BIO 310- EXAM 2

DNA replication

copying of genetic material

origin of replication

the site on the bacterial chromosome where DNA synthesis begins

bidirectionally

the synthesis of new daughter strands is initiated within the origin and proceeds in both directions

replication fork

the region where the parental DNA strands have separated and new daughter strands are being made

oriC

origin of chromosomal replication

3 sequences in oriC

AT rich region, DnaA box sequences, GATC methylation sites

AT rich regions

where the DNA strands will initially separate in Ecoli

DnaA boxes

sequences that provide binding sites for DnaA proteins which initiate the formation of a replication fork in Ecoli

GATC methylation sites

provide a mechanism for regulating DNA replication in Ecoli

Dna A protein

a protein that binds to a DnaA box sequence a the origin of replication in bacteria and initiates DNA replication

DNA helicase (DnaB)

an enzyme that separates the two strands of DNA

DNA gyrase (topoisomerase 2)

alleviates positive supercoiling

Single stranded binding proteins

keep the parental strands apart

Primase

synthesizes an RNA primer

DNA polymerase 3

synthesizes a daughter strand of DNA

DNA polymerase 1

excuses the RNA primers and fills In with DNA

DNA ligase

covalently links the Okazaki fragments together

DnaA proteins

bind to DnaA sequences within the origin of replication to initiate DAN replication

DnaC proteins

Aid DnaA in the recruitment of DNA helices to the origin

Tus

binds to ter sequences and prevent the advancement of the replication fork

RNA primer

a short strand of RNA, made by primate, that is used to elongate a stand of DNA during DNA replication

primase

an enzyme that synthesizes sort RNA primers during DNA replication

leading strand

a strand during DNA replication tat is synthesized continually toward the replication fork

lagging strand

a strand during DNA replication that is synthesized as short Okazaki fragments in the direction away form the replication fork

okapi fragments

short segments of DNA that are synthesized to produce that lagging strand during DNA replication

primosome

a protein complex that includes DNA helices and primase

replisome

a complex that consists of a primosome and dimeric DNA polymerase

dimeric DNA polymerase

a complex of two DNA polymerase holoenzymes that move as a unit during DNA replication

termination sequences

In Ecoli a pair og sequences in the chromosome that bind a protein known as the termination utilization substance (Tus), which stops the movement of the rep-liaison forks

catenanes

intertwined circular molecules

conditional mutants

a mutant whose phenotype depends on the environmental conditions, such as temperature sensitive mutants

processive enzyme

an enzyme, such as RNA or DNA polymerase, which glides along the template strand and does not dissociate from it while catalyzing the covalent attachment of nucleotides

fidelity

to describe the accuracy of a process: few mistakes = high fidelity

proofreading function

the ability if DNA polymerase to remove mismatched bases from a newly made strand

ARS elements

DNA sequences found in yeast that function as origins of replication

G-quadraplex

a four stranded structure in DNA that is stabilized by hydrogen bonding between four guanines

pre replication complex (preRC)

in eukaryotes, an assembly of at least 14 different proteins, including a group of proteins called the origin recognition complex (ORC) that are required to initiate DNA replication.

origin recognition complex (ORC)

a group of proteins found in eukaryotes that acts as the first initiator of preRC assembly to begin DNA replication

MCM helicase

a group of six proteins needed to complete a process called DNA replication licensing, which is necessary for the formation of two replication forks at an origin of replication in eukaryotes.

DNA replication licensing

in eukaryotes, occurs when MCM helicase is bound at an origin of replication, enabling the formation of two replication forks.

translation replicating polymerase

a type fo DNA polymerase that can replicate over a DNA region that contains an abnormal structure

flap endonuclease

an enzyme that removes small RNA flaps that are generated by the action of DNA polymerase sigma on an RNA primer during DNA replication

telomeres

specialized repeated sequences of DNA found at the ends of eukaryotic chromosomes

telomerase

the enzyme that recognizes telomeric sequences at the ends of eukaryotic chromosomes and synthesizes additional repeats of these sequences

senescent

describes a cell that no longer capable of dividing

Polymerase Chain Reaction (PCR)

another way to copy DNA without the help of a vector or host cell

primers

a short segment of DNA or RNA that initiates DNA replication

template DNA

a sample of DNA, such as chromosomal DNA, that used in a PCR experiment

Taq polymerase

a thermostable form of DNA polymerase used In PCR experiments

primer annealing

in PCR, the process where primers bind to a strand of template DNA

primer extension

in PCR, the step in which complementary strands of DNA are synthesized from the denatured template DNA, starting at the primers

thermocycler

a sevice that automates the timing of temperature changes in each cycle of a PCR experiment

reverse transcriptase PCR (RT-PCR)

a modification of PCR in which the first round of replication involves the use of RNA ad reverse transcriptase to make a complementary strand of DNA

quantitative PCR

a method of PCR in which the synthesis of DNA is monitored in real time. This method can quantitate the string amount of DNA in a sample

cycle threshold method

in quantitative PCR, a method of determining the starting amount of DNA based on a threshold level at which the accumulation of fluorescence is significantly greater than the background level

DNA sequencing

a method for determining the base sequence in a segment of DNA

dideoxy sequencing

a method of DNA sequencing that uses dideoxyribonucleotides to terminate the growth of DNA strands

dideoxyribonucleotide (ddNTP)

a nucleotide used in DNA sequencing that is missing the 3’ —OH group. If incorporated then it stops and further growth of the strand

chain termination

an event that stops the growth of a DNA strand, RNA strand, or polypeptide

automated DNA sequencing

the use of fluorescently labeled deoxyribonucleotides and a fluorescence detector to sequence DNA

sequencing ladder

a series of bands on a gel that can be followed in order to determine the base sequence of a strand of DNA

gene editing

experimentally altering the sequence of a gene

Crispr Cat technology

a method that uses the components of the CRISPR Cas system of genome defense found in prokaryotes to introduce mutations into genes

enhancements

changing traits that are not involved with causing a disease

northern blotting

a technique to detect a specific RNA within a mixture of many RNA molecules

western blotting

a technique used to detect a specific protein within a mixture of proteins

antibody

proteins that are produced by the immune systems of vertebrates, which recognizes foreign material and target it for destruction

epitomes

the structure on the surface of an antigen that is recognized by an antibody

antigen

foreign substances that elicit an immune response because that are recognized by antibodies

electrophoretic mobility shift assays

a technique for studying protein DNA interactions in which the binding of protein to a DNA fragment slows down its mobility during gel electrophoresis

DNase 1 foot printing

a method for studying protein DNA interactions in which the binding of a p[rotein to DNA protects the DNA from digestion by DNase 1