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BIOL101 > Ch. 17-18 > Flashcards

Ch. 17-18 Flashcards

Gene Expression, Mitosis and Meiosis

1
Q

gene expression

A

the process by which information encoded in DNA directs the synthesis of proteins, or RNAs that are not translated into proteins and instead function as RNAs

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2
Q

transcription

A

-the synthesis of RNA using a DNA template
-DNA is transcribed into RNA (same language)
-it starts and stops at specific sequences

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3
Q

translation

A

-the synthesis of a polypeptide using the genetic information encoded in an mRNA molecule
-RNA is translated into protein (different language; change of language from nucleotides to amino acids)

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4
Q

what bases does DNA use?

A

A, G, C, and T

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5
Q

what bases does RNA use?

A

A, G, C and U
(an RNA ‘U’ pairs with DNA ‘A’ during transcription)

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6
Q

what is the function of DNA in protein coding genes?

A

for protein coding genes, DNA serves as a template to produce a single strand messenger RNA (mRNA)

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7
Q

what does mRNA carry, and where to?

A

mRNA carries the genetic information to the ribosome

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8
Q

what occurs in the ribosome after mRNA carries the genetic information there?

A

the information is translated into proteins

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9
Q

how is transcription and translation different in bacteria?

A

in bacteria, transcription and translation are not separated into separate compartments, and they can occur simultaneously

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10
Q

where do eukaryotes export mRNA to and from, for translation?

A

eukaryotes must export the mRNA from the nucleus to cytoplasm for translation

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11
Q

pre-mRNA

A

-before the mRNA leaves the nucleus it starts out as pre-mRNA
-the pre-mRNA has certain regions removed, a cap is added to the 5’ end and additional ‘A’ nucleotides added to the 3’ end before it leaves the nucleus as a mature mRNA

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12
Q

primary transcript

A

the initial RNA transcript from any gene before it is processed; also applies to RNAs that are not translated into protein

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13
Q

template strand of DNA

A

-used to generate the mRNA
-during transcription the two strands of DNA separate, and only one of the two strands is used as the template for the mRNA
-for any gene, the same strand always serves as the template strand
-different genes on the same chromosome can use opposite strands of DNA as the template strand
-the mRNA is synthesized in the 5’ to 3’ direction, and it is antiparallel to the template strand

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14
Q

coding strand

A

-aka the nontemplate strand
-the nontemplate strand has the same nucleotide sequence as the mRNA, except that T is substituted for U

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15
Q

The Genetic Code

A

-there are only 4 bases in DNA and multiple nucleotides must be combined together to specify the different amino acids

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16
Q

triplet code

A

a genetic information system in which a set of three-nucleotide-long words specify the amino acids for polypeptide chains

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17
Q

codons

A

the mRNA nucleotide triplets

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18
Q

how was the genetic code determined?

A

by making synthetic mRNAs and combining them with ribosomes, amino acids, and other components in a test tube
-ex: an RNA molecule with only U (UUUUUUUUUUUU) would produce a polypeptide with only phenylalanine (PhePhePhePhe)

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19
Q

characteristics of the genetic code

A

-the genetic code is REDUNDANT, more than one codon is used for most amino acids
-the genetic code is NOT AMBIGUOUS, one codon codes for only one amino acid

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20
Q

AUG codon

A

-codes for methionine
-the start signal for translation

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21
Q

UAA, UAG, and UGA codons

A

-do not code for an amino acid
-they are the stop signals for translation

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22
Q

reading frame

A

-each mRNA will have three possible frames that can be translated into amino acids
-only one strand is used, called the reading frame
-generally begins from the first AUG in the mRNA sequence

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23
Q

the genetic code is universal

A

-the genetic code applies to all organisms
-same code used in bacteria, plants, and people
-implies that all life on earth had a common ancestor
-a useful feature for molecular biologists

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24
Q

RNA polymerase

A

-the enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand
-does not need a primer, unlike DNA polymerase
-works in a 5’ to 3’ direction
-unwinds the DNA as it goes to expose the template strand

