Molecular Biology Exam 2 Material IU

DNA Polymerase

-enzymes used to assemble DNA molecules by copying a template strand of DNA according to base-pairing interactions

-adds nucleotides to the 3' end of a growing chain

DNA primase

-a type of RNA polymerase which creates an RNA primer

-an enzyme involved in the replication of DNA

Helicase

-enzyme that separates double-stranded DNA into single strands allowing each strand to be copied

(think unzipping a zipper)

leading strand

-a strand of DNA that is being replicated continuously

lagging strand

-a strand of DNA that is being replicated non-continuously

okazaki fragments

short, newly synthesized DNA pieces that are formed on the lagging template strand during DNA replication

RNA primer

RNA strands that are added to the lagging strand of DNA by RNA polymerase, beginning replication of the lagging strand

replication bubble

the area or section where DNA replication occurs

replication fork

The point at which the two strands of DNA are separated to allow replication of each strand

DNA ligase

an enzyme that facilitates the joining of two DNA strands together by catalyzing the formation of a phosphodiester bond

origin of replication

a particular sequence in a genome at which replication is initiated

ori C

the DNA sequence that signals for the origin of replication in E. coli

SSBs: single stranded binding proteins

proteins responsible for holding the replication fork of DNA open and making sure the strand does not break apart

nucleosome remodeling complex

when a nucleosome is moved away from a histone in some way for a protein to be able to read the DNA sequence is known as...

DNA boxes

-a section of DNA sequencing that always results in a certain reaction from the protein

-also known as promoter sequence

point mutations

a single nucleotide substitution

transitions

a point mutation where a pyrimidine is replaced with another pyrimidine or a purine with another purine

transcription

the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase

messenger RNA

the form of RNA in which genetic information transcribed from DNA as a sequence of bases is transferred to a ribosome

ribosomal RNA (rRNA)

a type of RNA, distinguished by its length and abundance, functioning in protein synthesis as a component of ribosomes

transfer RNA (tRNA)

RNA consisting of folded molecules that transport amino acids from the cytoplasm of a cell to a ribosome

RNA polymerase

-an enzyme that produces primary transcript RNA

-necessary for constructing RNA chains using DNA genes as templates (transcription)

ribonucleotides

these are considered a molecular precursor of nucleic acids, consisting of a ribosome and a nucleotide

initiation

the assembly of the replication apparatus at a unique site

promoter

A DNA sequence at the beginning of a gene that functions as a signal to initiate transcription

consensus

the calculated order of most frequent amino acids

sigma factor / subunit

-a protein needed only for initiation of RNA synthesis

-a single protein molecule that assembles with other protein molecules to form a protein complex

closed promoter complex

-the structure formed during the initial step in assembly of the transcription initiation complex

-consists of the RNA polymerase and/or accessory proteins attached to the promoter, before the DNA has been opened up by breakage of base pairs

open complex

an enzyme locally unwinds at a promoter to form...

abortive initiation

a process in which RNA polymerase binds to a DNA promoter and enters into cycles of synthesis of short mRNA transcripts which are released before the transcription complex leaves the promoter

-10 box

a consensus sequence known as Pribnow box (TATAAT) that helps form a promoter

-35 box

a consensus sequence (TTGACA) that helps form a promoter

transcription bubble

an area where a small amount of DNA is unwound to synthesize RNA

coding strand / non-template strand

The non-template DNA strand that has the same nucleotide sequence as the transcribed RNA (except that T replaces U)

template strand

-a nucleotide sequence that provides the structural mold to create a sequence complementary to it

termination sequence

DNA sequences that serve to stop transcription

nonsense, missense, silent, and framshift

there are three types of point mutations (substitution, insertion, and deletion), what are the four main outcomes of point mutations?

leading strand

Which strand is synthesized in the 5' --> 3' direction?

lagging strand

Which strand is synthesized overall in the 3' --> 5' direction?

Bidirectional replication means that there are 2 forks that move in opposite directions.

What does the term bidirectional replication mean?

DNA polymerase needs DNA primase to lay down a primer to begin replication.

