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Biology 224 > EXAM 4 - Chapter 12, Gene Expression at Molecular Level > Flashcards

EXAM 4 - Chapter 12, Gene Expression at Molecular Level Flashcards

1
Q

In the early 1900’s…

A

Gregor Mendel’s work published in 1865 on genetics was rediscovered and finally understood

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2
Q

A British Physician in 1908 by the name of….was..

A

Archibald Garrod, who was studying the inheritance of disease Alkaptonuria

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3
Q

Garrod proposed…

A

a link between genes and the production of enzymes

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4
Q

By 1908 biochemists understood…

A

that metabolic pathways consisted of a series of enzymes, each one converting one chemical into another

they were linked series of reaction in which enzymes were involved

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5
Q

Garrod…

A

applied Mendel’s theory on genes to the pathway for the breakdown of Phenylalanine and the disease to Alkaptonuria

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6
Q

He made the connection that…

A

if the gene is broken/affected, enzyme cannot respond

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7
Q

Garrod knew that Alkaptonuria…

A

was inherited and proposed the disease was caused when an individual inherited recessive, defective genes from both parents

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8
Q

Garrod was the FIRST to…

A

link genes with enzyme production

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9
Q

Garrod termed the defective genes…and…

A

inborn errors of metabolism and began field of Human or Medical Genetics

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10
Q

He is considered the father of…

A

human or medical genetics

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11
Q

_________ saw Garrods work while….

A

Beadle and Tatum saw his work while wokring on the nutritional needs of a mold Neurospora

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12
Q

Beadle and Tatum exposed mold to…

A

x rays to produce mutations

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13
Q

After exposing molds to xrays they…

A

isolated a number of mutant strains which could not produce certain nutrients

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14
Q

They were working on…

A

inheritance or genetics of these mutant strains, in other words, could mutant pass mutant strains to next generation

they were intentionally trying to break parts in pathways

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15
Q

The metabolic pathway for ______ production was known to…

A

Arginine, be controlled by three enzymes

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16
Q

They had several strains of Neurospora which…

A

could not produce Arginine

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17
Q

Is starts with the precurser molecule then…

A

enzyme 1 produces OMITHINE -> enzyme 2 produces CITRULLIN -> enzyme 3 produces ARGININE

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18
Q

By seeing the products they could…

A

isolate which enzyme is blocked and broken and therefore which gene was mutated

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19
Q

They found that….

A

different strains had different mutations (in genes) which all prevented arginine synthesis, but at DIFFERENT STEPS in pathways

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20
Q

They (Beadle and Tatum) first proposed that…. which become known as…

A

each gene controlled a separate enzyme, “ONE GENE ONE ENZYME” theory

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21
Q

The one gene one enzyme theory…

A

has been modified over time because of a few exceptions that were found

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22
Q

Exception #1

A

Genes do control the production of enzymes, but not all genes code for enzymes

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23
Q

Exception #2

A

Not all enzymes consist of a single polypeptide

Some multimeric enzymes are formed by the product of multiple genes, each producing a separate polypeptide which combine to form mature/complete enzyme

One Gene - One Polypeptide

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24
Q

Exception #3

A

Some genes are alternatively spliced to produce multiple proteins, or versions of a proteins

so some genes produce multiple proteins

This is why 20,000 genes code for about 2 million proteins, because they can be spliced

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25
Q

The Central Dogma of biology:

A

traces the path of information flow within cells

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26
Q

Cycle is…

A

DNA (transcription) -> mRNA (translation) -> polypeptide (protein)

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27
Q

______ comes first, before _____

A

transcription, before translation

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28
Q

In transcription only..

A

one half will be copied

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29
Q

It goes from double helix to..

A

single mRNA

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30
Q

Transcription is also called

A

DNA-Directed RNA Synthesis

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31
Q

The one molecule/enzyme concerned with Transcription is

A

RNA Polymerase

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32
Q

The promoter is…

A

The region of gene where RNA Polymerase attached to transcribe the gene

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33
Q

Gene is the…

A

region of DNA linked to production of polypeptides

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34
Q

Transcription occurs on…

A

the template strand only

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35
Q

Transcription occurs on..

