1
Q
Mutation
A
A permanent change in the DNA sequence that can cause changes to the RNA sequence and protein.
2
Q
Point Mutation
A
A single nucleotide base is changed, inserted, or deleted.
3
Q
DNA Repair Steps
A
- During replication wrong base is added
2.Recognition of mistake causes DNA Polymerase (2) to back up and cut out wrong nucleotide - DNA polymerase adds the correct nucleotide
4
Q
How does DNA polymerase recognize a mistake?
A
Recognizes a distortion in helix structure.
5
Q
What checks the sequence if DNA polymerase misses a mistake?
A
DNA repair proteins.
6
Q
How do DNA repair proteins determine the parent vs new strand in prokaryotes?
A
They look for the unmethylated new strand. Temp strand will have methyl groups added to cystines and adenines.
7
Q
How do DNA repair proteins determine the parent vs new strand in eukaryotes
A
The new strand will have additional nicks and spaces.
8
Q
How are mistakes fixed if DNA polymerase misses mistake?
A
1.Wrong nucleotide is cut out (along with additional surrounding one) by DNA repair proteins.
2. DNA polymerase comes and fills in gap
3. Ligase bonds together strand.
9
Q
DNA Replication (compared to transcription)
A
- Occurs only once in cell’s lifetime
- All DNA is replicated
- Both strands are used as templates
10
Q
Transcription (compared to replication)
A
- Occurs through lifetime when RNA is needed
- Only a section of DNA is transcribed-one gene
- Only one template strand
- Promoters
11
Q
Gene
A
DNA sequence w/instructions to synthesize mRNA. Each gene directs synthesis of a type of RNA
12
Q
What are the four types of RNA
A
Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Other small RNAs
13
Q
Transcription
A
The process of creating a complementary RNA strand from a segment of DNA.
14
Q
Transcription Initiation Steps
A
- Proteins (sigma factors or transcription factors recognize promoter sequence
- DNA binding proteins recruit RNA polymerase.
15
Q
Promoter (Sequence)
A
The DNA sequence that signals the start of transcription of a gene.
16
Q
DNA Binding Proteins
A
Find and bind to promoters. Interact with DNA through major and minor grooves.
Sigma Factors in prok.
Transcription Factors in euk.
17
Q
What can DNA binding proteins non-specifically interact with?
A
Sugar phosphate backbone
18
Q
How do DNA biding protein interact specifically?
A
Through hydrogen bonds with different base pairs.
19
Q
What do DNA binding proteins recognize?
A
The unique atom patterns of the major and minor grooves.
20
Q
Prokaryotic Promoter (sequences)
A
- Varies by type of organism
- Most common region is behind start site (-)
*First nucleotide used is +1
*Has consensus sequence between -10 and -35 regions
21
Q
Consensus Sequence
A
Common sequence of nucleotides found in promoter region. IE TATA box in euk.
22
Q
What do DNA binding proteins bind to?
A
The consensus sequence of the promoter.
23
Q
Sigma Factors
A
Prokaryotic DNA binding proteins that bind to specific promoters.
Direct RNA polymerase to bind to promoters.
*Sigma factor is general name for set of proteins.
24
Q
Eukaryotic Promoter (sequences)
A
Host of transcription factors that bind to common TATA BOX.
*Designated by TF, #polymerse, and letter
25
Transcription Factors
Eukaryotic DNA binding proteins that binds to specific promoters
Directs RNA polymerase to promoters.
26
Formation of Basal Transcription Apparatus
1. First general transcription factors binds to the promoter at TATA box
2. Transcription factors continue to join
3. RNA polymerase joins after several transcription factors are bound
4. More factors are added
5. Apparatus if formed and RNA polymerase is ready to transcribe
27
What does RNA Polymerase do in Transcription?
RNA polymerase unwinds helix, bubble does not expands, moves down strand.
RNA polymerase takes two ribonucleotides and joins them using phosphodiester bonds.
28
What are the 3 eukaryotic RNA polymerase that carry out transcription?
RNA Polymerase 1
RNA Polymerase 2
RNA Polymerase 3
29
What RNA does RNA Polymerase 1 Transcribe?
18srRNA and 28srRNA
30
What RNA does RNA Polymerase 2 Transcribe?
mRNA
31
What RNA does RNA Polymerase 3 Transcribe?
5srRNA and tRNA
32
Transcription Elongation
RNA polymerase moves along DNA temp strand and produces RNA transcript adding nucleotides complementary to the DNA strand to the growing RNA 3' end.
