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Flashcards in Exam 1- Ch 10-14 Deck (184)
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1

Characteristics of Genetic Material

1. Genetic material must contain complex info
2. Genetic material must replicate faithfully
3. Genetic instructions must encode the phenotype
4. Must have capacity to vary

2

1. Genetic material must contain complex info

-Store large amounts of info
-Instructions for traits and functions of an organism

3

2. Genetic material must replicate faithfully

-Begins w single cell-> undergoes billions of divisions
-W/ each division, genetic instructions must be accurately transmitted to decendant cells
-When organisms reproduce and pass genes to progeny, genetic instructions must be copied w/ fidelity

4

3. Genetic instructions must encode phenotype

-Genotype must have capacity to be expressed as a phenotype (code 4 traits)
-Product of gene= protein or RNA molecule
--Must be mechanism 4 genetic instructions in DNA to be copied to RNAs and proteins

5

4. Must have capacity to vary--> Genetic info must have ability to vary

-Diff species and individual members of species differ in genetic makeup

6

Chargaff's Rule

-Developed by Chargaff and colleges concerning ratios of bases in DNA
-DNA from diff organisms varies in base comp
-A=T, G=C

7

Transforming principle

-Substance responsible 4 transformation
-Ex: DNA

8

Griffith Experiment

-Virulent strains= disease causing (S)
-Nonvirulent strains= non-disease causing (R)
-R strains lived, S strains killed, heat killed R mice lived, heat killed S w/ R died
-Conclusion= virulence is heritable

9

Avery, Macleod, and McCarthy experiment

-Showed DNA= transforming principle
-Virulent bacteria heat killed and added to nonvirulent
-Treated w/ RNAase, Protease, and DNAase
-RNAse and Protease--> virulent and nonvirulent bacteria
-DNAase--> only virulent bacteria

10

Hershey-Chase experiemnt

-T2 bacteriophage= virus that infects ecoli, reproduces by attaching to outer wall of cell and injecting its DNA into cell, cell synethsizes phage proteins
Q?- does phage protein or DNA transmitted in phage production
-DNA contains phosphorus, tagged w/ P isotope
-Protein contains Sulfer, tagged w S isotope
-S batch had no radioactivity, protein not transmitted
-P batch was radioactive, indicating DNA transmitted

11

Deoxyribose

-5 carbon sugar in DNA
-Lacks a hydroxyl group on 2' carbon atom
-Hydroxyl group on 1' and 3'

12

Nitrogenous base

-Nitrogen-containing base
-one of the 3 parts of a nucleotide

13

Purine

-Double-ringed
-Type of nitrogenous base in DNA and RNA
-Adenine and Guanine

14

Pyramidine

-Single ringed
-Nitrogenous bases in DNA and RNA
-Cytosine, Thymine (not in RNA), Uracil ( not in DNA)

15

Phosphate Group

-A phosphorus atom attached to 4 oxygen atoms
-One of 3 compoents of nucleotide
-5' end

16

Deoxyribonucleotides

-Basic building block of DNA
-Consisting of deoxyribose, phosphate group, and nitrogenous base

17

Ribonucleotides

-Basic building block of RNA, consisting of ribose, a phosphate group, and a nitrogenous base
-Ribose has OH on 1', 2' and 3'

18

Phosphodiether linkages

-A strong covalent bond that joins the 5' phosphate group of one nucleotide to the 3' hydroxyl group of the next nucleotide in a polynucleotide strand
-Connection of nucleotides

19

3' end

-End of a polynucleotide chain
-OH group is attached to 3' carbon of sugar in nucleotide

20

B-DNA

-Right-handed helical strucutres of DNA
-exist when water is abundent

21

Primary Structure

-DNA as nucleotide structure
-How nucleotides join together

22

Secondary Structure

-3D congifuration
-Helical structure
-H bonds link base pairs (3 bonds btwm G and C, 2 btwn T and A)
-DNA strands= antiparallel

23

DNA/ RNA backbone

-Alternating sugars and phosphate groups

24

Supercoiling

-Tertiary structure
-Forms when strain is placed on DNA helix by over or underwinding
-Takes up less space than relaxed DNA

