DNA Structure, Organization, Replication, Damage, and Repair Flashcards
1
Q
Gene
A
Part of the DNA that codes for a protein
2
Q
Coding (Sense Strand)
A
- Sequence of nucleotides that is the blueprint for a protein
- Similar to the mRNA made, as RNA Polymerase makes a complementary mRNA strand from the Template Strand and the Coding Strand is already complementary to the Template Strand.
- The only difference between the Coding Strand and mRNA are the differences between DNA and RNA
3
Q
Template (Anti-Sense Strand)
A
- Sequence of nucleotides complementary to the coding (sense) strand
- Strand that RNA Polymerase follows and makes a complementary mRNA form of
4
Q
Transcription General Steps
A
- ) De-helization exposes the individual genes (the two DNA strands are still attached)
- ) Pre-Initiation Complex (Proteins/Enzymes) form around the promoter region
- ) RNA Polymerase separates the two DNA strands within it making a transcription bubble
- ) RNA Polymerase follows the template strand and assembles mRNA
- ) RNA Polymerase reaches the terminator sequence (2 complementray sequences in a row on a single strand) which creates a mRNA hairpin loop when transcribed which detaches the RNA Polymerase from the DNA strand and Terminates transcription
5
Q
Promoter Region
A
- Repetative Non-Coding Sequence of DNA
- Starting point of a gene
- Common promoter is the TATA Box
6
Q
After mRNA is transcribed, what modifications are made?
A
- A 7-Methylguanosine Cap is added to the 5’ end
- Polyadenylate Polymerase adds a Poly-Adenine Tail (sequence of Adenine Nucleotides) to the 3’ end
- Spliceosome splices the Introns out, leaving only the Exons
- The mRNA now leaves the nucleus to go be translated
7
Q
Translation basic steps
A
- ) Ribosome grabs the mRNA
- ) Start Codon (AUG) starts transcription
- ) Stop Codon stops transcription (UAA) (UAG) (UGA)
8
Q
Codon
A
- Group of 3 nucleotides on mRNA
- Either translates into 1 amino acid, or gives a signal to start or stop translation
9
Q
How many codons are there?
A
64
10
Q
Translation Initiation
A
- Ribosome grabs the mRNA
- 40s subunit recognizes the start codon (AUG)
- 60s subunit begins translating
11
Q
Transfer RNA (tRNA)
A
- Short RNA sequence
- Finds specific amino acid in the cytosol
- Takes amino acids to the ribosome
- Anticodon: Three letter coding sequence that complements mRNA
12
Q
Ribosome binding sites
A
- ) Exit (E) site
- ) Peptidyl (P) site
- ) Aminoacyl (A) site
13
Q
Steps of Translation with Ribosome Sites
A
- ) The tRNA containing Methionine (for the start codon AUG) binds to the P site
- ) tRNA with complementary sequence for the next codon binds to the A site
- ) Peptide bond forms between the amino acid in the P and A site
- ) The growing polypeptide chain is transferred to the tRNA in the A site
- ) Everything moves down one site (A –> P –> E)
- ) The tRNA in the E site exits and the A site is open for another tRNA
- ) Repeat until you reach a stop codon (UAA) (UAG) (UGA)
14
Q
What conditions must be satisfied to successfully take a genomic DNA sequence all the way to a functional protein product?
A
- ) Genomic DNA seuence must be accessibly to regulatory factors and transcription machinery
- ) The right combination of transcription factors must be present to promote, not inhibit, transcription of the particular gene
- ) The mRNA transcript must be stable and survive to complete translation
15
Q
Constitutive heterochromatin
A
- Highly condensed
- Transcriptionally inactive
- Usually consists of highly repetitive DNA sequences
- Approximately 10% of interphase chromatin is in this state in all cells
16
Q
Facultative heterochromatin
A
- Highly consensed
- Transcriptionally inactive
- Does NOT consist highly of highly repetitive DNA sequences
- Amount of facultative heterochromatin varies between cells (this is one of the main ways cells differentiate)
17
Q
Epigenetics
A
- Study of heritable changes in cellular function or gene expression that can be transmitted from cell to cell (even generation to generation) as a result of chromatin-based molecular signals
- Reversible changes in the chromatin landscape that contribute to regulation of gene expression
18
Q
Complex epigenetic states can be established, maintained, and transmitted by what mechanisms?
A
- Modifications to the DNA such as DNA methylation
- Histone modifications that alter chromatin packaging or access
- Substitution of specialized histone variants that mark chromatin associated with particular sequences or regions in the genome
19
Q
DNA Methylation
A
- Modification of cytosine bases by methylation
- Typically occurs on the C of CpG dinucleotides
- Inhibits gene expression by preventing general transcription factors from binding to the promoter
- Important in cell differentiation and development
- Silences repetitive DNA sequences and endogenous transposons
- Stimulate Histone Deacetylation which further inhibits transcription
20
Q
Histone Modifications
A
- Post-translational modifications of histone proteins
- Can include: Methylation, Phosphorylation, Acetylation, Ubiquitylation, or Sumoylation
- Impacts gene expression by altering chromatin structure or recruiting histone modifiers
21
Q
Histone Acetylation
A
- Mediated by the enzyme Histone Acetyltransferase
- Opens the DNA and promotes transcriptional activation
- Can be removed by the enzyme Histone Deacetylase
22
Q
Histone Methylation
A
- Occurs at Lysine or Arginine residues
- Mediated by the enzyme Histone Methylatransferase
- Contributes to transcriptional activation or repression (including heterochromatin formation)
23
Q
Noncoding RNA
A
- Transcribed from DNA
- Not translated into protieins
- Play a variety of roles within the cell, including gene expression regulation at the transcriptional and post-transcriptional level
24
Q
microRNA
A
- Can function to block protein production by causing degradation of mRNA messages or by inhibiting translation
25
Q
How many methyl groups in Histone Methylation are added to increase or decrease transcription?
A
- Increase: 1 Methyl Group added –> Decreases the attraction between DNA and Histone –> Less tightly wound –> More accessible –> Increases transcription
- Decrease: 2 or 3 Methyl Groups added –> Histone Represses –> Locks down genes –> Prevens Transcription
26
Q
Activators
A
- Type of transcription factor
- Kickstart gene transcription through positive regulation
- Binds to DNA sequence called the Enhancer (near gene)
- Ligand/receptor on cell surface –> Signals the Activator to move from Cytosol to Nucleus –> Activator binds to Enhancer –> Loops the DNA making it easier for General Transcription Factors + RNA Polymerase to bind to the Promoter
- Also recruits Histone Acetyltransferase –> Further promotes Transcription
27
Q
Repressor
A
- When active, binds to DNA sequence called the Silencer (near gene)
- Prevents RNA Polymerase from binding to the Promoter –> Thus inhibiting Transcription
- Recruits Histones Deacetylases –> Further inhibits Trancription
28
Q
RNA Editing
A
- Changes in the nucleotides of RNA via enzymes. Includes the following 3 types:
1. ) Insertion
2. ) Deletion
3. ) Substitution
29
Q
Translation Elongation
A
Both Ribosome subunits translate codons into an amino acid sequence (primary structure of protein)
30
Q
Translation Termination
A
Ribosome recognizes stop codon (UAA) (UAG) or (UGA) and releases the protein
