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Intro to Molecular and Cellular Biology > Molec and Cell 5 > Flashcards

Molec and Cell 5 Flashcards

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1
Q

The role of DNA in heredity was first discovered by studying what?

A

bacteria and the viruses that infect them

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2
Q

Frederick Griffith

A

1928: worked with two strains of a bacterium, one pathogenic and one harmless

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3
Q

transformation

A

a change in genotype and phenotype due to assimilation of foreign DNA

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4
Q

Griffith’s experimental process

A

When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic

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5
Q

Oswald Avery, Maclyn McCarty, and Colin MacLeod

A

1944: announced that the transforming substance was DNA based on experimental evidence that only DNA worked in transforming harmless bacteria into pathogenic bacteria

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6
Q

bacteriophages (or phages)

A

viruses that infect bacteria

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7
Q

Alfred Hershey and Martha Chase

A

1952: experiments showing that DNA is the genetic material of a phage known as T2

they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection

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8
Q

Erwin Chargaff

A

1950: DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group

DNA composition varies from one species to the next

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9
Q

Chargaff’s rules

A

that in any species there is an equal number of A and T bases, and an equal number of G and C bases

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10
Q

Maurice Wilkins and Rosalind Franklin

A

X-ray crystallography to study molecular structure

Franklin produced a picture of the DNA molecule using this technique

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11
Q

Franklin’s X-ray crystallographic images of DNA did what?

A

enabled Watson to deduce that DNA was helical

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12
Q

DNA shape and X-ray advantage

A

The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases

The width suggested that the DNA molecule was made up of two strands, forming a double helix

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13
Q

Franklin’s conclusion

A

two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior

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14
Q

Watson and Crick

A

Determined pairing a purine with a pyrimidine resulted in a uniform width consistent with the X-ray

adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C) (Consistent with Chargaff’s rule)

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15
Q

Watson and Crick also suggested what?

A

that the specific base pairing suggested a possible copying mechanism for genetic material

Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication

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16
Q

Watson and Crick’s semiconservative model of replication

A

when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand

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17
Q

Matthew Meselson and Franklin Stahl

A

supported the semiconservative model

They labeled the nucleotides of the old strands with a heavy isotope of nitrogen, while any new nucleotides were labeled with a lighter isotope

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18
Q

origins of replication

A

where the two DNA strands are separated, opening up a replication “bubble”

A eukaryotic chromosome may have hundreds or even thousands of origins of replication

Replication proceeds in both directions from each origin, until the entire molecule is copied

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19
Q

replication fork

A

At the end of each replication bubble is a Y-shaped region where new DNA strands are elongating

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20
Q

Helicases

A

enzymes that untwist the double helix at the replication forks

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21
Q

Single-strand binding protein

A

binds to and stabilizes single-stranded DNA until it can be used as a template

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22
Q

Topoisomerase

A

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

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23
Q

Where are nucleotides added to DNA elongation?

A

they can only add nucleotides to the 3’ end

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24
Q

primer

A

short RNA initial nucleotide strand for DNA elongation

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25
Q

primase

A

An enzyme that can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template

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26
Q

DNA polymerases

A

catalyze the elongation of new DNA at a replication fork

Most DNA polymerases require a primer and a DNA template strand

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27
Q

Rate of elongation

A

The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells

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28
Q

Where DNA begins elongation?

A

a new DNA strand can elongate only in the 5’ to 3’ direction

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29
Q

leading strand

A

where the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork

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30
Q

lagging strand

A

The opposite strand of the leading strand which is replicated

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31
Q

Elongation of the leading strand

A

synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase

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32
Q

DNA ligase

A

Joins the 3’ end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand

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33
Q

“DNA replication machine”

A

The proteins that participate in DNA replication form a large complex

probably stationary during the replication process

Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules

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34
Q

DNA polymerases second function

A

proofread newly made DNA, replacing any incorrect nucleotides

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35
Q

Proofreading and Repairing DNA

A

In mismatch repair of DNA, repair enzymes correct errors in base pairing

DNA can be damaged by chemicals, radioactive emissions, X-rays, UV light, and certain molecules (in cigarette smoke for example)