25

Relaxed state

-Energy state of DNA molecule where there is no structural strain on molecule

26

Positive Supercoiling

-Tertiary structure
-Forms when strain is place on DNA helix by overwinding

27

Negative Supercoiling

-Tertiary structure
-Forms when strain is placed on DNA helix by underwinding
-Most DNA= neg supercoiled
-Advantages= separation of 2 strands easier during replication/ transcription, packed into smaller spaces

28

Topoisomerases

-Enzymes that add or remove rotations in a DNA helix by temporarily breaking nucleotide strands, rotating ends around each otherm, and rejoining broken ends
*Induces and relieves supercoiling

29

Euchromatin

-Chromatin that undergoes condensation and decondensation in course of cell cycle
-Majority of chromosomal material, where transcription takes place

30

Heterochromatin

-Chromatin that remains in highly condensed state throughout cell cycle
-Found at centromeres and telomeres
-Y chromosome= largely heterochromatin
-Lack of transcription
-Absence of crossing over and replication in S phase

31

Bacterial Chromosome

-Circular
-Looks like a clump
-Additional DNA in form of plasmids

32

Eukarytoic Chromosomes

-1 chromosome= 1 linear molecule of DNA (packed and folded)

33

Chromatin

-Complex of DNA and proteins
-Types= Euchromatin and Heterochromatin
-When in condensed form, nucleosomes fold on themselves into 30nm loop fibers, each anchored to base by proteins

34

Histones

-Small, + charged proteins
-H1, H2A, H2B, H3, H4
-Charge attracts DNA

35

Nucleosome

-Core of protein and DNA produced by digestion w/ nuclease enzymes
-Simplest level of chromatin structure (basic repeating unit)
-146 bp of DNA wrapped 2 times around 8 histone (2 copies of H2A, H2B, H3, H4)
-H1- Binds bp of DNA where DNA joins and leaves histone octamer and locks DNA into place
-Separated by linear DNA

36

DNAase I

-Enzyme that digests DNA

37

Semiconservative Replication

-Replication in which 2 nucleotide strands of DNA separate and each serveds as a temple for synthesis of a new strand
-All DNA replication is semiconservative

38

Replicon

-Unit of replication consisting of DNA from the origin of replication to the point at which replication on either side of the origin ends

39

Origin of Replication

-Site where DNA synthesis is initiated

40

Theta Replication

-Replication of circular DNA (Bacteria)
1. Double stranded DNA unwinds at origin of replication, producing ingle nucleotide strands to serve as templates 4 new DNA
2. Unwinding of double helix creates replication bubble
3. DNA replication on both template strands= simultaneous w/ unwinding (2 forks= bidirectional)
-Produces 1 new and 1 old strand

41

Replication Bubble

-Segment of DNA molecule that is unwinding and undergoes replication

42

Replication fork

-Point at which a double-stranded DNA molecule separates into two single strands that serve as templates for replication

43

Bidirectional Replication

-Replication at both ends of replication bubble

44

Rolling Circle Replication

-Replication of Circular DNA (Viruses)
1. Initiated by break in one of the nucleotide strands, exposing 3' OH and 5' Phosphate
2. New nucleotides are added to 3' end of broken strand using inner (unbroken) strand as template
3. New nucs. added to 3', 5' displaced from template
4. 3' grows around circle w each revolution around circle, 3' displaces nuc strand in preceeding rev
5. Linear DNA molecule cleaved from O
**Result= Double stranded O dna molecule and single stranded dna molecule

45

DNA Polymerase

-Enzyme that synthesizes DNA

46

Continuous Replication

-Replication of leading strand of DNA in same direction as unwinding
-Allows new nucleotides to be added continuously to the 3' ends of the new strands as template is exposed

47

Discontinous Replication

-Replication of the lagging strand of DNA in direction opposite to unwinding
-DNA must be synthesized in short fragments (Okazaki fragments)
--Frags eventually joined together

48

Conservative replication

-False
-Entire double-stranded DNA molecule serves as template 4 replication

49

Dispersive Replication

-Both nucleotide strands break down into fragments and reassemble into new DNA strands
-New molecules contain old and new frags
-None of original molecule is conserved