* Nucleotides are always added to 3'OH
*RNA is synthesized as a single strand
33
Template Strand
DNA strand used as a template to synthesize an RNA molecule.
34
Coding Strand
DNA strand not used as a template to synthesize RNA molecule, complementary to template strand.
35
The RNA strand that is synthesized is complementary to what strand and is essentially identical to what strand.
Template; Coding
36
Termination Site
A section of nucleic acid sequence that marks the end of a gene.
When RNA polymerase reach sit RNA transcript and polymerase release from template strand.
37
Transcription Termination in Prokaryotes
Rho-dependent termination
Rho-independent termination
38
Rho-Dependent Termination
1. Rho helicase bind to rut site after rut site is synthesized and leaves polymerase.
2. Rho helicase moves up the RNA being synthesized and catches up to RNA polymerase and pulls RNA strand. Breaks up RNA-DNA helix.
39
Rho-Independent Termination
1. RNA synthesis encounters very specific sequence at the end of the transcript, it transcribes termination sequence.
2. As soon as the sequence exits RNA sequence RNA molecule around terminator sequence folds and forms hairpin which disrupt DNA-RNA helix, pulls RNA out of RNA polymerase.
40
Transcription Termination in Eukaryotes
Each RNA polymerase has different termination.
41
Termination in RNA Polymerase 1
Transcriptions is terminated by a terminator proteins that recognizes a terminator sequence.
42
RNA Polymerase 3
Termination is similar to prokaryotes rho-independent termination, sequence forms hairpin, RNA pulled out.
43
RNA Polymerase 2
Transcript is modified prior to termination.
*Transcript is considered pre-mRNA
44
Untranslated Region
Any mRNA that is not going to be directly used in the polypeptide sequence.
45
RNA Polymerase in Modifications
1. RNA polymerase transcribes polyadenylation signal sequence.
2. Other proteins see signal and come
3. RNA transcript is transcribed 10-35 nucleotides past signal
46
Polyadenylation Signal Sequence
A sequence in a pre-mRNA molecule that signals where it should be cleaved and a poly(A) tail should be added.
47
Poly A Tail Modification
Polymerase adds a series of adenines to the 3' end of the transcript.
*Template Independent
48
5' Cap Modification
A modified nucleotide (guanine) is added to the 5' end to protect mRNA.
*Added through phosphate bonds
*Happens as soon as strand leaves polymerase
49
Eukaryotic Pre-mRNA
Has coding regions interspersed with non-coding regions.
50
Coding Regions
Exons eventually express, code for polypeptide regions.
51
Non-Coding Regions
Intervening or Intron that are not expressed.
52
RNA Splicing
Removes introns, joins exons.
Generates an mRNA molecule with continuous coding sequence.
53
Spliceosome
Complex of proteins and RNA that carries out RNA splicing.
54
How are Introns Recognized by Spiceosome?
Generally will have consensus sequences.
55
snRNPs
Complex of small RNAs and proteins.
56
Steps of RNA Splicing: 1
1.snRNPS bind to mRNA sequence at the 5' donor and branch point consensus sequence (end of exon, beginning on intron.
57
Steps of RNA Splicing: 2
2. Binding on snRNPs recruits other proteins, spliceosome assembles.
58
Steps of RNA Splicing: 3
3. A cut (broken phosphodiester bond) is made between the upstream (5') exon and intron.
59
Steps of RNA Splicing: 4
4. After the first cut at the 5' end, the intron forms a closed loop.
60
Steps of RNA Splicing: 5
5. The free 3' OH group at the end of the cut upstream exon reacts with the 5' phosphate group of downstream exon.
61
Steps of RNA Splicing: 6, 7
6. The downstream exon is cleaved at the intron junction and splices to the upstream exon.
7. Intron is degraded
62
Translation
The synthesis of a polypeptide, using information in the polypeptide.
* RNA is the bridge between genes and proteins for which they code
63
Ribosome
Molecular machine composed of two subunits that synthesizes proteins in eukaryotes and prokaryotes.
64
Ribosome Subunit
Small and large complex composed of multiple rRNAs and ribosomal proteins.
*Binds to mRNA during translation
65
tRNA
RNA that helps ribosome read current and next codon.
66
Codon
Three nucleotides that code for a specific amino acid. 63 total, 61 for amino acids, 3 stop codons.
67
What are the two functions of tRNAs
Recognize specific codons in mRNA; Carry amino acid to ribosome.
68
How do tRNAs recognize specific codons?
