steps does accurate translation require

A

A correct match between tRNA and an amino acid done by the enzyme aminoacyl-tRNA synthetase

A correct match between the tRNA anticodon and mRNA codon

110
Q

Ribosomes facilitate ____ in protein synthesis

A

specific coupling of tRNA anticodons with mRNA codons

111
Q

What are the 3 binding sites for tRNA in a ribosome

A

A, P, and E sites

112
Q

What does the A site do

A

holds the tRNA that carries the next amino acid to be added to the chain

113
Q

What does the P site do?

A

Holds the tRNA that carries the growing polypeptide chain

114
Q

What does the E site do

A

Is the exit site, where discharged tRNA’s leave the ribosome

115
Q

When does a tRNA fit into a binding site

A

When its anticodon base pairs with an mRNA codon

116
Q

What does the P site hold

A

The tRNA attached to the growing polypeptide

117
Q

What does the A site hold

A

tRNA carrying the next amino acid to be added to the polypeptide chain

118
Q

The initiation xtage of translation brings together

A

mRNA
tRNA with the first amino acid
2 ribosomal subunits

119
Q

Termination of Translation occurs when

A

a sstop codon in the mRNA reaches the A site of the ribosome

120
Q

The A site accepts a protein called a

A

release factor

121
Q

What does the release factor do?

A

causes the addition of water molecule instead of an amino acid

122
Q

What does the reaction of the release factor cause

A

It releases the polypeptide and the translation assembly then comes apart

123
Q

A number of ribosomes can translate a single mRNA simultaneously, forming a

A

Polyribosome

124
Q

What do polyribosomes do?

A

Enable a cell to make many copies of a polypeptide very quickly

125
Q

During and after synthesis a polypeptide chain spontaneously ____ into its 3D shape

A

coils and folds

126
Q

True or false: often translation is not sufficient to make a functional protein

A

True

127
Q

Proteins may require ____ modifications

A

post translational

128
Q

Completed proteins are ____ in the cell

A

Targeted to specific sites

129
Q

Protein synthesis begins in the

A

cytosol

130
Q

Synthesis finishes in the ___ unless the polypeptide signals the ribosome to attach to the ER

A

cytosol

131
Q

Polypeptides destined for the ER or for secretion are marked by a

A

signal peptide

132
Q

A ____ binds to the signal peptide

A

Signal-recognition particle SRP

133
Q

What are mutations

A

Changes to the genetic material of a cell or virus

134
Q

Spontaneous mutations can occur during

A

DNA replication, recombination, or repair

135
Q

___ are physical or chemical agents that can cause mutations

A

Mutagens

136
Q

What are point mutations

A

chemical changes in just one base pair of a gene

137
Q

What do point mutations lead to

A

production of an abnormal protein

138
Q

Point mutations are divided into 2 general categories

A

Nucleotide pair substitutions

one or more nucleotide pair insertions or deletions

139
Q

What are silent mutations

A

Have no effect on the amino acid produced by a codon because of redundancy in the genetic code

140
Q

What are missense mutations

A

Still code for an amino acid but not necessarily the right amino acid

141
Q

What are nonsense mutations

A

Change an amino acid codon into a stop codon nearly always leading to a nonfunctional protein

142
Q

What does a nucleotide pair substitution do

A

replaces one nucleotide and its partner with another pair of nucleotides

143
Q

What are insertions and deletions

A

Additions or losses of nucleotide pairs in a gene

144
Q

Insertions and deletions have a ___ on the resulting protein more often than ___ do

A

disastrous

substitutions

145
Q

Insertions or deletion of nucleotides may alter the ___ producing a ____

A

reading frame

frameshift mutation

146
Q

Prokaryotic cells __ a nuclear envelope allowing translation to begin while transscription progresses

A

Lack

147
Q

In a eukaryotic cell: the nuclear envelope ____ and extensive RNA processing occurs in the ____

A

separates transcription from translation

nucleus

148
Q

A gene is

A

discrete unit of inheritance

specific nucleotide sequence in a chromosome

dna sequence that codes for a specific polypeptide chain

149
Q

Define gene

A

a region of DNA that can be expressed to produce a final functional product either a polypeptide or an RNA molecule

150
Q

DNA—-> RNA—>

A

protein

151
Q

Prokaryotes and eukaryotes alter gene expression in response to their

A

changing environment

152
Q

In multicellular eukaryotes, genexpression regulates ____ and is responbsible for differences in ____

A

development

cell types

153
Q

Bacteria regulate _____ gene expression

A

their own

154
Q

Why do bacteria regulate their own gene expression?