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25
Q

promoter

A

the site where RNA polymerase attaches and begins transcription

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26
Q

terminator

A

a specific sequence in bacteria that signals the end of transcription (termination is different in eukaryotes)

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27
Q

transcription unit

A

the stretch of DNA that is transcribed into RNA

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28
Q

the 3 phases of producing an RNA:

A
  1. initiation
  2. elongation
  3. termination
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29
Q

downstream

A

the direction of transcription (the termination sequence is downstream from the promoter)

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30
Q

upstream

A

the opposite direction of transcription

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31
Q

initiation of transcription

A

-in bacteria, RNA polymerase binds to a specific sequence in the promoter

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32
Q

transcription factors

A

-other proteins in eukaryotes that bind that bind to the DNA first
-typically have a DNA binding domain and a protein interaction domain

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33
Q

general transcription factors

A

-a protein that binds to DNA to initiate the transcription of genetic information into messenger RNA, for eukaryotes
-poly A signal sequence

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34
Q

sigma factor

A

-a protein in bacteria/prokaryotes that is necessary for the start of transcription
-GC rich terminator sequence

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35
Q

transcription initiation complex

A

when RNA polymerase forms a complex with the transcription factors

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36
Q

RNA polymerase II

A

used to transcribe mRNA (eukaryotes have three RNA polymerases)

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37
Q

TATA box

A

-the many promoters in eukaryotes that contain a specific sequence TATAAAA, to which transcription factors bind in order to establish the transcription initiation complex

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38
Q

Pribnow box

A

-a six-nucleotide sequence of TATAAT that is a vital part of the promoter site on DNA for transcription to occur in bacteria/prokaryotes

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39
Q

start point

A

-the site where transcription actually begins
-the promoter consists of DNA sequences dozens of nucleotides upstream from the start point

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40
Q

elongation of transcription

A

-RNA polymerase untwists the DNA, exposing about 10-20 nucleotides at a time
-RNA nucleotides that are complementary to the DNA template are added to the 3’ end of the growing RNA molecule

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41
Q

termination of transcription in bacteria

A

-the terminator sequence in the DNA is transcribed into RNA, and the newly formed RNA forms a structure that causes the polymerase to fall off the DNA
-the mRNA in bacteria doesn’t need to be processed and translation can begin

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42
Q

termination of transcription in eukaryotes

A

-the RNA polymerase passes through a specific sequence in the DNA that creates a polyadenylation signal (AAUAAA) in the pre-mRNA molecule
- 10-31 nucleotides downstream of the polyadenylation signal proteins that associate with the newly formed pre-mRNA cut it free from the RNA polymerase

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43
Q

extensive processing of pre-mRNA in eukaryotes

A

-before the pre-mRNA can leave the nucleus it undergoes extensive processing that alters both ends of the RNA and cuts sequences out of the middle
-the 5’ end of the pre-mRNA receives a 5’ cap, which is a modified guanine nucleotide
-a special enzyme adds 50 – 250 adenine nucleotides to the 3’ end. This long stretch of As is called a poly-A tail
-the 5’ cap and poly-A tail protect the mRNA from degradation, are used to export the mRNA form the nucleus, and help to attach ribosomes to the 5’ end of the RNA

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44
Q

Untranslated Regions (UTRs)

A

the regions of RNA that are not translated (not all of the RNA nucleotides will be translated into amino acids)

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45
Q

RNA splicing

A

-most eukaryotic genes and the RNA transcripts produced from them have long stretches of nucleotides that are not translated into protein
-the sequence of DNA nucleotides that codes for a polypeptide are not contiguous, but are split into regions
-the 5’ UTR and 3’ UTR are included in exons, even though they are not translated into proteins

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46
Q

introns

A

-the noncoding regions of nucleotides that lie between coding regions
-aka intervening sequences

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47
Q

exons

A

the regions of nucleotides that are expressed (usually translated into protein)

