Biology 101 Exam 4

The double stranded parent DNA molecule unwinds into ______ ______ ______ of DNA.

2 single strands

Once the strands get unwind, each parent strand will act as a ______ to synthesize a new daughter strand

template

Semiconservative Replication Model

Type of DNA replication in which the replicated double helix consists of one old strand, derived from the parental molecule, and one newly made strand.

Half of the DNA in the newly synthesized DNA molecule belongs to the ______ and the other half is still ______

parent; conserved

5'

PO4

3'

OH

Erwin Chargaff's Rule

A=T and G=C

Replication begin at...

origins of replication

Origins of Replication

sites where the replication of a DNA molecule begins; where 2 parental DNA strands are separated

Replication Bubble

a region of DNA, in front of the replication fork, where helicase has unwound the double helix

How many origins of replication do eukaryotes have?

few hundred to thousands

Replication proceeds in ______ ______ from each origin

both directions

Helicases

Enzymes that unwind the double helix at the replication forks

Why does helicase unwind DNA?

In order to make it accessible for primate and polymerase to synthesize the new DNA strands

Single Strand Binding Proteins (SSB)

Bind to and stabilize the single stranded DNA left behind from the action of helicase

Topoisomerase

Corrects "overwinding" ahead of replication forks caused from unwinding at the replication forks

why does overwinding need to be resolved?

In order to relieve the strain on the DNA strands

How does topoisomerase correct overwinding?

By making cuts, twisting, and then rejoining the DNA strands

Primase

An enzyme that lays down a primer on the parental DNA strand

Primer

5 to 10 nucleotides of RNA segments; acts as an attachment point for the enzyme DNA polymerase

What happens when polymerase binds to a primer?

It causes the polymerase to scan the entire length of DNA by moving in a 5' to 3' direction

DNA Polymerase

Catalyzes DNA synthesis and requires a template along with all 4 deoxyribonucleoside triphosphates

DNA Polymerase III

Catalyze the elongation of new DNA by adding nucleotides to the free 3' of the daughter strand

In which direction does chain elongation occurs in?

5' to 3' direction

What is required when making a new daughter strand?

A primer and a template strand

DNA Polymerase I

An enzyme which removes the primers from the DNA stand and then it replaces the gaps with DNA

Why are the primers removed?

Because RNA doesn't belong with DNA

DNA Ligase

An enzyme that replaces the gaps left behind from the removal of primers with new DNA

DNA polymerases can only add nucleotides in the ______ ______ end of a growing chain

free 3'

A new strand can only be synthesized in the ______ to ______ direction

5'; 3'

DNA polymerase III can create only 1 of the 2 strands in a continuous manner called the...

leading strand

The other strand DNA polymerase III creates has to be done so by in small fragments called ______ ______ by using primers going in the 5' to 3' direction

Okazaki fragments

1st key issue resolved during replication:

Unwinding of the helix

2nd key issue resolved during replication:

Relieving the strain at one end generated during unwinding at the other end

3rd key issue resolved during replication:

Discontinuous synthesis of the lagging strand

4th key issue resolved during replication:

Removal of the RNA primers

5th key issue resolved during replication:

Joining the gaps in lagging strand of DNA, left by removal of primers

6th key issue resolved during replication:

Proofreading for errors and fixing if any found

What enzymes are involved in DNA replication?

Helicase, DNA polymerase I, DNA polymerase III, Ligase, Topoisomerase, Primase

Any incorrect ______ found are replaced with correct ones

nucleotides

What enzymes are involved in DNA repair?

DNA polymerases, Glycosylases, Endonucleases, Ligases

DNA can be damaged by:

Radioactive emissions, UV light, free radicals and chemicals

Mismatch Repair

Enzymes correct errors in base pairings; The cellular process that uses specific enzymes to remove and replace incorrectly base pairings.

How does mismatch repair work?

One enzyme detects the mismatch and the other gets endonuclease to cleave the new DNA at the point where the mismatch occurred

Base Excision Repair

Repairs damage to a single nitrogenous base

How does base excision repair work?

Glycosylases removes a single nitrogenous base to create an apurinic or aplyrimidinic site (AP site) then AP endonuclease nick the damaged DNA backbone at the AP site then DNA polymerase removed the damaged region using its 5' to 3' exonuclease activity and correctly synthesis the new strand

Nucleotide Excision Repair

Needed when a few DNA nucleotides are damaged

How does nucleotide excision repair work?