A

Natural selection has favored bacteria that produce only the products needed by that cell

155
Q

How do bacteria excersise this metabolic control?

A

Adjusting activity of metabolic enzymes

Regulating genes that encode metabolic enzymes

156
Q

Describe the regulation of tryptophan synthesis

A

An abundance of trp can inhibit the activity of the first enzyme in the pathway (feedback inhibition) a rapid response and repress expression of the genes for all the enzymes needed for the pathway, a longer-term response

157
Q

In bacteria, genes are often clustered into

A

operons

158
Q

What are operons made up of?

A

An operator (on/off switch)

a promoter

genes for metabolic enzymes

159
Q

An operon can be switched off by a protein called a

A

repressor

160
Q

Where does the repressor bind?

A

Only to the operon

161
Q

A repressible operon is one that is usually

A

On

162
Q

Binding of a repressor to the operator ____ transscription

A

Shuts off

163
Q

The ____ is a repressible operon

A

trp operon

164
Q

Repressible enzymes usually function in _____

A

anabolic pathways

165
Q

What is a corepressor

A

A small molecule that cooperates with a repressor to switch an operon off

166
Q

An inducible operon is one that is usually

A

Off

167
Q

A molecule (inducer) inactivates the repressor and _____ transcription

A

Turns on

168
Q

The lac operon is a ____ operon

A

Inducible

169
Q

Inducible enzymes usually function in _____

A

Catabolic pathways

170
Q

Regulation of the ______ involves negative control of genes because operons are switched off by the active form of the repressor

A

trp and lac operons

171
Q

Some operons are also subject to ____ through a stimulatory activator protein such as CAP

A

positive control

172
Q

The lac operon is under dual control: negative control by the lac ____ ; positive control by ____

A

repressor

CAP

173
Q

What is positive control

A

When glucose is scarce, the lac operon is activated by the binding of CAP

174
Q

When glucose levels increase, CAP ____ the lac operon turning it off

A

Detaches from

175
Q

A mutation that makes the regulatory gene of an inducible operon non functional would result in

A

Continuous transcription of the operon’s genes

176
Q

What are the two features of eukaryotic genomes that are a major information-processing challenge?

A
  1. typical euk. genome is much larger than that of a prokaryotic cell
  2. cell specialization limits the expression of many genes to specific cells
177
Q

Almost all the cells in an organism are genetically

A

Identical

178
Q

Differences between cell types result from

A

Differential gene expression

179
Q

What is differential gene expression

A

The expression of different genes by cells with the same genome

180
Q

Errors in gene expression can lead to

A

diseases (cancer)

181
Q

Muscle cells differ from nerve cells mainly because

A

They express different genes

182
Q

What is the most important control point of gene expression

A

Transcription

183
Q

Genes within hightly packed heterochromatin are usually _____

A

not expressed

184
Q

Chemical modifications to histones and DNA of chromatin influence both______ and ______

A

Chromatin structure

Gene expression

185
Q

What is histone acetylation

A

Acetyl groups are attached to a positively charged lysines in histone tails

186
Q

Histone acetylation seems to loosen chromatin structure thereby _____ the initiation of transcription

A

promoting

187
Q

What is DNA methylation

A

The addition of methyl groups to certain bases in DNA is accociated with reduced transcription in some species

188
Q

DNA methylation can cause ______ of genes in cellular differentiation

A

long term inactivation

189
Q

What is the epigenetic inheritance?

A

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

190
Q

Associtated with most eukaryotic genes are multiple ____

A

Control elements

191
Q

What are control elements

A

Segments of noncoding DNA that help regulate transcription by binding certain proteins

192
Q

To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called

A

Transcription factors

193
Q

What are proximal control elements

A

Located close to the promoter

194
Q

What are distal control elements

A

Groups of which are called enhancers, may be far away from a gene or even in an intron

195
Q

What is an activator

A

Specific transcription factor, a protein that binds to an enhancer and stimulates transcription of a gene

196
Q

What is repressor

A

Specific transcription facotr, inhibit expression of a gene

197
Q

Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a ___ and ____

A

promoter and control elements

198
Q

Transcription alone ____ account for gene expression

A

does not

199
Q

The lifespan of mRNA molecules in th cytoplasm is a key to determining

A

protein synthesis

200
Q

Eukaryotic mRNA is more ____ than prokaryotic mRNA

A

long lived

201
Q

What are differentiated cells?

