DNA Structure, Organization, Replication, Damage, and Repair

Question 1

Gene

Answer 1

Part of the DNA that codes for a protein

Question 2

Coding (Sense Strand)

Answer 2

• 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

Question 3

Template (Anti-Sense Strand)

Answer 3

• Sequence of nucleotides complementary to the coding (sense) strand
• Strand that RNA Polymerase follows and makes a complementary mRNA form of

Question 4

Transcription General Steps

Answer 4

1. ) De-helization exposes the individual genes (the two DNA strands are still attached)
2. ) Pre-Initiation Complex (Proteins/Enzymes) form around the promoter region
3. ) RNA Polymerase separates the two DNA strands within it making a transcription bubble
4. ) RNA Polymerase follows the template strand and assembles mRNA
5. ) 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

Question 5

Promoter Region

Answer 5

• Repetative Non-Coding Sequence of DNA
• Starting point of a gene
• Common promoter is the TATA Box

Question 6

After mRNA is transcribed, what modifications are made?

Answer 6

• 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

Question 7

Translation basic steps

Answer 7

1. ) Ribosome grabs the mRNA
2. ) Start Codon (AUG) starts transcription
3. ) Stop Codon stops transcription (UAA) (UAG) (UGA)

Question 8

Codon

Answer 8

• Group of 3 nucleotides on mRNA

- Either translates into 1 amino acid, or gives a signal to start or stop translation

Question 9

How many codons are there?

Answer 9

64

Question 10

Translation Initiation

Answer 10

• Ribosome grabs the mRNA
• 40s subunit recognizes the start codon (AUG)
• 60s subunit begins translating

Question 11

Transfer RNA (tRNA)

Answer 11

• Short RNA sequence
• Finds specific amino acid in the cytosol
• Takes amino acids to the ribosome
• Anticodon: Three letter coding sequence that complements mRNA

Question 12

Ribosome binding sites

Answer 12

1. ) Exit (E) site
2. ) Peptidyl (P) site
3. ) Aminoacyl (A) site

Question 13

Steps of Translation with Ribosome Sites

Answer 13

1. ) The tRNA containing Methionine (for the start codon AUG) binds to the P site
2. ) tRNA with complementary sequence for the next codon binds to the A site
3. ) Peptide bond forms between the amino acid in the P and A site
4. ) The growing polypeptide chain is transferred to the tRNA in the A site
5. ) Everything moves down one site (A –> P –> E)
6. ) The tRNA in the E site exits and the A site is open for another tRNA
7. ) Repeat until you reach a stop codon (UAA) (UAG) (UGA)

Question 14

What conditions must be satisfied to successfully take a genomic DNA sequence all the way to a functional protein product?

Answer 14

1. ) Genomic DNA seuence must be accessibly to regulatory factors and transcription machinery
2. ) The right combination of transcription factors must be present to promote, not inhibit, transcription of the particular gene
3. ) The mRNA transcript must be stable and survive to complete translation

Question 15

Constitutive heterochromatin

Answer 15

• Highly condensed
• Transcriptionally inactive
• Usually consists of highly repetitive DNA sequences
• Approximately 10% of interphase chromatin is in this state in all cells

Question 16

Facultative heterochromatin

Answer 16

• 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)

Question 17

Epigenetics

Answer 17

• 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

Question 18

Complex epigenetic states can be established, maintained, and transmitted by what mechanisms?

Answer 18

• 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

Question 19

DNA Methylation

Answer 19

• 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

Question 20

Histone Modifications

Answer 20

• 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

Question 21

Histone Acetylation

Answer 21

• Mediated by the enzyme Histone Acetyltransferase
• Opens the DNA and promotes transcriptional activation
• Can be removed by the enzyme Histone Deacetylase

Question 22

Histone Methylation

Answer 22

• Occurs at Lysine or Arginine residues
• Mediated by the enzyme Histone Methylatransferase
• Contributes to transcriptional activation or repression (including heterochromatin formation)

Question 23

Noncoding RNA

Answer 23

• 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

Question 24

microRNA

Answer 24

• Can function to block protein production by causing degradation of mRNA messages or by inhibiting translation

Question 25

How many methyl groups in Histone Methylation are added to increase or decrease transcription?

Answer 25

- 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

Question 26

Activators

Answer 26

- 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

Question 27

Repressor

Answer 27

- 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

Question 28

RNA Editing

Answer 28

- Changes in the nucleotides of RNA via enzymes. Includes the following 3 types: 1. ) Insertion 2. ) Deletion 3. ) Substitution

Question 29

Translation Elongation

Answer 29

Both Ribosome subunits translate codons into an amino acid sequence (primary structure of protein)

Question 30

Translation Termination

Answer 30

Ribosome recognizes stop codon (UAA) (UAG) or (UGA) and releases the protein