Either endonuclease or exonuclease cuts out the damaged nucleotides then DNA polymerase I lays down new DNA in the space that is available then ligase joins the newly laid DNA to the existing DNA strand

Transcription and translation are also called...

gene expression

Transcription

The synthesis of RNA by using the information stored in DNA

Where does transcription take place?

Inside the nucleus

Translation

The synthesis of proteins by using the information stored in RNA

Where does translation take place?

Cytoplasm

What are the types of RNA?

mRNA, rRNA, tRNA, miRNA, snRNA

mRNA

Messenger RNA; the one that makes proteins; DNA transcription

rRNA

Ribosomal RNA; the one that makes ribosomes; nucleolus

tRNA

Transfer RNA; the one that makes the transfer molecule; transfer amino acids

miRNA

Micro RNA; one that play a role in RNA silencing

snRNA

Small nuclear RNA, plays a role in RNA silencing

Which RNA's are the building proteins?

mRNA, rRNA, tRNA

Which RNA's are the destroying proteins?

miRNA, snRNA

In Prokaryotes mRNA ______ undergo additional processing from transcription

doesn't

Prokaryotes is translated into proteins ______

immediately

In Eukaryotes mRNA ______ undergo additional processing from transcription

does

Eukaryotes yields a ______ mRNA which is translated into proteins

modified

RNA polymerase reads ______ and makes ______

3' to 5'; 5' to 3'

Stages of transcription:

Initiation, elongation, termination

Transcription - initiation in prokaryotes

Starts at the promoter region; RNA polymerase binds to the promoter region to read and transcribe DNA into RNA

What binds to the promoter region?

RNA polymerase

What is inside the promoter region?

Pribnow Box

Pribnow box

TATAAT

Transcription - elongation in prokaryotes

RNA polymerase adds nucleotides to the growing strand

Transcription - termination in prokaryotes

Ends at the terminator region on the template strand

Terminator Region

a certain sequence on the transcription unit that signals the RNA polymerase to end transcription

Transcription - Initiation in eukaryotes

Begins with the uncoiling of the chromatin; inside the promoter region there is a TATA box; RNA polymerase rely on transcription factors to bind to DNA along a promoter and needs enhancers and silencers to control transcription regulation

TATA Box

TATATA

Transcription - elongation in eukaryotes

RNA polymerase adds nucleotides to the growing strand; RNA polymerase adds 40 nucleotides per second

Transcription - termination in eukaryotes

RNA polymerase reads DNA until the gene length is exhausted and falls off; RNA polymerase continues even when pre-mRNA is sliced out of the growing RNA chain

RNA processing and editing modify the mRNA ______ after transcription

immediately

RNA Processing

Ends of the pre-mRNA (5' and 3') are altered; The removal of introns and the combining of exons

What is the alteration of the pre-mRNA on the 5' end?

A nucleotide cap

What is the alteration of the pre-mRNA on the 3' end?

A poly-A tail

How do the alteration of the pre-mRNA affect it?

It helps facilitate the export of mRNA outside of the nucleus and into the cytoplasm; It helps protect the degradation of mRNA from hydrolytic enzymes; It helps the mRNA slide into the ribosome

Introns

Non-coding sequences

Exons

Coding sequences

RNA splicing

The removal of introns and the joining of exons

RNA splicing is carried out by the enzyme ______

Spliceosome

RNA Editing

a process by which some cells can make distinct changes to specific nucleotide sequences within an RNA transcript

RNA editing is ______ ______ as RNA processing

not common

How many types of RNA editing are there?

2

Substitution editing

Individual nucleotide bases are altered

Insertion/Deletion Editing

Nucleotides are added/deleted from the total number of bases

What is required for translation?

mRNA, tRNA, ribosomes, amino acids

mRNA function in translation

The ribosome reads mRNA in codons to make proteins

How many codons are there?

64

How many codons code for amino acids?

61

What are the 3 codons that don't code for amino acids called?

Stop codons

What are the stop codons?

UGA, UAG, UAA

1 out of the 61 codons is a ______ ______

start codon

What is the start codon called?

AUG