Why can't DNA polymerase synthesize DNA on its own?

elongation

The leading strand is synthesized continuously. Lagging strand is synthesized discontinuously.

This stage is known as...

termination

the 2 replication forks meet about halfway around the bacterial chromosome in E. coli

This stage is known as...

5' --> 3' direction

In what direction does helicase travel along the DNA?

Topoisomerases

enzymes that release the stress on DNA from unwinding a section for replication

DNA gyrase

this enzyme travels ahead of the helicase and alleviates supercoils (aka Type II Topoisomerase)

Holoenzyme

a general term used for multiprotein complexes in which a core enzyme is associated with additional protein components that complete its structure and lead to its function

DNA polymerase I

specialized to remove remaining RNA primer and synthesize DNA across the gap

DNA polymerase III

a specific enzyme used to replicate the majority of the DNA on the leading and lagging strands

DNA ligase connects the Okazaki fragments by making phosphodiester bonds between base pairs.

What does DNA ligase do? How?

DnaA protein

binds to DnaA boxes within the origin to initiate DNA replication

Type I Topoisomerase

this type of enzyme makes a single cut or break in the DNA to avoid supercoiling

Type II topoisomerase

this type of enzyme makes two cuts (or a double stranded break) and a second DNA double helix is passed through the temporary gap before the cut DNA is religated (reconnected)

Type II topoisomerase

Which type of topoisomerase needs ATP in order to function?

Telomeres

protects the ends of DNA chromosomes

Endonuclease

a nuclease that acts within a strand

Exonuclease

a nuclease that acts only at the end of a strand

Vector

an organism that contains all the information needed to propagate inserted DNA inside a host cell (bacteria)

Endogenous agents

structure that damages DNA and is formed insides the cell

Exogenous agents

structure that damages DNA and comes from the surrounding environment

Deamination

the loss of an amino group from a nucleotide base is known as...

Depurination

the loss of one of the purines from a nucleotide is known as...

Induced mutations

mutations due to agents that can damage DNA are known as...

Mutagens

agents that generate mutation inducing DNA damage are called...

Homologous recombination and nonhomologous end joining (NHEJ)

What are the two major pathways to repair double-strand breaks?

Homologous recombination

-a type of recombination in which nucleotide sequences are exchanged between two similar molecules of DNA

-used when double-strand breaks occur

NHEJ (nonhomologous end joining)

-a type of double-strand break repair mechanism that usually occurs when cells haven't duplicated their DNA yet

-joins broken ends of DNA together

Translesion DNA synthesis

-when DNA polymerase gets derailed from the template strand because an error, a special DNA poly comes in to extend the primer passed the error

-this can also introduce mutations in the DNA

nucleotide excision repair, base excision repair, mismatch repair

What are the three types of single stranded repair?

nucleotide excision repair

If a strand of DNA is exposed to UV light, what type of repair will be needed to fix the DNA?

Covalent bonds will form between adjacent pyrimidines (pyrimidine dimers). Endonucleases will cut out the damaged nucleotides, DNA poly will add new bases and DNA ligase connects them

What happens when DNA is exposed to UV light? How is this damage repaired? (name specific enzymes)

Base excision repair. Glycosylase recognizes and removes damaged base, endonuclease cuts the phospodiester backbone

What type of repair occurs when a base is damaged? How is this damage repaired? (name specific enzymes)

Missmatch repair

What type of repair occurs when errors happen during DNA replication (not necessarily damaged)?

The damaged base is first detected and then is flipped away from the double helix to allow for easy access

How do glycosylase enzymes gain access to damaged bases during base excision repair?

XP - Xeroderma pigmentosum

a human disease caused by mutations in any one of several nucleotide excision repair genes that can cause skin disorders when exposed to UV light

1. Ionizing radiations (X-rays, Gamma rays)

2. Physical constraints

3. reactive oxygen species (free radicals)

What are three ways in which a double strand break can occur?

Base excision repair

This type of repair recognizes specific chemical modifications on a single base within the DNA structure

1.presences of Uracil in DNA

2. methylated bases

3. oxidized bases

repairs a single base on a strand of DNA

What does base excision repair correct for? Be specific (3).