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48
Q

splicing

A

the process in which intervening sequences (introns) are cut out of the pre-mRNA (primary transcript)

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49
Q

splicesosome

A

-a large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron, and joining the two adjacent exons
-contains several small nuclear ribonucleoproteins (snRNPs)

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50
Q

ribonucleoproteins (snRNPs)

A

each snRNP contains a small nuclear RNA (snRNA) that can act as a catalyst in the splicing process

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51
Q

ribozymes

A

-are RNA molecules that function as catalysts (therefore not all biological catalysts are made of protein)
-some organisms only use snRNAs to catalyze splicing without using any proteins

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52
Q

why can RNAs operate as enzymes?

A

-because they can adopt specific three dimensional shapes, and the bases contain functional groups that can interact with other molecules

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53
Q

what gives RNA a high degree of specificity?

A

the ability to form complementary bonds with other nucleic acids gives RNAs a high degree of specificity

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54
Q

alternative RNA splicing

A

-a process that creates different mRNA molecules from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
-multiple proteins can be produced from the same gene (with alternative splicing different, but related proteins can be made from the same gene)

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55
Q

domains

A

-discrete structural and functional regions that proteins can have (ex: a DNA binding domain, or an active site for an enzyme, or a kinase domain)
-different exons can code for different domains

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56
Q

how can alternative splicing produce proteins with different functions?

A

by adding or removing specific domains

57
Q

Prokaryotes versus Eukaryotes

A

-cellular location: cytoplasm (prok) vs nucleus (euk)
-AT rich promoter: Pribnow box (prok) vs TAT box (euk)
-proteins aid in RNA polymerase binding: sigma factor (prok) vs general transcription factors (euk)
-no mRNA modification, translation immediately occurs after mRNA synthesis (prok) vs extensive mRNA modifcation occurs prior to transport out of nucleus (euk)

58
Q

what does translation bring together in order to make a protein?

A

mRNA, rRNA, and tRNA

59
Q

mRNA

A

carries the genetic information from the DNA

60
Q

rRNA molecules

A

are ribozymes that are integral parts of ribosomes where translation occurs

61
Q

tRNA

A

converts the codons in the mRNA to the proper amino acid in the polypeptide

62
Q

tRNA molecule

A

-a tRNA molecule is a short, single strand of RNA that adopts a specific shape, containing three loop domains
-one of the loops contains a triplet anticodon that is complementary to the codon in mRNA
-each tRNA molecule with a specific anticodon carries a specific amino acid

63
Q

anticodon

A

complementary to the codon in mRNA

64
Q

aminoacyl-tRNA synthetases

A

-link the correct amino acid to the correct tRNA
-there are 20 different aminoacyl-tRNA synthetases, one for each amino acid

65
Q

active site of the aminoacyl-tRNA synthetase

A

-fits only a specific combination of amino acid and tRNA
-this molecular recognition ensures that the correct amino acid is associated with the correct tRNA

66
Q

what are ribosomes made of?

A

-rRNA and protein
-each ribosome is made of two subunits, a large subunit and a small subunit
-each subunit contains one or more rRNA molecules
-the rRNA molecules are ribozymes and carry out the main functions of the ribosomes
-the proteins support the function of the ribozymes

67
Q

ribosomes

A

-are essentially large ribozymes
-because there are so many ribosomes in a cell, rRNA is the most abundant type of RNA in the cell
-also have entry sites for the mRNA and exit tunnels for the polypeptide

68
Q

P site, A site, and E site

A

the 3 locations that ribosomes contain for tRNAs to bind to an mRNA

69
Q

P site

A

holds the tRNA that is attached to the growing polypeptide

70
Q

A site

A

holds the tRNA attached to the next amino acid to be added to the polypeptide

71
Q

E site

A

the exit site for the prior tRNA that has incorporated its amino acid already

72
Q

3 phases of translation

A
  1. initiation
  2. elongation
  3. termination
    (like transcription)
73
Q

what 3 things are brought together during translation initiation?