50

Meselson and Stahl Experiment

-Used nitrogen isotopes of different weights and a centrifuge to prove that DNA is semiconservative in replication

51

Linear Eukaryotic Replication

-Multiple origins of replication
-A each origin, DNA unwinds and produces replication bubble
-Replication takes place at both strands at each end of the bubble w/ 2 replication forks spreading outward
-Replication forks run into each other, fuse to form large stretches of DNA

52

Requirements of Replication

-Template consisting of single-stranded DNA
-Raw materials to be assembled into new nucleotide strand
-Enzymes and other proteins that read template and assemble DNA molecule

53

DNA Replication

5'--> 3' direction, nucs added to 3' end

54

Initiator Proteins

-Proteins that bind to an origin of replication
-Unwinds a short stretch of DNA, allowing helicase and other single-strand-binding proteins to bind and initiate replication

55

DNA Helicase

-Enzyme that unwinds double-stranded DNA by breaking hydrogen bonds
-cannot initiate strands unwinding
-Binds to laggin strands temp at replication fork and moves in 5-->3 direction along strands (moves rep fork)

56

Single-Stranded-Binding Proteins (SSBs)

-Protein that binds to single-stranded DNA during replication after helicase
-Protect single-strand nuc chains and prevent seconardy structures
-Indiff to base sequence--> bind to any single-stranded DNA
-Form tetramer

57

DNA Gyrase

-Topoisomerase enzyme in ecoli that relieves torsional strain that builds ahead of replication fork
-Creates double-strand breaks
-Inhibition results in cessation of DNA synthesis

58

Primase

-Enzyme that synthesizes short stretch of RNA on DNA template
-Fxns in replication to provide a 3' OH group for attachment of DNA nucleotide

59

Primers

-Short stretch of RNA on a DNA template
-Provides a 3' OH group for the attachment of DNA nucleotide at initiation of replication

60

DNA Polymerase III

-Bacterial DNA polymerase that removes RNA primers and places them w DNA nucleotides
-Main replicator, adds nucs to 3' end (5-->3 polymerase activity
-3'-->5' exonuclease acitivity (removes nucs in this direction to remove errors)
-High processivity

61

B Sliding Clamp

-A ring-shaped polypeptide component of DNA pol III,
-Encircles DNA during replication and allows pol to slide along DNA template strand

62

DNA Pol I

-Bacterial DNA pol that removes RNA primers and replaces them w DNA nucleotides
-Has 5--3' polymerase, exonuclease and 3'-->5' exonuclease activity
---Removes primers and replaces w/ DNA nucs after DNA pol III initiated sythesis at downstream primers

63

Proof-reading

-Process by which DNA pols remove and replace incorrectly paired nucleotides in the course of replication

64

Mismatch Repair

-Process that corrects mismatched nucleotides in DNA after replication has been completed
-Enzymes excise take out nuc and use original nuc strand to replace it

65

Initiation, Replication - Bacteria

-1 origin of replication
-Initiator protein binds to origin and causes DNA to unwind (allows helicase to attach to strand)

66

Unwinding, Replication-Bacteria

-DNA helicase
-SSBs
-DNA Gyrase

67

Elongation, Replication -Bacteria

-All DNA pol require nuc w/ 3' OH group to add nucs to
-All newly synthesized DNA molecules have short RNA primers embedded in them, later removed and replaced w/ DNA nucs
-Lagging strand= new primer generated at beginning of each Okazaki
-Leading strand= primer required at 5' end of new strand
-Primase forms complex w helicase at fork
-DNA Pol I and III

68

DNA Ligase

-Break that remains in sugar-phosphate backbone of new DNA strand is sealed
-3' OH attaches to 5' phosphate group

69

Termination--Bacteria

-Terminates when replication forks meet or reach termination sequences

70

Origin-Recognition Complex

-Eukaryotes
-Multiprotein complex that binds to an origin of replication
-Unwinds the DNA around it to initiate replication