A

one gene only (one at a time)

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36
Q

First RNA Polymerase…

A

attached to DNA at promoter and denatures (unwinds) DNA

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37
Q

In Eukaryotes…

A

a variety of proteins are involved in the attachment process

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38
Q

These variety of proteins are called…

A

Initiation and Transcription factors

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39
Q

RNA Polymerase…

A

unwinds then winds it back

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40
Q

The second step is _____ ….then the enzyme _______…

A

Ribonucleoside Triphosphates (ribose sugar and 3 phosphates) line up opposite DNA template strand and then RNA polymerase connects them together in the 5 to 3 direction

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41
Q

Template strand is running….so…

A

3 to 5, so built in 5 to 3, adding new nucleotides at the 3 end

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42
Q

Ribonucleoside triphosphates are…

A

precursors for transcription

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43
Q

What happens to ribonucleoside triphosphate is…

A

removal of pyrophosphate (2 phosphates) and polymerization of nucleotide to 3 end of the growing RNA chain

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44
Q

Three types of RNA are

A

mRNA, rRNA, tRNA

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45
Q

mRNA…

A

carries info (message) from DNA to ribosome

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46
Q

rRNA…

A

they are a component of ribosomes

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47
Q

tRNA…

A

“escorts” (i.e. transfers) amino acids to the ribosomes

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48
Q

All three of these…*

A

are all TRANSCRIBED in the same way

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49
Q

_______ occurs in a variety of different ways in RNAs

A

termination

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50
Q

The final product…..is not…

A

Primary Transcript (Pre-RNA) is NOT the final product

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51
Q

So the main three steps of Transcription are…

A
  • INITIATION - (RNA Polymerase binds to promoter and starts to unwind DNA strands
  • ELONGATION - Ribonucleoside Triphosphates line up opposite DNA template strand and RNA Polymerase connects them together in 5 to 3
  • TERMINATION - final product (Primary Transcript/pre-RNA) is not final product
52
Q

Within a single chromosome..

A

different strands of the double stranded DNA form the template strand

(Can be bottom or top strand)

53
Q

RNAs are all…

A

post-transcriptionally modified in a variety of ways

54
Q

There are ____ types of modification

A

8 TYPES

55
Q

The 8 types are…

A

1.) Addition of 5’ 7-methyl Guanosine Cap
2.) Addition of a Poly-A Tail
3.) Splicing
4.) Pre-RNA may be cut into more than 1 RNA
5.) Removal of nucleotides from 5/3 end
6.) Addition of CCA to 3’ end
7.) Chemical modification of bases
8.) RNA Editing

56
Q

1.) Addition of 5’ 7-methyl Guanosine Cap occurs in…and its function is…

A

mRNA ONLY

Allows mRNA to exit nucleus and bind to ribosome

57
Q

2.) Addition of Poly-A tail occurs in…function..

A

mRNA ONLY

Allow mRNA to be exported from nucleus and persist in cytosol

58
Q

3.) There are…

A

two types of splicing

59
Q

3.) Splicing A is

A

removal of introns (intervening regions) can occur to ANY TYPE OF RNA by action of SPLYCEOSOMES which is a complex of RNA and proteins

60
Q

The exon…

A

is expressive, this is the part than turns into a protein

61
Q

The intron..

A

is intervening, non-exon region

62
Q

3.) Result of Splicing A is…

A

removal of introns results in RNA Transcript much shorter than corresponding gene (DNA)

63
Q

3.) Spicing B is…

A

Since not all exons always included in final mRNA

If different combinations of exons are used to produce different RNAs, different proteins are produced in different cells or tissues FROM THE SAME GENE

so some exons spliced out, different number of exons = different everything

64
Q

3.) ______always comes before _____

A

intron splicing…alternative splicing

65
Q

4.) The Pre-RNA may be cut into more than one RNA occurs in…its function…

A

ALL RNAs, but ALWAYS occurs in rRNA

After introns cut out, can be left with separate pieces, that why it can be so diverse

66
Q

5.) Removal of nucleotides from 5 and/or 3 end occurs in….and…

A

ALL RNAs

just simply removing nucleotides

67
Q

6.) The addition of CCA to 3 end occurs in…and..