A

a small ribsomal subunit, an mRNA, and an initiator tRNA carrying Met

74
Q

translation initiation in bacteria vs eukaryotes

A

-in bacteria, the small ribosomal subunit can bind the mRNA and tRNA in any order
-in eukaryotes, the small ribosomal subunit binds the 5’ cap of the mRNA and then scans along the mRNA until it finds the start codon (AUG). then the initiator tRNA hydrogen bonds to the start codon

75
Q

translation initiation complex

A

-once the mRNA and tRNA are in place on the small ribosomal subunit, the large ribosomal subunit binds to create the translation initiation complex
-this step requires an input of energy, which comes from the hydrolysis of GTP (very similar to ATP)
-initiation factors help to assemble the complex
-the initiator tRNA sits in the P site of the ribosome

76
Q

initiation factors

A

other proteins that help to assemble the translation initiation complex

77
Q

elongation factors

A

other proteins necessary for elongation and helps elongation to occur

78
Q

translation elongation

A

-the codon in the A site of the ribosome base pairs with the appropriate tRNA (this step requires an energy input, GTP hydrolysis, which ensures the accuracy and efficiency of codon recognition)
-the energy input (GTP hydrolysis) moves the mRNA through the ribosome
-a peptide bond forms between the carboxyl group on one amino acid (in the P site) and the amino group on the next amino acid (in the A site)
-the tRNA in the A site moves to the P site moves to the E site and is released
-empty A site to receive next tRNA

79
Q

peptide bond

A

-a covalent bond that forms between the two adjacent amino acids and the growing polypeptide is attached to the tRNA in the A site
-rRNA molecules in the ribosome catalyze the peptide bond

80
Q

N-terminus and C-terminus

A

-the Met amino acid is at the N-terminus of the polypeptide
-the last amino acid added to the polypeptide chain is at the C-terminus
-polypeptides are always listed in order from the N-terminus to the C-terminus
-the codons for the amino acids at the N-terminus of a polypeptide are found at the 5’ end of a molecule

81
Q

release factor

A

-binds to the codon when a stop codon enters the A site of the ribosome
-is a protein, shaped like a tRNA
-promotes the hydrolysis of the covalent bond between the amino acid and the tRNA sitting in the P site of the ribosome, freeing the polypeptide

82
Q

translation termination

A

-stop codon on mRNA in A site
-release factor into A site
-release polypeptide chain
-release mRNA
-release ribosomal subunits
-release uncharged tRNAs
[hydrolysis of two additional GTP molecules breaks apart the ribosomal complex; parts are recycled to be used again]

83
Q

polyribosome

A

the whole complex of many ribosomes found on one mRNA molecule

84
Q

post-translational modifications

A

-the polypeptide begins to fold into its secondary and tertiary shapes as it is being synthesized
-after synthesis, a polypeptide may undergo modification: (add sugars, lipids, or phosphate groups to specific amino acids; enzymes can remove one or more amino acids, particularly from the N-terminus; enzymes may cleave the polypeptide into multiple pieces)

85
Q

chaperonin

A

a protein that assists with protein folding

86
Q

signal peptide

A

a sequence of about 20 amino acids at or near the N-terminus of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell
(other kinds of signal peptides for other organelles in the cell are recognized after the polypeptide has completed synthesis from a free ribosome in the cytoplasm)

87
Q

signal recognition particle (SRP)

A

binds to the signal peptide and carries the ribosome to the ER so that the polypeptide is inserted into the ER lumen

88
Q

mutations

A

are changes to the nucleotide sequence of DNA

89
Q

point mutation

A

-a change in a single nucleotide pair in a gene
-can result in three difference classes of mutations

90
Q

the 3 different classes of mutations

A
  1. silent mutations
  2. missense mutations
  3. nonsense mutations
91
Q

silent mutations

A

-occur when a nucleotide-pair substitution results in a codon that codes for the same amino acid in the polypeptide
-there is no functional change in the polypeptide

92
Q

missense mutations

A

-occur when a nucleotide-pair substitution results in a codon that codes for a different amino acid in the polypeptide
-sometimes doesn’t affect the protein function very much
sometimes changing one amino acid significantly impairs the function of the protein
-sometimes results in a protein with improved function because the new amino acid improves upon the previous amino acid

93
Q

when would a missense mutation not affect the protein function much?