71

Replication Licensing Factors

-Eukaryotes
-Protein that ensureds replication takes place only once at each origin of replication
-Required at origin b4 replication can be initiated and removed after DNA is replicated
-Ensures DNA is not replicated until cell has passed through mitosis

72

DNA Polymerase a (alpha)

-Eukaryotes
-DNA pol that initiates replication by synthesizing RNA primer, followed by short string of DNA nucleotides
-Primase activity
-High fidelity

73

DNA pol d (delta)

-Eukaryotic
-DNA pol that replicates lagging strand during DNA synthesis
-Carries out DNA repair and translesion DNA synthesis
-High fedelity

74

DNA Pol E (epsilon)

-Eukaryotic
-DNA pol that replicates leading strand during DNA synthesis
-High fedelity

75

Translesion DNA pols

-Specialized DNA pols
-Able to bypass distortions in template to synthesize DNA
-Makes more errors than other DNA pols
-Low fedelity

76

G-rich 3' overhang

-A guanine rich sequence of nucs
-Protrudes beyond complementary C-rich strand at end of chromosome

77

Telomerase

-Ribonucleoprotein enzyme
-Replicates telomeres of eukaryotic chromosomes
-RNA part of enzyme has template that is complementary to repeated sequences in the telomore, base pairs w them
-Provides template for the synthesis for add copies of repeats

78

Eukaryotic Genomes

-Greater size than prokaryotes
-Linear chromosomes
-DNA template associated w/ histone proteins in nucleosomes, nucleosome assembly must follow DNA replication

79

Lincensing of DNA Replication Eukaryotes

1. Origins are licensed/approved for replication
--Early in cell cycle when replication licensing factors attach to each origin
2. Replication machinery initiates replication at each licensed origin
---ORC w/ 2 licensing factors allow MCM2-7 to bind to origin

80

Unwinding in Replication, Eukaryotes

-Helicases, SSBs and topoisomerases all fxn like DNA gyrase

81

Nucleosome Assembly Eukaryotes

1. Distribution of the original nucleosomes on parental DNA molecule ahead of replication fork
2. Redistribution of prexisiting histones on new DNA molecules
3. Addition of newly synthesized histones to complete formation of new nucleosomes
-New DNA= mix of old and new histones

82

Replication at Telomeres

-At end if DNA, no crucial 3' OH group
-Chromosomes shorten each time cell divides
---Problem solved by telomeres
----Sequence= TTAGGG (grich overhang), usually after a C
-RNA sequence pairs w/ overhang and provides template for add. DNA copies of the repeats
---As nucs added, RNA sequence moves down strand
-Telomerase can extend 3' end w/o use of complementary template
**WHEN TELMERES GONE, CELLS DIE

83

Ribozymes

-RNA molecule that can act as a biological catalyst

84

Ribosomal RNA

-RNA molecule that is a structural component of the ribosome
-large ribosomal subunit and small ribosomal subunit
--Each 1 of 2 units of fxnal ribsome
-rRNA

85

Messenger RNA

-mRNA
-RNA molecule that carries genetic info for the amino acid sequence of a protein

86

pre-Messenger RNA

-pre-mRNA
-Eukaryotic RNA molecule that is modified after transcription to become mRNA

87

Transfer RNA

-tRNA
-RNA molecule that carries an amino acid to the ribosome and transfers it to a growing polypeptide chair in translation
-Interacts w codons in mRNA, placing the amino acids in their proper order of synthesis
-Each tRNA can only attach to 1 TYPE OF amino acid

88

Small Nuclear RNA

-snRNA
-Small RNA molecule found in the nuclei of eukaryotic cells
-Fxn in processing pre-mRNA

89

Small nuclear ribnucleoproteins

-snRNPs
-Structure found in the nuclei of eukaryotic cells
-Consist of snRNA and proteins
-Fxn in processing pre-mRNA

90

Small nucleolar RNAs

-Small RNA molecule found in nuclei of eukaryotic cells
-Fxn in processing of rRNA and assembly of ribosomes

91

MicroRNAs

-Small RNA molecules
-21-22 bps in length
-Produced by cleavage of double-stranded RNA arising from small hairpins w/in RNA that is mostly single stranded
-Combine w proteins to form a complex that binds to mRNA and inhibits their translation

