lecture 8 intro to cell and molecular biology

What is a gene?

A gene is a sequence that codes for a functional product —> this could be an RNA but usually a polypeptide

What are the 2 stages of gene expression and describe generally what they do:

The 2 stages of gene expression are transcription which is the synthesis of RNA using information in DNA, performed by enzyme RNA polymerase. In translation, this is the synthesis of polypeptide, using info in mRNA, performed by Ribosomes

what performs transcription?

performed by the enzyme RNA polymerase

What performs translation?

Performed by the ribosome

What are proteins the links to?

the genotype and phenotype

what is mRNA the bridge to?

genes and proteins

what is the central dogma? how does this information flow?

DNA —> RNA —> Polypeptide. Information flows from center outward such as nucleus —> cytosol (ribosomes)

What is an example of a violation of central dogma?

Telomerase —> uses short stretch of RNA to build out extra lengths on telomeres …goes from RNA to DNA

Who first suggested that genes dictate phenotypes through enzymes?

Archibald Garrod

How do genes dictate phenotype (through what)?

through enzymes

Explain how Garrod originally came up with his experiment?

Basically Garrod working with a fungus called Neurspora crass where when he grew it in minimal medium, the cells would grow + survive like usual. However, he observed that in a mutant neurospora crass, the cells did not grow or divide. He wanted to know why this is

What is the name of the experiment that was inspired by Garrod? Describe what the experiment did:

The beadle and Tatum experiment. The experiment exposed bread mold to x-rays creating mutants that were unable to survive on minimal medium. The X-Rays were used to damage the DNA of the fungus causing mutation. We could now look at mutants and narrow down which gene had been mutated which didn’t allow enzyme to function.

Desribe the mutants in Neurospora crassa experiment?

The mutants in the neurospora crass lacked enzymes that could produce arginine. Each class had a defect in one of the genes that produced the enzymes in Arginine.

What was the big point that came from the beadle and Tatum experiment?

the big point was that this led to the formation of the one gene- one enzyme hypothesis where each gene dictates the production of a special enzyme. Back in the day this was how scientists discovered metabolic pathways by mutating genes that code for functional proteins allowing them to figure other elements.

Why was the one gene-one protein hypothesis revised?

this was revised because not all proteins are enzymes

Why is one-gene, one-protein not correct (provide more details on the structure of protein)

Proteins are composed of several polypeptides which form the quartnery structure suggesting that it’s multiple genes that create different polypeptides that form the quartenary structure

What was the hypothesis revised to?

one gene, one polypeptide

What does piRNA do?

\re-arranges/positions chromatin and creates euchromatin

Enhancer RNAs

Add enhancers to enhance expression of gene

What does snoRNA do?

it’s related to many of the functions in the nucleolus because that is where rRNA is made

How does RNA form hairpin structures?

It can bend back on itself

What is the antisense strand?

Has the same sequence as mRNA and is the template strand for the creation of mRNA

What is the sense strand?

The sense strand is the NON template DNA strand which has the same sequence for mRNA (we have to substitute T for U though)

Where are codons located?

The sense strand

How does the synthesis of transcription start?

it starts by opening strands of DNA at the promoter

Why is the promoter easy to pry open?

It’s easy to pry open because it is made of the TATA box to which A:T only have 2 hydrogen bonds making them easy to break

In transcription, which DNA sequence has the starting point

the promoter

Why can we not say the starting point is similar to the start and stop codon in translation?

Start and stop codons signal for the initiation and termination of translation, not transcription

What are the 3 stages of transcription?

the 3 stages of transcription are initiation, elongation, and termination

What do promoters signal for?

the start of transcription

How far is the promoter and actual start point?

promoter is upstream of start point

What 2 things do we need for transcription?

1) we need RNA polymerase II which will bind to the promoter 2) we need transcription factors which are proteins that help the binding of RNA polymerase to the promoter.

Name the 3 roles for transcription factors?

1) they help RNA polymerase bind to DNA 2) help recognize the TATA box 3) open up double stranded DNA

What is the name for RNA and transcription factors that are bound to the promoter?

transcription factor complex

What kind of organisms rely on the formation of the TATA box for initiation?

eukaryotes

What happens during the elongation stage

RNA polymerase untwists the helix to which the DNA strand re-twist and re-anneal behind the RNA polymerase as it moves forward. As the two strands of DNA are coming together (because again RNA polymerase re twists and brings back the strands together) the primary mRNA strand is forced off the antisense strands

What is the rate of transcription for eukaryotes?

40 base pairs per second

How many RNA polymerases can transcribe DNA to RNA on a gene?

multiple RNA polymerase 😉

What can prokaryotes do during elongation that eukaryotes can NOT do

Prokaryotes can transcribe and translate before the RNA molecule is fully synthesized

To what end are ribonucleotides added to the growing mRNA

the 3 end so mRNA is made in the 5 to 3’ direction

What is the process for termination in bacteria?

Bacteria have a terminator sequence that tells RNA polymerase to stop. As well, bacteria termination can stop termination itself or mediate itself through Rho proteins

How do Rho proteins work?

Rho proteins work when RNA polymerase moves along DNA, it creates an mRNA copy, at certain points mRNA folds into C-G rich hairpin structure. Eventually rho protein will recognize and attach to the mRNA transcript following RNA polymerase. Eventually RNA polymerase will encounter the C-G rich structure and stop so Rho protein can catch up to it. Once rho catches up, it releases the mRNa-DNA hybrid and disrupts transcroption causing ca