A

-if the location of the amino acid in the protein is not in a critical spot
-or if the new amino acid may have properties very similar to the old amino acid and can function in its place (ex: changing Lys for Arg, which are both positively charged)

94
Q

when would a missense mutation significantly impair the function of the protein?

A

-if the change occurs in a critical location, such as the active site of a protein
-if the new amino acid is very different from the old amino acid (ex: changing Lys for Phe, a hydrophilic to a hydrophobic change)

95
Q

nonsense mutations

A

-occur when a nucleotide-pair substitution creates a stop codon and terminates a polypeptide prematurely
-almost always produce nonfunctional proteins

96
Q

insertions

A

a type of mutation when there are additions of nucleotide pairs in a gene (can be single or many nucleotide pairs)

97
Q

deletions

A

a type of mutation when there are losses of nucleotide pairs in a gene (can be single or many nucleotide pairs)

98
Q

frameshift mutation

A

-when inserting or deleting nucleotide pairs alter the reading frame, which subsequently alters all of the amino acids that follow the insertion or deletion (lots of missense mutations)

99
Q

mutagens

A

-are physical and chemical agents that interact with DNA in ways that cause mutations (ex: x-rays, UV light, chemicals that mimic nucleotides, chemicals that insert into DNA and distort the DNA structure)
-are usually carcinogenic

100
Q

carcinogens

A

-cancer causing chemicals
-usually mutagenic

101
Q

the central dogma

A

genetic information flows in one direction only, from DNA to RNA to protein, meaning that the information encoded in DNA is transcribed into RNA, which is then translated into a protein

DNA—>RNA—>protein

102
Q

functional RNAs

A

rRNA, tRNA, and miRNA

103
Q

when are genes turned “on”?

A

when they are transcribed and the mRNA is translated into protein

104
Q

when are genes turned “off”?

A

when they are not transcribed

105
Q

how does regulation of gene expression enable cells to respond to environmental conditions?

A

-all organisms must regulate which genes are expressed at any given time
-genes are turned on and off in response to signals from their external and internal environments
-enables cells to maintain internal conditions within a narrow range (homeostasis)

106
Q

homeostasis

A

maintaining internal conditions within a narrow range

107
Q

constitutively expressed

A

-some genes are always “on”
-the presence of the protein or RNA is essential for the function of the cell (ex: rRNA, tRNA, actin, tubulin, enzymes for glycolysis and cellular respiration, etc.)
-the amount of the RNA or protein stays at a fairly constant level in the cell

108
Q

how does regulation of gene expression allow cells to efficiently control cellular resources?

A

-bacterial cells don’t waste energy making tryptophan, if it is available in the environment (no need to go through transcription and translation to produce enzymes necessary to make tryptophan)
-in multicellular organisms, cells have specific jobs, requiring specific proteins (each cell type has the same DNA content, but uses different sets of genes to generate cell specific proteins)

109
Q

tryptophan

A

an essential amino acid that the body needs to function properly but cannot produce on its own

110
Q

bacterial operons

A

a cluster of functionally related genes can be coordinately controlled by a single “on-off” switch

111
Q

operator

A

-the “switch”, or segment of DNA usually positioned within the promoter
-sequences of nucleotides between the promoter and the transcriptional start where active repressors can bind

112
Q

operon

A

the entire stretch of DNA that includes the operator, the promoter, and the genes that they control

113
Q

repressors

A

proteins that can inhibit transcription

114
Q

trp operon

A

-a group of genes in bacteria that are transcribed together to produce enzymes that synthesize the amino acid tryptophan
-is ON when tryptophan is absent
-is OFF when tryptophan is present