92

Small Interfering RNAs

-siRNAs
-Single-stranded RNA molecule
-21-25 bps
-Produced by cleavage and processing of double-stranded RNA that binds to complementary sequences in mRNA and brings about cleavage and degradation of mRNA
-Bind to complementary sequences in DNA and brings out methylation

93

Piwi interacting RNAs

-Small RNA molecule belonging piwi protein class that they interact w/
-Similar to microRNA and siRNA
-Thought to have role in supressing expression of transposable elements in reproductive cells

94

CRISPR RNAS (crRNAs)

-small RNA molecules found in prokaryotes that assist in the destruction of foreign DNA

95

Long Noncoding RNAs

-lncRNAs
-Class of relatively long RNA
-Found in Eukaryotes
-Do not code 4 proteins but provide a variety of other fxns
-Regulation of gene expression

96

Template Strand

-Strand of DNA that is used as a template during transcription
-RNA synthesized during transcription is complementary and antiparallel this

97

Nontemplate strands

-DNA strand that is complementary to template strand
-Also known as coding strand
-Not ordinarily used as a template during transcription
-Written 5'-->3'

98

Transcription Unit

-Sequence of nucleotides in DNA
-Encodes a single RNA molecule and the sequence necessary for its transcription
-Normally contains a promoter, an RNA-coding sequence, and a terminator

99

Promoter

-DNA sequence to which the transcription apparatus binds to to initiate transcription
-Indicates direction of transcription, which of the two DNA strands is read and template, and starting point of transcriptor
*Not itself transcribed

100

RNA Coding Region

-Sequence of DNA nucs that encodes an RNA molecule

101

Terminator

-Sequence of DNA molecules that causes termination of transcription
-Stops once coded into RNA

102

Ribonucleoside Triphosphates

-Substrate of RNA synthesis
-Consists of ribose, nitrogenous base, and 3 phosphate groups linked to the 5' carbon atom of ribose
-In transcription, 2 of 3 phosphates r cleaved, producing RNA nucleotide

103

RNA Polymerase

-Enzyme that synthesizes RNA from DNA template during transcription
-Bacterial
-Core enzyme and sigma factor
-Can proofread errors by backtracking and cleaving last 2 nucs

104

Core enzyme

-Set of 5 subunits at heart of most bacterial RNA polymerases
-During transcription, catalyze elongation of RNA molecule by the addition of RNA nucleotides
-Consist of 2 copies of beta, alpha, beta prime, and w

105

Sigma Factor

-Subunit of bacterial RNA polymerase
-Allows RNA polymerase to recognize promoter and initiate transcription
-W/o it, transcription eould occur along random pt in DNA

106

Holoenzyme

-Complex of an enzyme and other protein factors necessary for fxn
-Core enzyme+ sigma factor
-RNA pol binds stabily only to promoter and initiates transcription at start site
--Sigma detaches from core enzyme when RNA binds to promoter and transcription begins

107

RNA Pol I

-Eukaryotic RNA pol
-Transcribes large ribosomal RNA molecules

108

RNA Pol II

-Eukaryotic RNA pol
-Transcribes pre-mRNA, snRNA, and microRNA
-Transcribes promoters w/ core promoter and reg. promoter

109

RNA Pol III

-Eukaryotic RNA pol
-Transcribes tRNA, small ribosomal RNA, snRNA, and microRNA

110

Central Dogma

Dna--transcription--> RNA-- translation--> protein

111

Transcription vs Replication

R: all nucleotides in DNA copied
T: only parts of DNA molecule are made into RNA, highly selective--> individual genes transcribed only when products r needed

112

3 Components of Transcription

1. DNA template
2. Raw materials (ribonucleotides triphosphate) to build RNA
3. Transcription appartus--> proteins necessary 4 catalyzing synthesis of RNA

113

DNA Template- Transcribed Strand

-Complementary and antiparallel to RNA strand
-same polarity and sequences, but T instead of U

114

Downstream vs Upstream

-Transcription apparatus moves downstream
-Downstream= +#
-Upstream= -#

115

Transcription Aparatus

-RNA polymerase carries out all steps

116

Consensus Sequence

-Sequence that comprises the most commonly encountered nucleotides found at a specific location in DNA or RNA

