Genetics Exam 2

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DNA Replication

Makes DNA copies that are transmitted from cell to cell and parent to offspring

Chromosomal DNA

Stores information in genes

Transcription

Produces and RNA copy of a gene

Messenger RNA

A temporary copy of a gene containing information to make a polypeptide

Translation

Produces a polypeptide using the information in mRNA

Polypeptide

Becomes part of a functional protein that contributes to an organisms traits

What defines the end and beginning of a gene?

DNA base sequences

What does DNA base sequences help regulate?

The level of RNA synthesis

What must happen for transcription to occur?

Proteins must recognize and act on DNA

What is gene expression?

The overall process by which information within a gene is used to produce a functional product

What determines a trait?

Gene expression in concert with environmental factors

What are codons?

3 nucleotide sequences within mRNA that specify particular amino acids

Define start codon

Specifies first amino acid in a polypeptide sequence, usually a formylmethionine or methionine

What is the start codon usually found in eukaryotes?

Methionine

What is the start codon typically found in bacteria?

Formylmethionine

Define stop codon

Specifies the end of a polypeptide synthesis

What does polycistronic mean?

Codes for two or more polypeptides

What are the three transcription stages?

Initiation, elongation, and termination

First part of initiation in transcription?

The promoter functions as recognition site for transcription and lets RNA polymerase on

Second part of initiation in transcription?

Transcription factors enable RNA polymerase to bind to promoter

The third step of initiation?

After RNA polymerase binds, DNA denatures into an open transcription bubble 

What happens during elongation of transcription?

RNA polymerase slides along DNA in an open complex to synthesize RNA

What happens in termination of transcription?

A terminator is reached that causes RNA polymerase and RNA transcript to dissociate from DNA

With transcription in bacteria, what’s special about the -10 sequence?

It is A-T rich

What does RNA polymerase do?

It’s the enzyme that catalyzes the synthesis of RNA

What is the RNA polymerase holoenzyme in E. coli composed of?

Cove enzyme (five subunits) and sigma factor (one subunit)

Where is the thing you need more of located?

Closer to the consensus sequence 

What does the RNA polymerase holoenzyme do?

Binds loosely to DNA, scans the DNA until it finds a promoter

What can the sigma factor recognize in DNA?

Both the -35 and -10 sequences

What forms the closed complex?

The binding of RNA polymerase to the promoter 

What forms an open complex?

When the TATAAT box in the -10 sequence is unwound

What gets made within the open complex? What ends up releasing?

A short RNA strand, the sigma factor releases marking the end of initiation

What does the promoter specify?

The direction of transcription  

What exactly is termination?

The end of RNA synthesis

When does termination occur?

The RNA-DNA hybrid of the open complex is forced to separate

What happens when RNA-DNA hybrid separates?

Releases the newly made RNA as well as RNA polymerase

What is E. coli’s two different mechanisms for termination?

rho-dependent termination and rho-independent termination

Rho-dependent termination

Requires a protein known as p (rho)

Rho-independent termination

Does not require the protein p (rho)

How many polymerases is nuclear DNA transcribed by? 

Three different RNA polymerases 

What does RNA polymerase I do?

Transcribes all rRNA genes (except 5s rRNA)

What does RNA polymerase II do?

Transcribes all protein-coding (structure) genes

What does RNA polymerase III do?

Transcribes all tRNA 

What does the rho-independent and rho-dependent both need?

A stem and loop structure

What does eukaryotic genes have?

A core promoter and regulatory elements

What does eukaryotic genes consist of?

The TATA box, transcriptional start site, and one or more downstream promoter elements 

What is basal transcription?

Low level of transcription core promoter produces by itself

What do enhancers contain?

Contain one or more regulatory element

How big are enhancers?

Usually 50 bp to 1000 bp 

What influences the rate of transcription in eukaryotes?

Regulatory transcription factors (proteins) binding to enhancers

What do activators do?

Stimulate transcription 

What do repressors do?

Inhibit transcription

Where are enhancers usually located?

The -50 to -100 region

What are the two general types of factors that regulate gene transcription?