A

ONLY tRNA

if it doesnt already have a cap it adds, the CCA is an amino acid attachment site

68
Q

7.) Chemical modification of bases occurs in…and…

A

tRNA ONLY

Reactions happening on pre-RNA to change bases, change into weird bases that can affect other things, shown as weird shapes or different letters other than the normal A,C,G,T,U

69
Q

8.) RNA Editing is…

A

process by which one or more nucleotides in an RNA can be changed, added, or removed

70
Q

8.) Two kinds of editing are

A

Substitution Editing, Insertion/Deletion Editing

71
Q

8.) In substitution editing…

A

one nucleotide is substituted for another

enzymes modify or change one base into another

Cytidine deaminase converts C in RNA to U

Adenosine deaminase converts A to I, which ribosomes translates as a G

72
Q

8.) In insertion/deletion editing…

A

uses guide RNAs produced by separate genes to bind and indentify the RNA molecles where a nucleotide will be added or removed

73
Q

8.) RNA editing…(2)

A

has been found in all three major types of RNA

Error in RNA editing can cause mental disorders such as schozophrenia

74
Q

MEMORIZE ONLINE TABLE

A

MEMORIZE ONLINE TABLE

75
Q

Translation is…

A

the second step, comes after transcription

76
Q

The 3 letters codes made after transcription called…

A

codons

77
Q

The bottom amino acids made after translation have…

A

anticodons on tail that match with the codon

78
Q

_________ are used for translation..

A

all three RNAs (mRNA, rRNA, tRNA)

79
Q

mRNA in translation…

A

carries the information

80
Q

tRNA in translation…

A

brings the amino acids (transfers from cytoplasm to ribosome)

81
Q

rRNA in translation…

A

is a component of ribosomes

82
Q

other enzymes used during translation are ________ and the purpose of them is…

A

Aminoacyl-tRNA Synthetase….are also used to “load” amino acids onto corresponding tRNA molecules

Makes sure the right amino acids get on/become the right RNA

83
Q

Triplet Code:

A

3 bases make up a codon

84
Q

A codon is…

A

a sequence of 3 bases in mRNA which code for an amino acid

85
Q

Transfer RNA (tRNA)…

A

speak both nucleotide and amino acid language

86
Q

The start codon is…and…

A

AUG, it is initiation/start codon, it marks the point where translation begins

87
Q

The codons that stop translation…

A

are called the terminators, which stop translation rather than insert an amino acid

They are UAA, UAG, UGA

88
Q

The genetic code is…since…

A

degenerate (redundant) since most amino acids are represented by more than one codon

89
Q

2D shape of tRNA is…

A

3 leaf clover

90
Q

The stem of 2D shape is…

A

the acceptor stem - amino acid is attached to the 3’ end of tRNA

connected with H bonds

91
Q

3D shape of tRNA is

A

L-shaped, anticodon on one end and then the 3’ single stranded region on the other end (acceptor stem)

92
Q

The ______ is across from the acceptor stem on tRNA and it…

A

anticodon loop, pairs with the codon on mRNA

93
Q

Aminoacyl-tRNA Synthetases….

A

loads proper amino acid onto tRNA using energy from ATP

94
Q

First, Aminoacyl-tRNA Synthetases…

A

binds ATP and the specific amino acid recognized by that activating enzyme

the energy from ATP is transferred to amino acid as AMP (breaks off pyrophosphate to make AMP, and AMP holds onto amino acid)

95
Q

Then….

A

the specific tRNA recognized by the synthetase is bound and the amino acid is transferred from the AMP to the tRNA

AMP is there to give energy and help hold things, once transferred, AMP is released

96
Q

Finally…

A

the tRNA, charged with the appropriate amino acid is released, as is the enzyme (in an unaltered state) and the AMP

enzymes are not changed during course of reactions

97
Q

This whole process above is how…

A

join together the correct amino acid with tRNA with the correct codon

98
Q

This whole process happens in…

A

cytoplasm, or rough ER, wherever there are ribosomes

99
Q

Structure of ribosomes

A

large and small subunits each constrcuted of one or more rRNA and 20-50 proteins

100
Q

Sedimentation rates…

A

based on mass, density, and shape, CANT BE ADDED SIMPLY

101
Q

The ribosome subunits…

A

can be apart, but during translation they come together during process

102
Q

Eukaryotic ribosomes are…

A

larger

103
Q

Self assembly in ribosomes mean…

A

the rRNAs and proteins come together naturally, enzymes and charges involved in building small and large subunits