117

-10 Consensus Sequence

-TATAAT
-Found in most bacterial promoters approximately 10 bp upstream of transcription
-Where unwinding begins

118

-35 Consensus Sequence

-TTGACA
-Found in many bacterial promoters
-35 bp upstream of transcription start site

119

Upstream element

-Consensus sequence found in some bacterial promoters that contain a number of A-T pairs
-Located 40-60 bps upstream of transcription start site

120

Abortive Initiation

-Process during initiation of transcription
-RNA polymerase repeatedly generate and release short transcripts (2-6 bp in length) while still bound to promoter
-Euks and proks

121

Rho-dependent terminators

-Sequence in bacterial DNA
-Requires presence of Rho factor to terminate transcription
-Causes RNA pol to pause
-No hairpins
-Rut site= binding site for rho factor
-Rho has helicase properties

122

Rho Factor

-A protein that binds to a baterial RNA polymerase and facilitates termination of transcription in some genes

123

Rho-independent terminators

-Sequence in bacterial DNA
-Does not require presence of rho factor to terminate transcription
-Inverted repeats, sequence of nucleotides on same strand that are inverted and complementary (hairpins)
-String of uracil
**Intrinsic termination

124

3 Stages of Bacterial Transcription

1. Initiation
2. elongation
3. termination

125

Bacterial Initiation Transcription

1. Promoter region recognition by transcription apparatus
2. Formation of transcription bubble
3. Creation of 1st bonds btwn rNTPs
4. Escape of transcription apparatus from promoter

126

Down vs Up mutations

-Down= slows transcription down
-Up= speeds transcription up

127

Elongation Bacterial RNA synthesis

-RNA polymerase undergoes shape change at end of initiation, can no longer bind to promoter
-Can now transcribe downstream
-Unwinds DNA downstream of transciption bubble, joining nucs to growing RNA molecule according to sequence of template
-rewinds DNA at upstream edge of bubble

128

Transcription Bubble Bacterial RNA Synthesis

-RNA continuoisly synthesized here
-Neg supercoiling behind bubble, pos ahead of it

129

Termination Bacterial RNA Synthesis

-RNA polymerase transcribes terminator at 3' end
-once transcribed, RNA pol stops
-New RNA released and fully disociated from DNA

130

General Transcription Factors

-protein that binds to eukaryotic promoter near transcription start site
-Part of basal transcription apparatus that initiates transcription
-Added to RNA pol

131

Basal Transcription Apparatus

-Complex of general transcription factors, RNA pol II, and proteins that assemble on the promoter and are cabale of initiating minimal levels of transcription
-Mediator= TFIID

132

Transcriptional Activator Proteins

-Protein in eukaryotic cells that binds to consensus sequences in regulatory promoters or enhances and initiates transcription by stimulating the assembly of basal transcription apparatus

133

Core promoter

-Dna sequence located immediately upstream of a eukaryotic gene
-Where basal transcription app. binds
-Ex: TATA box

134

TATA Box

-Consensus sequence TATAAAA
-found in eukaryotic RNA pol II promoters
-Usually located 25-35 bps upstream of transcription site
-Determine transcription start site

135

Regulatory promoter

-DNA sequence located immediately upstream of eukaryotic core promoter
-Contains consensus sequences which transcriptional regulator proteins bind

136

Enhancers

-Sequence that stimulates maxial transcription of distant genes
-Affects only genes on same DNA molecule
-Contains short consensus sequence
-Is not fixed in relation to transcription start site
-Can stimulate almost any promoter in its vicinity
-May be upstream or downstream of gene
-Fxn: Independent of sequence orientation

137

Internal Promoters

-Promoter located w/in sequence of DNA that are transcribed into RNA

138

Tata-binding protein (tbp)

-Polypeptide chain found in several diff transcription factors that recognizes and binds to sequences in eukaryotic promoters

139

Promoters in Eukaryotes

-Carried out by accesory proteins that bind to promoter and then recruit a specific RNA pol