A

All have a complete genome, and potential to express all of an organism’s genes

202
Q

What is a totipotent cell?

A

One that can generate a complete new organism

203
Q

Differentiated plant cells have the ability to develop into

A

A whole new organism

204
Q

What is nuclear transplantation

A

Involves replacing nuclei of egg cells with nuclei from differentiated cells

205
Q

In most transplantation studies only a ____ of cloned embryos developed normally to birth

A

small percentage

206
Q

Dolly’s death indicated her cells were not as healthy as those of a normal sheep, possibly reflecting

A

Incomplete programming of the original transplanted nucleus

207
Q

Many epigenetic changes such as acetylation of histones or methylation of DNA must be ______

A

Reversed

208
Q

Embryonic stem cells

A

Can give rise to specific types of differentiated

209
Q

Adult stem cells

A

Generate replacements for nondividing differentiated cells

210
Q

How are adult stem cells unlike embryonic stem cells?

A

They are partway along the road to differentiation

211
Q

_____ and placenta provide another source of stem cells

A

Umbillical cord blood

212
Q

Therapeutic cloning

A

Produces embryonic stem cells

213
Q

Human therapeutic cloning

A

Cloning of embryos for the production of embryonic stem cells for medical use

214
Q

Transformed cells from Skin cells to ES cells are called

A

iPS cells

215
Q

iPS cells can be used to

A

treat some diseases and to replace nonfunctional tissues

216
Q

Genes that normally regulate cell growth and division include

A

Genes for growth factors

Their receptors

Intracellular molecules of signaling pathways

217
Q

What are oncogenes

A

Cancer causing genes

218
Q

What are proto oncogenes

A

Normal cellular genes that code for proteins that stimulate normal cell growth and division

219
Q

What are tumor suppressor genes

A

Help prevent uncontrolled cell growth

220
Q

What are the functions of tumor supressor proteins

A

Repair damaged DNA

Control Cell adhesion

Inhibit cell cycle in the cell-signaling pathway

221
Q

Many human cancers involve mutations in

A

Ras (proto oncogene—>oncogene)

p53 (tumor suppressor)

222
Q

A virus ma promote cancer by:

A

donating an oncogene to the cell

disrupt a tumor suppressor gene

convert a proto oncogene to an oncogene

223
Q

Viruses seem to play a role in ___% of human cancer cases worldride

A

15

224
Q

What are genomics?

A

The study of whole sets of genes and their interactions

225
Q

What is bioinformatics

A

Application of computational methods to the storage and analysis of biological data

226
Q

What is the Human Genome Project

A

Mapping of the human genome

227
Q

Whole genome shotgun approach

A

skips genetic physical mapping and sequences random DNA fragments directly

228
Q

What was Griffith’s experiment

A

Injected pnemonia into mice and discovered a “transformed” strain of bacteria that was lethal. R and HS= +
S and R&HS= -

229
Q

What were the hershey chase experiments

A

Confirmed DNA was a genetic material, showed bacteriophages DNA enters the host bacterial cell, but most of their protein does not

230
Q

What was Chargoff’s experiments

A

Contributed to two rules to the double helix structure of DNA:

  1. # G= # C and #A=#T
  2. Relative amounts of G,C,A,T bases vary from one species to another
231
Q

What was franklin’s experiments

A

Did x-rays of DNA which led to discovery of DNA double helix

232
Q

Describe chromatin packing

A

DNA wraps around histones forming a nucleosome, the building block. Nucleosomes looped around till densly packed chromosomes.

233
Q

DNA polymerase vs RNA polymerase

A

DNA: Synthesizes DNA, require a primer, has a base T, double stranded, continuous till work done, faster, cannot initiate new strand

RNA: synthesizes RNA, does not require a primer, capable of initiating a new strand, has base U, single stranded, RNA polymerase continues to a stop cycle, slower

234
Q

Describe Trp Operon

A

repressible, negativ control, anabolic pathways, corepressor needed

235
Q

Describe lac operon

A

Inducible, negative control and positive control, catabolic pathways, inactive repressor and active repressor needed

BIOL 190 (4 decks)

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