104
Q

The parts of the ribosome…

A

3 positions to hold tRNAs:
- A site - holds new RNA **(EXCEPT FOR FIRST, THE FIRST GOES INTO THE SECOND P SITE)
- P site - hold tRNA with polypeptide chain
- E site - holds empty tRNA to exit the ribosome

large subunit on top, small on bottom

A site, anticodon matches with codon right at that moment

P site, holds what has been built so far

RIGHT TO LEFT, A-P-E

105
Q

RNA Directed Polypeptide synthesis (Translation) step #1:

A

Small ribosomal subunit attaches to 5’ end of mRNA (not yet connected to large subunit)

ribosomal binding sequence matches with 3 codons on the ribosome, this is so they can bind

106
Q

RNA Directed Polypeptide synthesis (Translation) step #2:

A

First tRNA attaches to small subunit P site

107
Q

RNA Directed Polypeptide synthesis (Translation) step #3:

A

Large ribosomal subunit attaches to form the complete ribosome

108
Q

RNA Directed Polypeptide synthesis (Translation) step #4:

A

One first aminoacyl-tRNA has attached to P-site, second aminoacyl-tRNA attaches at A-site of ribosome, matching the 2nd codon on the mRNA

matches codon of mRNA to anticodon on tRNA

the mRNA-ribosome-tRNA complex positions the amino acids so they are adjacent to one another

109
Q

RNA Directed Polypeptide synthesis (Translation) step #5:

A

Peptidyl Transferase catalyzes a peptide bond between first two amino acids by transferring (backwards) the 1st amino acid from the 1st tRNA to the 2ns amino acid on the 2ns tRNA

110
Q

RNA Directed Polypeptide synthesis (Translation) step #6:

A

Translocation moves the ribosome toward the 3’ end, to the right, to the next codon with the release of the 1st tRNA from the exit (E) site

first amino acid is alreayd attached to the 2nd, both are attached to the second tRNA (in the P site)

mRNA is relatively stable, but ribosome moves (5 to 3)

when ribosome moves to the right, tRNA is moved down from A to P to E

111
Q

RNA Directed Polypeptide synthesis (Translation) step #7:

A

The 3rd aminoacyl-tRNA anitocodn attaches to the A-site of the ribosome accoding to the 3rd mRNA codon

112
Q

RNA Directed Polypeptide synthesis (Translation) step #8:

A

Peptidyl transferase catalyzes the next peptide bond, ribosome translocates in the 3’ direction once more

tRNA in P site passes all amino aids to the tRNA in A site, then moves out and another one can come in

113
Q

RNA Directed Polypeptide synthesis (Translation) step #9:

A

Repeat steps 6-8

114
Q

anticodon is on…codon is on..

A

ANTICODON on tRNA

CODON on mRNA

115
Q

RNA Directed Polypeptide synthesis (Translation) step #10:

A

Upon reaching a termination (stop) codon, a releasing protein attaches to the A-site instead of an aminoacyl tRNA

releasing facotr binds to A-site and causes release of last tRNA and polypeptide

Two ribosomal subunits are released from the mRNA and are recycled to same the same or another mRNA to translate

116
Q

mRNA is translated my…

A

numerous ribosomes AT THE SAME TIME, once first ribosome clears the 5’ end, the next attaches

all translating different parts at same time

117
Q

A Polysome is…

A

one mRNA and all the multiple ribosomes translating it at the same time

118
Q

Once synthesized…

A

(or during synthesis), proteins with transit sequences may be exported to various organelles

119
Q

Post-Translational Modifications of proteins can me…(3 types)

A
  • proteolysis
  • glycosylation
  • phosphorylation
120
Q

Proteolysis

A

cleaving or cutting polypeptide allow the fragments to fold into different shapes

121
Q

Glycosylation

A

add sugars, important for targeting and recognition

122
Q

Phosphorylation

A

added phosphate groups alter the shape of the protein

123
Q

Example of glycosylation is

A

Glycoprotein synthesis

124
Q

Role of ER in Glycoprotein synthesis…

A

signal sequence - causes the ribsosome to be transported to the ER (co-translational sorting)

125
Q

Once completed…

A

the eventual glycoprotein is released into lumen of ER and the ribosomal subunits are released to the cytoplasm

Biology 224 (18 decks)

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