140

Accessory Proteins

1. Gen transcription factors
2. Basal transcription apparatus
3. Transcriptional activator proteins

141

RNA pol 1 and 3 promoters

-Each recognize promoters that are distinct

142

Initiation Eukaryotic RNA transcription

-Initiated through assembly of transcription machinery on promoter
-Regulatory proteins bind near promoter and modify chromatin structure so transcription can take place
-Reg proteins recruit basal transcription apparatus to core promoter

143

Steps of Initiation Eukaryotes

1. Binding of TFIID to TATA box on core promoter
--TFIID consists of TBP
2. RNA Pol II and general transcription factors assemble promoter, confirmation changes take place in DNA and pol
3. DNA template positioned w/in active site of RNA pol, creating open complex

144

Elongation Eukaryotes

-RNA pol leaves premoter and begins elongation
-GTFs left behind the promoter, serve to quickly reinitiate transcript w/ another rna pol
-RNA pol II maintains transcription bubble
-DNA doubkle helix enters cleft in pol and gripped by jawlike extensions of enzyme
-2 strands DNA unwind, comp nucs added to 3' end of RNA mol
-DNA-RNA hybrid hits amino acid wall and bends
-RNA separates from DNA and runs through cleft b4 exiting from pol

145

Termination eukaryotic transcription

-RNA pol I--> requires termination similar to rho factor , which binds to DNA sequence downstream of terminator
-RNA pol III--> Ends transcription after transcribing terminator sequence that produces string of uracil
-RNA pol II-> continues to synthesize 100-1000 bps past coding sequence necessary to produce mRNA
---Cleavage cuts pre-mRNA into -->mRNA that codes for protein, and RNA w/ 5' end trailing out
----Rat1= 5'-->3' exonuclease, degrades tail

146

Colinear

-Concept of direct correspondence btwn nucleotide sequence of a gene and the continuous sequence of amino acids in a protein

147

Exons

-Coding region of a gene that is interupted by introns
-After transcription and post-transcriptional processing, exons remain in mRNA

148

Introns

-Noncoding sequence btwn coding regions in eukaryotic gene
-Removed from RNA after transcription
-Rare in bacteria
-More introns=more complex organism

149

Group I introns

-A class of introns in some ribosomal RNA genes that are capable of self-splicing (catalyze own removal)
-Bacteria, bacteriophages, eukaryotes

150

Group II introns

-A class introns in some protein-coding genes that are capable of self-splicing
-found in mitochrondria, chloroplasts, and eubacteria

151

Nuclear pre-mRNA

-A class of introns in nuclear protein-encoding genes that are removed by splicosome -mediated splicing
--Requires snRNA and proteins

152

Transfer RNA introns

-A class of introns in tRNA genes whose splicing relies on enzymes

153

Characteristics of Splicing Process

1. splicing of pre-mRNA introns takes place in nucleus
2. Order of exons in DNA usually maintained in spliced rna
-Coding sequences may be split up, but not jumbled

154

Gene

-All sequences in DNA that are transcribed into a single rna molecule
--Includes exons, introns, sequences at beginnning and end of RNA not translated into protein

155

Codon

-Sequence of 3 nucleotides that encodes one amino acid in a protein

156

5' untranslated region

-Sequence of nucleotides at end of 5' end of mRNA, does not encode amino acids of a protein

157

Shine-Dalgarno Sequence

-Consensus sequence found in bacterial 5' untranslated region of mRNA
-Contains ribosome-binding site

158

Protein-coding region

-Part of mRNA consisting of the nucleotides that specify the amino acid sequence of a protein

159

3' Untranslated regions

-Sequence of nucleotides at 3' end of mRNA
-Does not encode the amino acid of a protein, but affects both stability of mRNA and its translation

160

5' Cap

-Modified 5' end of eukaryotic mRNA
-Consisting of extra methylated nucleotide and methyl groups @ 2' position of ribose suger in one or more subsequent nucleotides
-Plays a role in the binding of the ribosome to RNA and affects mRNA stability and removal of introns

161

Poly (A) tail

-String of adenine nucleotides added to 3' end of eukaryotic mRNA after transcription