115
Q

repressible operon

A

-is one that is usually on
-binding of a repressor to the operator shuts off transcription
-ex: trp operon

116
Q

inducible operon

A

-is one that is usually off
-a molecule called an inducer inactivates the repressor and turns on transcription
-ex: lac operon

117
Q

lac operon

A

-is inducible
-contains genes that codes for enzymes used in the hydrolysis and metabolism of lactose (when lactose is present a bacteria will turn on these genes in order to digest the lactose)
-is OFF when lactose is absent
-is ON when lactose is present

118
Q

lac repressor

A

-by itself, the lac repressor is active and switches the lac operon off
-the presence of lactose inactivates the repressor, turning the lac operon on

119
Q

beta-galactosidase

A

enzyme that binds to lactose and breaks it down into glucose and galactose (encoded by lacZ gene)

120
Q

permease

A

a transmembrane transporter protein that allows lactose to permeate/flood into the cell (encoded by lacY gene)

121
Q

cyclic AMP (cAMP)

A

-a small, hydrophilic molecule that acts as a second messenger, or cellular signal, in many biological processes
-high cAMP means low glucose or low energy

122
Q

abundant lac mRNA synthesized (high operon expression) occurs with:

A

low glucose, high lactose

123
Q

little lac mRNA synthesized (“leaky” gene expression) occurs with:

A

high glucose, high lactose

124
Q

operon “off” with:

A

-low/absent glucose, low/absent lactose
-or high glucose, low/absent lactose

125
Q

heterochromatin

A

highly packed, genes within this structure are usually not expressed

126
Q

euchromatin

A

loosely packed, genes within this structure are more active

127
Q

histone acetylation

A

-acetyl groups are attached to an amino acid in histone tails
-opens up chromatin structure and promotes transcription

128
Q

DNA methylation

A

-the addition of methyl groups to certain bases in DNA
-can condense chromatin and reduce expression (ex: methyl cytosine in eukaryotes, methyl adenine and cytosine in prokaryotes)
-can cause long-term inactivation of genes in cellular differentiation

129
Q

eukaryotic transcriptional regulation

A

-RNA requires the assistance of transcription factors to initiate transcription
-general transcription factors are essential for the transcription of all protein-coding genes
-a few bind to the TATA box within the promoter
-many bind to proteins , including other transcription factors and RNA polymerase II

130
Q

control elements

A

-segments of noncoding DNA that serve as binding sites for transcription factors, which help regulate transcription
-eukaryotic genes generally have multiple
-can be located near the promoter (proximal) or at a distance (distal) from the promoter

131
Q

enhancers

A

-for genes that are not expressed all the time, high levels of transcription depend on the presence of additional, specific transcription factors
-some of these transcription factors bind to enhancers, specific sequences of DNA, which can be distantly located from the promoter
-can be located upstream, downstream, or within an intron
-the DNA is bent, allowing the transcription factors bound to the enhancers to interact with the transcription initiation complex and RNA polymerase

132
Q

activators

A

activate transcription

133
Q

differential gene expression

A

the expression of different genes by cells with the same genome

134
Q

post transcriptional regulation

A

after an mRNA is produced a cell has additional mechanisms to control the amount of protein produced

135
Q

microRNAs (miRNAs)

A

-are short RNA molecules that can bind to 3’ UTR of other mRNAs
-can inhibit protein translation by causing the degradation of the mRNA or preventing translation at the ribosome

136
Q

differentiation

A

-the process by which a cell or group of cells becomes specialized in structure and function
-during development signals between cells activate specific transcription factors that begin the differentiation process

137
Q

Myoblasts

A

are cells determined to form muscle cells and produce large amounts of muscle-specific proteins

138
Q

MyoD

A

a “master regulatory gene” that encodes a transcription factor that commits the cell to becoming skeletal muscle

BIOL101 (4 decks)

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