In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA

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36
Q

Replicating the Ends of DNA Molecules

A

The usual replication machinery provides no way to complete the 5’ ends, so repeated rounds of replication produce shorter DNA molecules

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37
Q

telomeres

A

Eukaryotic chromosomal DNA molecules have at their ends nucleotide sequences

Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules

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38
Q

telomerase

A

catalyzes the lengthening of telomeres in germ cells

If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce

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39
Q

Telomere potential focus

A

The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions

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40
Q

Proteins are the links between what?

A

genotype and phenotype

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41
Q

Gene expression

A

process by which DNA directs protein synthesis, includes two stages: transcription and translation

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42
Q

Archibald Garrod

A

1902: Suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions

He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme

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43
Q

George Beadle and Edward Tatum

A

exposed bread mold to X-rays, creating mutants that were unable to survive on minimal media

one gene–one enzyme/protein/polypeptide hypothesis

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44
Q

Adrian Srb and Norman Horowitz

A

Identified three classes of arginine-deficient mutants

Each lacked a different enzyme necessary for synthesizing arginine

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45
Q

Point of RNA

A

RNA is the bridge between genes and protein synthesis

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46
Q

Transcription

A

the synthesis of RNA using information in DNA

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47
Q

Translation

A

the synthesis of a polypeptide, using information in the mRNA

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48
Q

Ribosomes

A

the sites of translation

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49
Q

Transcription and translation in prokaryotes.

A

translation of mRNA can begin before transcription has finished

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50
Q

Transcription and translation in eukaryotes.

A

the nuclear envelope separates transcription from translation

Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA

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51
Q

primary transcript

A

the initial RNA transcript from any gene prior to processing

The central dogma is the concept that cells are governed by a cellular chain of command: DNA → RNA → protein

52
Q

The Genetic Code

A

20 amino acids, but there are only four nucleotide bases in DNA

53
Q

triplet code

A

a series of nonoverlapping, three-nucleotide words

These words are then translated into a chain of amino acids, forming a polypeptide

54
Q

the template strand

A

One of the two DNA strands provides a template for ordering the sequence of complementary nucleotides in an RNA transcript. The template strand is always the same strand for a given gene

However, further along the chromosome, the opposite strand may be the template strand for a different gene

55
Q

codons reading order

A

the mRNA base triplets are read in the 5′ → 3′ direction

56
Q

coding strand

A

the non-template strand because the nucleotides of this strand are identical to the codons, except that T is present in the DNA in place of U in the RNA

57
Q

64 codons

A

deciphered by the mid-1960s

61 code for amino acids; 3 triplets are “stop” signals to end translation

Codons must be read in the correct reading frame (correct groupings) in order

58
Q

Evolution of the Genetic Code

A

The genetic code is nearly universal, shared by the simplest bacteria and the most complex animals

Genes can be transcribed and translated after being transplanted from one species to another

59
Q

the first stage of gene expression

A

Transcription

60
Q

RNA synthesis is catalyzed by what?

A

RNA polymerase

61
Q

RNA polymerase

A

pries the DNA strands apart and joins together the RNA nucleotides

does not need primer

62
Q

promoter

A

The DNA sequence where RNA polymerase attaches

63
Q

terminator

A

In bacteria, the sequence signaling the end of transcription

64
Q

transcription unit

A

The stretch of DNA that is transcribed

65
Q

The three stages of transcription:

A

Initiation
Elongation
Termination

66
Q

Initiation

A

Promoters signal the transcription start point and usually extend several dozen nucleotide pairs upstream of the start point

67
Q

Transcription factors

A

help guide the binding of RNA polymerase and the initiation of transcription

68
Q

transcription initiation complex

A

The completed assembly of transcription factors and RNA polymerase II bound to a promoter