162

RNA splicing

-Process by which introns are removed from RNA and exons are joined together
-Takes place in nucleus

163

5' splice site

-5' end of an intron where cleavage takes place in RNA splicing
-Ribosomes bind here

164

3' splice site

-3' end of an intron where cleavage takes place in RNA splicing

165

Branch Point

-Adenine nucleotide in nuclear pre-mRNA introns that lie 18-40 nucleotides upstream of 3' splice site

166

Splicosome

-Large complex consisting of several RNAs and many proteins that splices protein encoding pre-mRNA
-Contains 5 small nuclear ribonucleoprotein particles
---U1,U2,U4,U5,U6
-snRNAs associated w/ snRNPS

167

Trans-spilicing

-Process of splicing together exons of 2 or more pre-mRNAs

168

Recursive splicing

-A variation of splicing in which some long introns are removed in multiple steps

169

Alternative processing pathways

-One of several pathways by which a single pre-mRNA can be produced in diff ways to produce alt types of mRNA

170

Alternative splicing

-Process by whicha single pre-mRNA can be sliced in more than one way to produce diff types of mRNA

171

Multiple 3' cleavage sites

-The presence of more than 1 3' cleavage site on a single pre-mRNA
-Allows cleavage and polyadenylation to take place at diff sites
-Produces mRNA of diff lengths

172

RNA editing

-Process by which protein coding sequence of an mRNA is altered after transcription, so that amino acids specified by the altered mRNA are diff from those encoded by the gene

173

Guide RNAs

-gRNAs
-RNA molecule that serves as a template for an alteration made in mRNA duing RNA editing
-Partly complementary segments of unedited mRNA, and the two molecules that undergo base pairing at these sequences

174

Stop codon and start codon

-Start near 5' untranslated
-stop near 3' untranslated

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3 Primary Regions of RNA

1. 3' untranslated
2. 5' untranslated
3. protein-coding region

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Protein-coding region

-Comprises the codons that specify the amino acid sequence of proteins
-Begins and ends w/ start and stop codon

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Addition of 5' cap

-Modification of pre-mRNA
-extra guanine added to 5' end of mRNA
-extra methyl added to base of guaninie and 2' OH group of sugar of 1 or more nucleotides at 5' end
-Fxns initiating translation
---Cap binding proteins recognize cap and attach to it
---Ribosome then binds to these proteins and moves downstream along mRNA until start codon is reached
-Enzyme of addition of RNA pol II

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Addition of poly (A) tail

-20-50 nucleotides at 3' end
-Not encoded into DNA, added through polyadenylation after transcription (extra material at end of 3' cleaved and tail added)
-Requires polyadenylation signals (AAUAAA)--> Determines point where cleavage occurs
-W/ 5' cap increases mRNA stabiity

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Splicing code

-5' splice site
-3' splice site
-branch point
---Changing prevents splicing

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Process of splicing

1. pre-mRNA cut at 5' splice site
--Cut exon 1 from intron, 5' end of intron attaches to branching point
--Guanine at 5' splice w/ adenine at branch point through transesterfication rxn (5' phos group at guanine becomes attached to 2' OH of adenine at branch pt)
2. pre-mRNA cut at 3' splice site
--3' end of exon 1 covalently bonds to 5' end of exon 2
--Intron released as lariat

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tRNA modifying enzymes

-Enzymes that creates a modified base in tRNA by catalyzing a chemical change in the standard base

182

RNA interference

-Process in which cleavage of a double-stranded RNA produces small RNAs (siRNA or miRNAs) that bind to mRNAs containing complementary sequences and bring about their cleavage and degradation
-Used to limit invasion of foreign genes and censor expression of genes

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RNA-induced silencing complex (RISC)

-Complex of a siRNA or miRNA w/ proteins that can cleave mRNA, leading to degradation of the mRNA or repressing its translation

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Classes of small RNA molecules

1. siRNAs
2.miRNAs
3.piRNAs/ piwi-interacting RNAs
--Eukaryotes
--FXN: regulation of gene expression, defense against viruses , supression of transposons, modification of chromatin structure
**In prokaryotes--> ciRNAs