Cis-acting elements and trans-acting factors 

What do cis-acting elements regulate?

DNA sequences exert their effect only over a particular gene

What do trans-acting factors regulate?

General and regulatory transcription factor proteins that bind to DNA sequences

What are the three categories of proteins required for transcription to occur at promoter?

RNA Polymerase III, general transcription factors, and mediators 

What are general transcription factors?

It’s made up of six different proteins, it’s just a big cluster

What is a mediator?

A protein complex

What is the allosteric model?

Change in shape 

What is the torpedo model?

Shoots straight through, very quick

What did analysis of bacteria in the 60’s and 70’s discover?

DNA in coding strand corresponds to nucleotides in mRNA. Sequence of codons in mRNA provides instruction for sequence of amino acids in the polypeptide

What is colinearity?

Sequence of codons in mRNA provides instruction for sequence of amino acids in the polypeptide

What are exons?

Coding sequences

What are introns?

intervening sequences

What is removed and what is spliced together?

Introns are removed/ excised while exons connect together/ spliced

What is RNA splicing?

Common genetic phenomenon in eukaryotes that also occurs occasionally in bacteria

What is initially transcribed as larger precursor RNAs?

Many genes for non-coding RNA

What can RNA transcripts be cleaved into?

Smaller functional pieces 

Where are transfer RNSs cleaved?

At both the 5’ and 3’ ends to produce mature, functional tRNA’s

What cleaves transfer RNAs?

Exonucleases and endonucleases

What do exonucleases cleave?

Covalent bonds between 2 nucleotides at one end of a strand

What can endonucleases cleave?

Bonds within a strand

What is RNaseP?

An endonuclease ribozyme that is composed of RNA

What does transcription in eukaryotes produce?

A long transcript known as pre-mRNA

How is pre-mRNA altered?

Splicing and other modifications to it before it leaves the nucleus 

What is a splicosome?

A multicomponent structure that aids splicing

What does splicing require?

The aid of a splicosome

What are snRNPs?

Small nuclear RNA and a set of proteins that make up several subunits of the spliceosome

What is the benefit of genes with introns?

A phenomenon called alternative splicing 

What happens with a pre-mRNA with multiple introns?

It can be spliced in different ways which results in mature mRNA’s with different combinations of exons

What’s something interesting about polypeptides?

Two or more can be derived from a single gene which allows an organism to carry fewer genes in its genome yet have a large diversity of polypeptides

How can the degree of splicing and alternative splicing vary?

Varies greatly among different species 

What does tropomyosin play a role in?

Muscle contraction

What regulates alternative splicing?

Splicing repressors and splicing enhancers

What does each cell type express?

Its own unique set of splicing repressors and enhancers

What are SR proteins?

Contain a domain at c-terminal end rich in serine and arginine (amino acids) and RNA-binding domain at their amino-terminal end 

What do most mature mRNA’s have at their 5’ end? How is it attached?

A 7-methyl-guanosine, it’s covalently attached

How does capping occur?

As the pre-mRNA is being synthesized by RNA polymerase II, typically when transcript is only 20 to 25 bases long

What is exon-skipping?

When some exons get skipped

What do cap-binding proteins recognize?

The 7-methylquanosine cap structure 

What do cap-binding proteins play roles in?

Movement of some RNA’s in and out of nucleus, early stages of translation, and splicing of introns

What is the polyA tail?

A string of adenine nucleotides at mature mRNA’s 3’ end

When is the polyA tail added?

Enzymatically after the gene is completely transcribed 

What does the 7-methylguanosine cap allow for RNA’s?

It allows it to get out of the nucleus

What is RNA editing?

Change in the base sequence of an RNA after it’s already made. This occurs by changing the one base to another

What is deamination? 

Converts RNA nucleotides into new forms, can involve addition/ deletion of bases or conversion of a base   

Why are polyA tails and 7-methylguanosine caps important?

Helps to prevent the degradation of RNA

What are the active participants in cell structure and function?

Proteins 

What are protein-coding genes?

Genes that code polypeptides