69
Q

TATA box

A

promotor crucial in forming the initiation complex in eukaryotes

70
Q

Elongation

A

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

Nucleotides are added to the 3′ end of the growing RNA molecule

Transcription progresses at a rate of 40 nucleotides per second in eukaryotes

A gene can be transcribed simultaneously by several RNA polymerases

71
Q

Termination in bacteria

A

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

72
Q

Termination in eukaryotes

A

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

73
Q

After transcription in eukaryotes

A

Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm

74
Q

RNA processing

A

both ends of the primary transcript are altered

Also, in most cases, certain interior sections of the molecule are cut out and the remaining parts spliced together

75
Q

Each end of a pre-mRNA molecule is modified in a particular way

A

The 5′ end receives a modified nucleotide 5′ cap

The 3′ end gets a poly-A tail

76
Q

Purpose of pre-mRNA molecules caps

A

They seem to facilitate the export of mRNA to the cytoplasm

They protect mRNA from hydrolytic enzymes

They help ribosomes attach to the 5′ end

77
Q

RNA splicing

A

Removing eukaryotic genes and their RNA transcripts that are long noncoding stretches of nucleotides that lie between coding regions

78
Q

introns

A

The noncoding segments in a gene are called intervening sequences

79
Q

exons

A

coding sections that are eventually expressed, usually translated into amino acid sequences

80
Q

The removal of introns is accomplished by what?

A

Spliceosomes that consist of a variety of proteins and several small RNAs that recognize the splice sites

The RNAs of the spliceosome also catalyze the splicing reaction

81
Q

Ribozymes

A

catalytic RNA molecules that function as enzymes and can splice RNA

82
Q

Three properties of RNA that enable Ribozymes to function as an enzyme

A

It can form a three-dimensional structure because of its ability to base-pair with itself

Some bases in RNA contain functional groups that may participate in catalysis

RNA may hydrogen-bond with other nucleic acid molecules

83
Q

alternative RNA splicing

A

Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing

84
Q

domains

A

Proteins often have a modular architecture consisting of discrete regions

different exons code for the different domains in a protein

85
Q

Exon shuffling

A

may result in the evolution of new proteins by mixing and matching exons between different genes

86
Q

A cell translates an mRNA message into protein with the help of what?

A

transfer RNA (tRNA)

tRNAs transfer amino acids to the growing polypeptide in a ribosome

87
Q

tRNA specificity

A

enables translation of a given mRNA codon into a certain amino acid

88
Q

tRNA 2-D structure

A

Each carries a specific amino acid on one end

Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA

consists of a single RNA strand that is only about 80 nucleotides long

89
Q

tRNA 3-D structure

A

twists and folds into a three-dimensional molecule

tRNA is roughly L-shaped with the 5′ and 3′ ends both located near one end of the structure

The protruding 3′ end acts as an attachment site for an amino acid

90
Q

Accurate translation requires two instances of molecular recognition

A

First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase

Second: a correct match between the tRNA anticodon and an mRNA codon

91
Q

wobble

A

Flexible pairing at the third base of a codon allows some tRNAs to bind to more than one codon

92
Q

ribosomal RNAs (rRNAs)

A

two ribosomal subunits (large and small) are made of proteins

93
Q

ribosome has three binding sites for tRNA

A

P site
A site
E site

94
Q

P site

A

holds the tRNA that carries the growing polypeptide chain

95
Q

A site

A

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

96
Q

E site

A

the exit site, where discharged tRNAs leave the ribosome

97
Q

The three stages of translation:

A

Initiation
Elongation
Termination

98
Q

Translation Initiation

A

When the small ribosomal subunit binds with mRNA and a special initiator tRNA

The initiator tRNA carries the amino acid methionine

Then the small subunit moves along the mRNA until it reaches the start codon (AUG)

Proteins called initiation factors bring in the large subunit that completes the translation initiation complex

99
Q

Translation Elongation

A

amino acids are added one by one to the C-terminus of the growing chain
Each addition involves proteins called elongation factors

Translation proceeds along the mRNA in a 5′ → 3′ direction
The ribosome and mRNA move relative to each other, codon by codon

100
Q

Translation Termination

A

Elongation continues until a stop codon in the mRNA reaches the A site
The A site accepts a protein called a release factor
The release factor causes the addition of a water molecule instead of an amino acid
This reaction releases the polypeptide, and the translation assembly comes apart

101
Q

Translation Elongation 3 Steps

A

codon recognition, peptide bond formation, and translocation

Energy expenditure occurs in the first and third steps

Empty tRNAs released from the E site return to the cytoplasm, where they will be reloaded with the appropriate amino acid

102
Q

Often translation is not sufficient to make a functional protein so what happens?