Through base-pairing interactions-"anticodon"
69
Carry Amino Acids to Ribosome
*tRNA is modified after transcription, *Amino acid is attached covalently (by synthetase)
*Before amino acid is attached all tRNAs are modified by the addition of the nucleotides CCA at the 3' end.
70
tRNA Charging is done by what?
tRNA Synthetase
71
tRNA Synthetase
Attach amino acids to the correct tRNA and anticodon.
*Synthetases only bind to one amino acid and one tRNA
*Recognizes unique tRNA structure
72
Charged tRNA (Aminoacyl)
tRNA attached to an amino acid.
73
What is required for a tRNA synthetase to attach an amino acid?
ATP or GTP Hydrolysis.
74
The 1st position nucleotide codon pairs with what position anticodon?
First codon nucleotide pairs with the third anticodon nucleotide.
75
Wobble Base Pair Rules
Base pairing between 3rd (3'end) codon and 1st (5'end) anticodon is flexible, non Watson-crick.
76
Wobble Base Pairs
G-U, U-G, I-A, I-U, I-C
77
What do ribosomes bind to during translation?
mRNA and charged tRNA
78
Translation Initiation Step: 1
The small ribosomal subunit binds to the mRNA at the 5' end and locates start codon.
79
Initiation Step 1 Prokaryotes
Small ribosomal subunit recognizes specific sequence near start codon and binds start codon. Shine Dalgarno Sequence
80
Initiation Step 1 in Eukaryotes
Small ribosomal subunit recognizes and binds to 5' cap, scans mRNA to find "correct" start codon.
*Correct codon depends on consensus sequence around it (kozak)
81
Translation Initiation Step: 2
Methionine charged tRNA binds to AUG start codon completing initiation complex.
*modified fmet in prok.
*modified met in euk.
82
Translation Initiation Step: 3
Large ribosomal subunit joins initiation complex at P-site. Methionine charged tRNA now in P-site.
83
A-Site
Holds the tRNA that carries the next amino acid to be added.
84
P-Site
Holds the tRNA that carries the polypeptide chain.
85
E-Site
Exit site, where discharged tRNAs leave ribosome
86
What does assembly of the initiation complex require?
ATP or GTP Hydrolysis
87
Translation Elongation Step 1:
The anticodon of the incoming tRNA binds to the codon at the A site.
88
Translation Elongation Step 2:
Methionine is linked to the amino acid in the A-site by peptidyl transferase activity of large subunit.
The bond between the amino acid and the tRNA in the P-site is broken.
Peptide bond is formed between new and existing amino acid of polypeptide.
89
What is peptide bond formation catalyzed by?
Ribosomal RNA in the large ribosomal subunit.
90
Peptidyl Transferase
Enzyme that catalyzes the formation of peptide bonds between amino acids.
91
Translation Elongation Step 3:
After the peptide bond forms the ribosome moves and shifts the tRNAs to the next site.
-----> Subunit
<----- tRNA
92
What us GTP Hydrolysis Needed For?
To bind the charged tRNA to the A-site and to move the tRNA to P-site
93
What do Elongation Factors Faciliate?
1. Binding of the charged tRNAs to the A-site
2. Ensuring the correct charged tRNA is bound to A-site
3. Movement of the tRNA within ribosomes
94
Translation Termination Step 1:
1. Release factors bind to the complex (subunits, mRNA,etc) when a stop codon enters the A-site.
95
Translation Termination Step 2:
Release factors triggers hydrolysis (cut) of the bond between the polypeptide and tRNA.
The release factor disconnects the polypeptide from the tRNA in the P-site.
96
Translation Termination Step 3:
The mRNA and subunits separate.
97
Translation in Prokaryotes (when does it start)
As soon as shine Dalgarno sequence is transcribed (co-transcriptional RNA processing).
98
What Post Translation Modifies Occur?
Initial methionine is cleaved off N-terminus.
99
Phosphorylation
Protein shape is modified by addition of phosphate group.
*Depends on type of protein
100
Glycosylation
The addition of sugars for targeting and recognition.
*Depends on type of protein
101
Proteolysis
Cleaving of polypeptide to allow fragments to fold into different shapes, and be "turned" on and off.
102
Mutation
A permanent change in a cell's or organism's genetic material, resulting from alterations to the DNA sequence which affects mRNA and proteins.
103
Insertions and Deletions (1-2 nucleotides)
May alter reading frame of the mRNA, producing frameshift mutations.
104
105
BSCI 170
flashcards
Decks in class (8)
# Cards
