BIS2A MT3 PT 2

Lecture 21-25

What are the 3 parts of the central dogma and what do they each do?

1. Replication: DNA copies itself for cell division

2. Transcription: DNA is transcribed into RNA

3. Translation: RNA is translated into proteins

What is the difference between the Thymine and Uracil structures?

Thymine has a methyl group, uracil does not.

Where does DNA replication occur in eukaryotes and prokaryotes?

The nucleus and cytoplasm

Where does DNA transcription occur in eukaryotes and prokaryotes?

The nucleus and cytoplasm

Where does DNA translation occur in eukaryotes and prokaryotes?

The ribosome

What type of RNA is generated through transcription?

• mRNA, tRNA, rRNA, any type of RNA

What direction is RNA built in?

5’ to 3’

What is reverse transcription?

Generating DNA using an RNA template

What is a promoter?

• A special sequence of DNA required to initiate transcription

• Where RNA polymerase binds

• Determines which strand of DNA is read

What is RNA polymerase?

• Enzyme that synthesizes RNA from the DNA template during transcription initiation and elongation

• Requires a promoter to work

What direction does RNA polymerase read DNA?

3’ to 5’ direction

What direction does RNA polymerase synthesize RNA?

5’ to 3’

What is the process of transcription elongation?

RNA polymerase moves along the DNA strand and synthesizes RNA

What does the newly synthesized RNA molecule resemble?

It resembles the coding strand, except the T’s are replaced with U’s

What is the purpose of adding nucleotide triphosphates (NTP’s) to RNA during transcription?

To break the phosphoanydride bonds and supply energy from exergonic reactions to add nucleotides to the free 3’ -OH

What is the coding/sense/non-template strand?

• The strand of DNA not used as a template for transcription

• Is identical to the RNA transcript except there are U’s instead of T’s

• Runs in 5’ to 3’ direction

What is the non-coding/anti-sense/template strand?

• The template for RNA synthesis during transcription

• 3' to 5’ direction

What sites must be present in DNA so the RNA polymerase can transcribe the DNA to RNA?

• RNA binding site

• Transcription start site

• Transcription stop site

What does mRNA do?

• Messenger RNA

• Carries genetic information to ribosomes

What does tRNA do?

• Transfer RNA

• Helps decode mRNA into proteins

• Acts as a bridge between nucleic and amino acids

What is rRNA

• Forms a major part of ribosomes

• Synthesizes proteins

What is the purpose of the 5’ G-Cap in post-transcription and what is it?

• Protects mRNA and helps ribosome binding

• 5’ end of guanosine is attached to the 5’ end of the mRNA by an enzyme complex attached to RNA polymerase II

What is the poly-A-tail and what does it do?

• Adenine molecules attached to the 3’ end of mRNA

• Increases mRNA stability

• Shortens over time and mRNA is degraded when it reaches a certain length

What sites are present when a gene is encoding an mRNA in order?

1. Promoter

2. Transcription initiation site

3. Ribosome binding site

4. Translation initiation site

5. Translation termination site

6. Transcription termination site

What occurs simultaneously in prokaryotes and where does it take place?

• Transcription and translation

• Cytoplasm

What occurs simultaneously in eukaryotes and where does it take place?

• mRNA processing (transcription) finishes in the nucleus, and translation occurs in the ribosomes of the cytoplasm separately

What is splicing?

• Newly made mRNA transcript is transformed into a mature mRNA

• Removes introns and splices exons together

What is an intron?

• Segment of a DNA/RNA molecule that does not code for proteins and interrupts gene sequence

What is an exon?

• Coding region that contains information for making a protein

• Kept in final mRNA sequence

How is mRNA read and what direction?

• Read by triplets (codons)

• 5’ to 3’

What is splicing carried out by?

• Spliceosome

• Has a helper RNA molecule

• RNA-protein enzyme complex

What is a codon?

• Unit of code that maps the language of nucleotides onto that of proteins

Which RNA has the sequence for codons?

mRNA

Which RNA has the sequence for anti-codons?

tRNA

What are anti-codons?

• Complementary to codons

• 3 nucleotide sequence in tRNA

What are the 3 steps of translation intiation?

1. mRNA binds to the small subunit

2. Intiatior aminoacyl tRNA binds to the start codon

3. Large subunit of the ribosome binds

What does the ribosome do in translation?

• Responsible for making proteins

• Pairs the codon and anticodons together

What direction does tRNA attach to mRNA?

