Exam 1- Ch 10-14 Flashcards
(184 cards)
1
Q
Characteristics of Genetic Material
A
- Genetic material must contain complex info
- Genetic material must replicate faithfully
- Genetic instructions must encode the phenotype
- Must have capacity to vary
2
Q
- Genetic material must contain complex info
A
- Store large amounts of info
- Instructions for traits and functions of an organism
3
Q
- Genetic material must replicate faithfully
A
- 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
Q
- Genetic instructions must encode phenotype
A
- 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
Q
- Must have capacity to vary–> Genetic info must have ability to vary
A
-Diff species and individual members of species differ in genetic makeup
6
Q
Chargaff’s Rule
A
- Developed by Chargaff and colleges concerning ratios of bases in DNA
- DNA from diff organisms varies in base comp
- A=T, G=C
7
Q
Transforming principle
A
- Substance responsible 4 transformation
- Ex: DNA
8
Q
Griffith Experiment
A
- 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
Q
Avery, Macleod, and McCarthy experiment
A
- 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
Q
Hershey-Chase experiemnt
A
-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
Q
Deoxyribose
A
- 5 carbon sugar in DNA
- Lacks a hydroxyl group on 2’ carbon atom
- Hydroxyl group on 1’ and 3’
12
Q
Nitrogenous base
A
- Nitrogen-containing base
- one of the 3 parts of a nucleotide
13
Q
Purine
A
- Double-ringed
- Type of nitrogenous base in DNA and RNA
- Adenine and Guanine
14
Q
Pyramidine
A
- Single ringed
- Nitrogenous bases in DNA and RNA
- Cytosine, Thymine (not in RNA), Uracil ( not in DNA)
15
Q
Phosphate Group
A
- A phosphorus atom attached to 4 oxygen atoms
- One of 3 compoents of nucleotide
- 5’ end
16
Q
Deoxyribonucleotides
A
- Basic building block of DNA
- Consisting of deoxyribose, phosphate group, and nitrogenous base
17
Q
Ribonucleotides
A
- Basic building block of RNA, consisting of ribose, a phosphate group, and a nitrogenous base
- Ribose has OH on 1’, 2’ and 3’
18
Q
Phosphodiether linkages
A
- 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
Q
3’ end
A
- End of a polynucleotide chain
- OH group is attached to 3’ carbon of sugar in nucleotide
20
Q
B-DNA
A
- Right-handed helical strucutres of DNA
- exist when water is abundent
21
Q
Primary Structure
A
- DNA as nucleotide structure
- How nucleotides join together
22
Q
Secondary Structure
A
- 3D congifuration
- Helical structure
- H bonds link base pairs (3 bonds btwm G and C, 2 btwn T and A)
- DNA strands= antiparallel
23
Q
DNA/ RNA backbone
A
-Alternating sugars and phosphate groups
24
Q
Supercoiling
A
- 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
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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
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Bidirectional Replication
-Replication at both ends of replication bubble
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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
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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
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DNA Replication
5'--> 3' direction, nucs added to 3' end
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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
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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
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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
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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
175
3 Primary Regions of RNA
1. 3' untranslated
2. 5' untranslated
3. protein-coding region
176
Protein-coding region
- Comprises the codons that specify the amino acid sequence of proteins
- Begins and ends w/ start and stop codon
177
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
178
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
179
Splicing code
- 5' splice site
- 3' splice site
- branch point
- --Changing prevents splicing
180
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
181
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
183
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
184
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
