PCB3063C Module 2 Review

What is transcription?

when information from DNA is converted into information carried by RNA

DNA -> RNA

What is translation?

When information from mRNA is converted into information carried by a protein

mRNA -> protein

What is the goal of transcription and translation?

To turn DNA into proteins

What is DNA replication?

How you make copies of DNA during mitosis and meiosis

DNA -> DNA

T or F: Our cells are constantly making more mRNA and proteins.

True. mRNA and proteins have very short half-lives so we constantly need more

Why do we need proteins?

They do literally EVERYTHING in our body. They are how our body functions

Which parts of the gene determine when and where the gene is turned on?

Promoter, enhancer, and silencer

What parts of the protein determine protein sequence?

Exons

What are the steps of transcription?

1. Transcription factors bind to DNA at the enhancer and silencers

2. RNA polymerase binds to the promoter

3. RNA polymerase starts transcription

4. Premature mRNA becomes mature mRNA

Where do activator transcription factors bind?

They bind to a gene's enhancers to increase the expression of the gene

Where do repressor transcription factors bind to?

They bind to a gene's silencers to decrease the expression of the gene

What has to happen to the transcription factors for transcription to start on a gene?

1. Activators have to bind to the enhancers

2. Repressors have to fall off pf the silencers

How do transcription factors help RNA polymerase bind to the promoter?

They open the DNA so the RNA polymerase can get in and stabilize the RNA polymerase and allow it to bind to the DNA

What does RNA polymerase do?

makes RNA from DNA

How does RNA polymerase carry out transcription?

It reads through the ENTIRE template to create a premature mRNA molecule

(includes untranslated regions and exons and introns)

What stops transcription once it has started?

When RNA polymerase hits a stop sequence (found AFTER the stop codon)

What is premature mRNA?

RNA that contains the introns, exons, and untranslated regions of a gene

What is mature RNA?

RNA that has the exons and untranslated regions of a gene with a poly-A cap on the 3' end

What is alternative splicing?

mRNA processing events that lead to different combinations of exons being spliced together

the way that a single gene can make more than one protein

What is the final product of transcription?

the mature mRNA molecule

What are the steps of translation?

1. Ribosome binds to mRNA at AUG (start codon)

2. tRNAs match to the codons in mRNA

3. Polypeptide chain grows

4. Ribosome hits the stop codon, causing the release factor to come in and end translation

5. The polypeptide chain folds into a protein

What are tRNAs?

Transfer RNAs that carry a specific amino acid

What is a ribosome?

A protein-RNA complex that makes proteins from mRNA

What are the steps of the ribosome binding to the mRNA?

1. The small subunit of the ribosome binds to the mRNA

2. The tRNA that matches the start codon binds to the start codon

3. The large subunit of the ribosome binds to the mRNA

T or F: The tRNA carries amino acids that match to the anticodon sequence of the tRNA

True. The anticodon sequence is 3 nucleotides long and matches to the codon in the mRNA

T or F: The anticodon is the same sequence as the mRNA codon

False. The anticodon is 3 sequences long and is opposite of the mRNA codon following base pair rules.

What is a polypeptide?

a string of amino acids

What is a release factor?

A protein that binds to the stop codons, causing the ribosome to fall off and end translation

What gives a protein its function?

The 3D shape of the protein

How do you predict mRNA and the protein sequence from the DNA?

1. Figure out which strand of the DNA is coding vs. template

2. Figure out the mRNA sequence (transcribe)

3. Figure out what the codons are

4. Translate

What is the coding strand of the DNA?

The strand that is identical to the mRNA, except it has thymines (T) instead of uracils (U)

This strand ALWAYS has a ATG sequence

What is the template strand of the DNA?

The strand that the RNA polymerase reads to make the mRNA

What are codons?

Sets of three nucleotides that correspond to an amino acid

Why do we need the start codon?

It makes sure the right "frame" is read. Without it you will get the wrong protein.

T or F: There is a stop amino acid.

False! There is only a stop codon, not a stop amino acid.

What is the N-terminus?

The start of a protein

(N = "new" for a new protein)

What is the C-terminus?

The end of a protein

(C= "conclude" for the end of a protein)

What is the start codon?

AUG

What are the stop codons?

UAA, UAG, UGA

Why aren't genes "on" all the time?

Genes are turned on/off depending on the environment and mutations

T or F: Every cell in your body contains your entire genome

True. The thing that makes cells different is what genes are turned on and off

(Gametes are the exception)

What is gene expression?

When a gene is turned "on", and being made into mRNA and protein

What are the factors that affect gene expression?

1. Stage of development

2. Internal environment

3. External environment

4. Mutations in the gene

How does stage of development affect gene expression?

As you develop, your body has to turn the right genes on at the right time in order to build the proteins that you need for the development of organs, limbs, etc.

How does your internal environment affect gene expression?

Different tissues have different functions, which require different proteins, so those cells are only expressing the genes they need

How does your external environment affect gene expression?

Things like the season, stress, and diet affect how your body is responding to that environment which in turn affects the proteins your body is creating

T or F: Genes are turned on and off

False. Genes are not turned on/off, they are expressed at high/low levels

What is gene regulation?

How the cell controls what genes are expressed

What does it mean to be up-regulated?

To increase the gene expression

What does it mean to be down-regulated?

To decrease the gene expression

How do transcription factors regulate gene expression and transcription?

They can attract or block RNA polymerase, methylate or un-methylate DNA, and modify histones to make the chromatin more open or more closed

What are mutations?

Change in a DNA sequence

T or F: Alleles are formed through mutations occurring in a gene.

True. If a mutation occurs within a gene, it creates a new allele

T or F: Different alleles ALWAYS affect how the gene and its protein work differently.

False. Different alleles SOMETIMES affect how the gene/protein work, but not always

Where do new mutations come from?

1. Errors in DNA replication

2. The environment

3. Spontaneous lesions

What are spontaneous lesions?

Naturally occurring damage to DNA that leads to a nucleotide change

What is DNA repair?

The mechanisms our cells have for finding and fixing mutations

T or F: DNA repair can only work on specific kinds of mutations.

False. DNA repair can work on any kind of mutation, no matter where it comes from

What are somatic mutations?

Mutations in body cells that cannot be passed down to the next generation.

What are germ-cell mutations?

Mutations in sperm/eggs that are passed down to the next generation through meiosis.

T or F: All mutations affect phenotype.

False. Most mutations do not affect phenotype

What are the ways that mutations can affect phenotype?

1. Mutations can change the structure of a protein by changing the amino acid(s)

2. Mutations can change gene expression

What is insertion?

The addition of a nucleotide or nucleotides

What is substitution?

When one nucleotide is replaced with another

What is deletion?

The removal of a nucleotide or nucleotides

How do we study gene expression?

1. RNAseq

2. Reporter genes

What does RNAseq show you?

How much of every gene in the genome is being expressed

What are the steps of RNAseq?

1. Get your sample

2. Extract mRNA

3. Sequence the mRNA

4. Using a computer, figure out where the mRNA matches the genome

5. Use that data to calculate how much a gene is expressed

What does a reporter gene show you?

Where in the organism the gene is expressed

What are the steps of using a reporter gene?

1. Find the regulatory region of the target gene

2. Attach a glowing protein (ex: GFP)

3. When transcription/translation happen, the glowing protein is expressed instead of the gene

4. Find where the glowing protein is expressed in the organism