• Antiparallel

• mRNA is read 5’ to 3’ so tRNA is 3’ to 5’

What are the 3 ribosomal sites?

A, P, E

What is the purpose of the A site?

Point of entry for tRNA (except for the first tRNA, which enters at the P site)

What is the purpose of the P site?

Where tRNA is held in the ribosome and adds to the peptide chain

What is the purpose of the E site?

Exit site of the tRNA after it gives its amino acid to the growing peptide chain

What the the process of translation elongation?

• Ribosome moves along the mRNA in 5’ to 3’ direction

• tRNAs enter the A site, bringing in the correct amino acids.

• The ribosome catalyzes peptide bond formation between amino acids.

• The ribosome shifts, moving the tRNA to the P site, and the empty tRNA exits from the E site.

• Energy for elongation is provided by GTP hydrolysis.

What are sense codons?

They correspond to an amino acid

What are nonsense codons?

• They do not correspond to an amino acid

• They signal translation termination

What are the 3 steps of translation termination?

1. Release factor binds to stop codon, signaling it to initiate termination

2. Polypeptide is released

3. Ribosome subunits separate

What is a promoter?

The region of DNA to which RNA polymerase and transcription factors can bind to help initiate transcription

What are transcription factors?

Proteins that bind to specific DNA sequences and affect transcription

What is the difference between strong and weak promoters?

Strong promoters do not need external aid for RNA polymerase to initiate transcription, while weak promoters do

What are repressors?

• Transcription facots that bind to regulatory sequences and inhibit transcription

• Can bind to DNA and prevent RNA polymerase from interacting with strong promoters

What are activators?

• Transcription factors that bind to regulatory sequences and enhance transcription

What is positive gene regulation?

• Binding of a protein (transcription factors) stimulates transcriptions

What is negative gene regulation?

• Binding of a protein (transcription factor) that prevents transcription

What are operons?

Groups of genes regulated together under a single promoter

What are operators?

DNA sequences where transcription factors bind to regulate gene expression

What is promoter strength?

Determines how efficiently RNA polymerase binds and transcribes genes

What is the trp Operon?

Controls tryptophan biosynthesis in E. coli.

What happens if there are high tryptophan levels?

Tryptophan binds to Trp repressor, which binds to the operator and blocks transcription.

What happens if there is low tryptophan levels?

The repressor does not bind, allowing transcription of tryptophan synthesis genes.

What is negative regulation?

Transcription is turned off by a repressor

What does the lac Operon control?

Controls lactose metabolism in E. Coli.

What are the two regulators in the lac Operon?

1. Lac repressor

2. CAP-cAMP complex

What does the Lac Repressor do?

Binds operator and blocks transcription in the absence of lactose

What does the CAP-cAMP complex

Enhances transcription when glucose is low

When is the lac operon induced?

1. When lactose is present (repressor inactive)

2. Glucose is absent (CAP-cAMP activates transcription)

What is an enhancer?

Regulatory DNA sequence that increases gene expression

What is a silencer?

A regulatory sequence that helps inhibit/decrease gene expression.

What is DNA packaging?

DNA that is wrapped around histones, forming nucleosomes

What are histones?

• Proteins abundant in lysine and arginine residues

• Order DNA into structural nucleosomes

What are nucleosomes?

• Structural units

• Control the access of proteins to specific DNA regions

What is an effector?

A molecule that binds to transcription factors to change transcription

What is an inducer?

A molecule that binds to repressors to deactivate them (prevent binding to DNA) or binds to activators to activate them (allow binding to DNA)

What is an inhibitor?

A molecule that binds to activators and prevent from binding to DNA (opposite of inducer)

What is a corepressor?

A molecule that binds to repressors and allows binding to DNA (opposite of inducer)

What is a silent mutation?

No change in the amino acid sequence

What is a missense mutation?

Changes an amino acid, potentially altering protein function

What is a nonsense mutation?

Introduces a stop codon, truncating the protein

What is a transition substituition?

A purine (A/G) is replaced by another purine or pyrmidine (C/T) by another pyrimidine

What is a frameshift mutation?

Insertion or deletion of bases shifts the reading frame, leading to a nonfunctional protein

What is translocation?

A DNA segment moves to a different chromosome or a new location on the same chromosome

What is a wild type?

The “normal” or reference sequence found in a population

What is a mutant?

An organism with a genetic change that differs from the wild type

What are alleles?

Different versions of a gene in a population

What is haploid?

One set of chromosomes (bacteria, gametes)

What is diploid?

2n. Two sets of chromosomes (humans, animals)