BIOL 300 - Exam 3 (Module 9: Gene Expression)

DNA stands for?

Deoxyribonucleic acid

Shape of DNA?

Double helix

What is a nucleotide? What do they consist of?

They are the monomers of DNA. They consist of a phosphate, a sugar, and a nitrogenous base.

What are the four nucleotides of DNA?

ATCG - Adenosine, Thymine, Cytosine, and Guanine.

What are the pairings between the four nucleotides of DNA? (Include the # of hydrogen bonds involved)

1) A and T pair up (2 H-bonds)

2) C and G pair up (3 H-bonds)

What is considered the “blueprint” for all of life? And why?

DNA because it codes for all of the proteins needed for life

What are the three kinds of proteins? What does each one do and give an example of each one?

1) Structural proteins - they hold things together inside and outside the cell (e.g. cytoskeleton)

2) Transport proteins - they move things into and out of the cell (e.g. NAD+)

3) Enzymes - they catalyze chemical reactions, such as building and breaking down molecules (e.g. glucose)

What is the central dogma of biology?

DNA —> RNA —> Proteins

What are the two steps of gene expression?

Transcription and Translation

What is Transcription?

RNA is assembled by RNA polymerase using the DNA code as a template

What is Translation?

Proteins are assembled by the ribosome using the RNA code

Define gene expression

Building a specific protein from a specific gene

What is a gene?

Any DNA sequence that encodes a polypeptide (aka protein)

What are the four main differences in DNA vs RNA?

1) DNA is double-stranded; RNA is single-stranded

2) DNA is found in the nucleus; RNA is found in the nucleus and cytoplasm in eukaryotes

3) DNA is created once by DNA polymerase in the cell cycle; RNA is created thousands of times by RNA polymerase in the cell cycle

4) A pairs with T in DNA; A pairs with U in RNA

What are the 3 RNA types in Gene expression?

1) Messenger RNA

2) Ribosomal RNA

3) Transfer RNA

What are the three facts about Messenger RNA? Where it goes, when it’s made, and what it does?

1) It shuttles from the nucleus to the cytoplasm

2) Made during transcription by RNA polymerase

3) Carries a transcript of a gene to a ribosome

Ribosomal RNA

part of the ribosome and helps build the ribosomes

Transfer RNA

Brings single amino acids to the ribosome

What RNA has a specific sequence called Anticodon?

Transfer RNA (tRNA)

What is a codon? What does it encode?

A codon is a 3-letter code on mRNA. It encodes an amino acid.

What is an anticodon?

A complementary 3-letter code on the tRNA

Difference in gene expression process in Eukaryotes vs. Prokaryotes?

Translation and transcription happen separately in Eukaryotes; But they happen simultaneously in prokaryotes

Where does transcription occur in eukaryotes? Prokaryotes?

Transcription occurs in the nucleus of eukaryotes; It occurs in the cytoplasm of prokaryotes

What are the 3 steps of Transcription?

Initiation, Elongation, Termination

Explain the step of Initiation?

A small section of DNA is unwound. Helicase breaks the hydrogen bonds between the bases, unzipping the DNA strands. RNA polymerase attaches to a specific spot of the DNA called the promoter (it marks the beginning of the gene that needs to be copied) of the template strand

Explain the step of Elongation?

RNA polymerase moves along the template strand, reading the bases. As it moves, it is making complementary RNA. DNA closes behind. (A→U, T→A, C→G, G→C).

Explain the step of Termination?

RNA polymerase detaches from the DNA and stops transcribing mRNA. The Poly-A tail forms (only in eukaryotic cells).

Define the Poly-A tail.

A sequence of adenine nucleotides added to the 3' end of eukaryotic mRNA after transcription, increasing its stability.

How do we process the mRNA to close out the Transcription process?

By using introns and exons

Define Introns

Introns are sequences that will not be translated. They are cut out of the mRNA sequence by enzymes.

Define Exons

Exons are sequences that will be translated and are spliced together.

What are the first two steps of Translation?

1. mRNA leaves the nucleus through nucleus pores

2. mRNA attaches to the ribosome, which reads the mRNA to build the protein

What are the third and fourth steps of Translation?

3. the ribosome moves down the mRNA transcript until it reaches a start codon (with the sequence AUG).

4. the ribosome grabs the tRNA with the complementary anticodon (UAC); together, this pair (AUG + AUC) will carry the amino acid “Met”.

What are the fifth, sixth, and seventh steps of Translation?

5. the ribosome moves down the mRNA to the next codon and down the tRNA to the next anticodon, creating more nucleotides.

6. the ribosome stops adding amino acids when it hits any of the following stop codons: UAA, UAG, or UGA.

7. the ribosome detaches and the mRNA transcript can be read again.

Is DNA code ambiguous or redundant?

it is redundant; more than one codon can encode the same amino acid.

What are the three ways that genes can be regulated?

1. Enhancers/Activators

2. mRNA degradation

3. Alternative splicing (in eukaryotes only)

How do Enhancers/Activators regulate gene expression?

Enhancers are segments of DNA that can be bound by proteins called activators to promote transcription

What is mRNA degradation?

enzymes breakdown mRNA after use. mRNA can be translated many times over, as it has a lifetime of anywhere between seconds to weeks depending on the organism. you can also add a Poly-A tail.

What is alternative splicing?

cells can change which parts of mRNA are exons and which are introns, i.e. one gene can lead to multiple proteins.

When do DNA mutations occur?

During the formation of gametes

What are the two ways that DNA mutations can occur?

1. copying error in DNA polymerase, which makes copies of DNA down the wrong nucleotide, hence causing point mutations

2. exposure to radiation or certain chemicals, which may cause nucleotides to be physically removed, hence causing frameshift mutations [a factor in colorectal cancer]

Define point mutations

Single nucleotide changes

What is a frameshift mutation? Is it a type of point mutation?

Frameshift mutations are when a number of nucleotides are removed that are not divisible by three. Can lead to a completely different protein.

What are the four types of Point Mutations?

1. Silent mutations

2. Neutral mutations

3. Missense mutations

4. Nonsense mutations

Silent mutations

the new codon encodes the same amino acid

Neutral mutations

those where the altered codon codes for a similar amino acid. no selective advantage or disadvantage.

Missense mutations

the altered codon is different, resulting in a different protein. can be good or bad, depending on the resulting protein.

Name a disease that is the result of a missense mutation?

Sickle cell disease

Nonsense mutations

Results in a premature stop codon.

What are the three types of mutations effects?

1. No effect

2. Partial effect

3. Drastic

What mutations results in no effect?

Neutral or silent mutations.

What would be a partial mutation effect?

If the protein’s function is slightly altered or if a non-essential protein is harmed

What is the universal code?

DNA

True or False: All organisms have the same 4 nucleotides A-T-C-G?

True

What is a transgenic organism?

Those with dna from one organism spliced into another organism, e.g. GloFish.