A

Polypeptide chains are modified after translation or targeted to specific sites in the cell

103
Q

Post-Translational Modifications

A

a polypeptide chain begins to coil and fold spontaneously into a specific shape: a three-dimensional molecule with secondary and tertiary structure

104
Q

Two populations of ribosomes are evident in cells

A

Free ribosomes mostly synthesize proteins that function in the cytosol

Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell

Ribosomes are identical and can switch from free to bound

105
Q

Polypeptide synthesis always begins where?

A

in the cytosol

106
Q

Synthesis finishes in the cytosol unless what?

A

unless the polypeptide signals the ribosome to attach to the ER

107
Q

signal peptide

A

Polypeptides destined for the ER or for secretion are marked by this.

It is a sequence of about 20 amino acids at or near the leading end of the polypeptide

108
Q

signal-recognition particle (SRP)

A

binds to the signal peptide

The SRP escorts the ribosome to a receptor protein built into the ER membrane

The signal peptide is removed by an enzyme

109
Q

polyribosome (or polysome)

A

Multiple ribosomes can translate a single mRNA simultaneously

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

110
Q

coupling transcription and translation

A

bacterial cell streamlined process

newly made protein can quickly diffuse to its site of function

111
Q

Mutations

A

changes in the genetic information of a cell

112
Q

Point mutations

A

changes in just one nucleotide pair of a gene

113
Q

change of a single nucleotide a DNA template strand

A

can lead to the production of an abnormal protein

114
Q

Point mutations within a gene can be divided into two general categories:

A

Single nucleotide-pair substitutions
Nucleotide-pair insertions or deletions

115
Q

nucleotide-pair substitution

A

replaces one nucleotide and its partner with another pair of nucleotides

116
Q

Three types of nucleotide-pair substitution

A

Silent mutations
Missense mutations
Nonsense mutations

117
Q

Silent mutations

A

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

118
Q

Missense mutations

A

still code for an amino acid, but not the correct amino acid

119
Q

Nonsense mutations

A

Nonsense mutations change an amino acid codon into a stop codon; most lead to a nonfunctional protein

120
Q

Insertions and deletions

A

additions or losses of nucleotide pairs in a gene

These mutations have a disastrous effect on the resulting protein more often than substitutions do

121
Q

frameshift mutation

A

may alter the reading frame which could affect how the gene is expressed

122
Q

Spontaneous mutations

A

can occur during errors in DNA replication or recombination

123
Q

Mutagens

A

physical or chemical agents that can cause mutations

Chemical mutagens fall into a variety of categories

Most carcinogens (cancer-causing chemicals) are mutagens, and most mutagens are carcinogenic

124
Q

CRISPR-Cas9

A

In bacteria, the protein Cas9 acts together with a guide RNA to help defend bacteria from viral infection

Cas9 protein will cut any sequence to which it is targeted

Scientists can introduce a Cas9–guide RNA complex into a cell they wish to alter

The guide RNA is engineered to target a gene

Cas9 cuts both strands of the targeted gene

The broken ends trigger a DNA repair system

The repair enzymes remove or add some random nucleotides while joining the broken ends

This is a way for researchers to “knock out” (disable) a given gene, to study what the gene does in an organism

They can introduce a template with a normal (functional) copy of the gene to be corrected

In this way, the CRISPR-Cas9 system edits the defective gene and corrects it

125
Q

gene editing

A

altering genes in a specific way

Intro to Molecular and Cellular Biology (5 decks)

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