Bio Exam 3

a segment of DNA that varies in copy number among members of same species

copy number variation

bind to and stabilize single-stranded DNA

single strand binding proteins

A protein that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

Topoisomerase

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

origin of replication

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

RNA primer

An enzyme that creates an RNA primer for initiation of DNA replication.

RNA primase

DNA polymerase III

synthesizes new DNA only in the 5' to 3' direction

Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides

DNA polymerase I

each new DNA molecule contains one strand from the original parent strand and one newly synthesized daughter strand

semiconservative model

which is heavier the parent or daughter strand?

parent

which isotope is used to make parent strands?

15 N

which isotope is used to make daughter strands?

14 N

new strands of DNA are made from \_____ to \_____ ends

5' to 3'

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

DNA Polymerase

what must be present for a new dNTP addition

3'-OH

building blocks of DNA

dNTPs

strand with continuous DNA synthesis

leading strand

strand with discontinuous DNA synthesis

lagging strand

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

okazaki fragments

Which strand has Okazaki fragments?

lagging strand

replication starts with a

primer

Are DNA strands parallel or antiparallel?

antiparallel

What does antiparallel mean?

side by side but in opposite directions

do DNA strands grow towards or away from the replication fork?

away from

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

DNA ligase

An enzyme that untwists the double helix of DNA at the replication forks.

helicase

What proofreads DNA?

DNA polymerase

How many origins of replication do eukaryotes have?

multiple

how many origins of replication do prokaryotes have?

one

why can't the lagging strand copy all the way to the end?

DNA polymerase needs a primer to start strand synthesis

is the lagging or leading strand shorter?

lagging

Telomeres job

protect the ends of chromosomes

chromosomes shorten every cell division. chromosome gets too short, cell dies

telomere shortening

An enzyme that catalyzes the lengthening of telomeres. The enzyme includes a molecule of RNA that serves as a template for new telomere segments.

telomerase

types of cells that express more telomerase

germ cells, stem cells, cancer cells

what can cells with telomerase do?

divide indefinitely

Do somatic cells have telomerase?

no, they can only divide a certain number of times

What is PCR used for?

replicating DNA sequence many times so it can be amplified and studied

Steps of PCR

1. Denaturation 2. Annealing 3. Extension 4. Repeat

unzipping DNA by raising the temperature

denaturation

primers attach to complimentary base-pairing

annealing

DNA adds dNTPs starting at the primer

extension

Ingredients of PCR

template DNA, Primers, dNTPs, DNA polymerase

What does PCR stand for?

polymerase chain reaction

Role of dNTPs in PCR

serve as building blocks for new DNA strands

role of template DNA in PCR

contains the region of interest to be amplified by PCR

Role of primers in PCR

to define the target region and provide a 3' end that can be extended by taq polymerase

Role of DNA polymerase in PCR

makes new strands of DNA

A DNA synthesis enzyme that can withstand the high temperatures of PCR

Taq polymerase

Where does Taq polymerase come from?

Thermus aquaticus

If you started with a single DNA molecule, how many would you have at the end of six PCR cycles?

64

If you started with a single DNA molecule, how many would you have at the end of 5 PCR cycles?

32

If you started with a single DNA molecule, how many would you have at the end of 4 PCR cycles?

16

Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel

gel electrophoresis

what parts of DNA get stuck first

large DNA segments

Charge of DNA

negative

Enzyme that cuts DNA at a specific sequence of nucleotides

restriction enzyme

reading the same backwards and forwards

palindromic

Specific site where a restriction enzyme cuts the DNA

restriction sites

Restriction maps show

the lengths of DNA fragments between restriction sites

DNA produced by combining DNA from different sources

recombiant DNA

Organisms that contain functional recombinant DNA from a different organism

transgenic organism

DNA for cloning is made with

donor DNA and vector DNA

ddNTP function

terminators, fluorescent

Why do ddNTPs terminate synthesis?

they have no hydroxl group causing synthesis to stop

DNA editing tool

CRISPR

DNA editing

a process by which changes to the DNA sequence of genes can be achieved; also termed gene editing.

Why is the polymerase isolated from a heat-tolerant bacteria used when performing PCR

During the denaturation step of PCR, most polymerases would also denature as the DNA dissociates, but heat-tolerant bacteria possess DNA polymerase that can survive the high temperatures.

DNA replication starts at specific locations in chromosomes. They are called origin of replication. Apparently, the DNA sequence of origin of replication is rich in A-T pairs. What would be a reason for that?

A-T pairs have two H-bonds between them while G-C pairs have three; therefore, regions rich in A-T pairs will be easier to break apart making them ideal for origins of replication.

After replication you are left with a daughter DNA molecule that contains many small pieces of RNA between long stretches of DNA. Which enzyme, involved in replication, is likely malfunctioning?

DNA polymerase I

Can the BamHI and the Sau3AI ends be connected? If so, explain

yes, the sticky ends made by both restriction enzymes are the same

genetic makeup of a cell or organism

genotype

common mutations in a population

polymorphisms

different forms or versions of a given gene

alleles

how many alleles are in a genotype of any given gene

2

Where do the two alleles come from?

one from each parent

2 alleles are the same

homozygous

2 alleles are different

heterozygous

observable expression of a trait

phenotype

Are mutations spontaneous or induced?

both

sources of induced mutations

X-ray, UV light, chemicals

germ line cells

egg, sperm, and cells giving rise to them

somatic cells

Any cells in the body other than reproductive cells

do mutations in germ-line cells transmit through generations?

yes

do mutations in somatic cells transmit through generations?

no

gene mutation in which a single base pair in DNA has been changed

point mutation

do point mutations have an effect on genes?

they can, but most times they do not

change in nucleotide sequence does not change amino acid sequence

silent/synonymous mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

missense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

nonsense mutation

Part of a gene sequence is missing-causes a frameshift mutation

deletion mutation

a mutation in which one or more nucleotides are added to a gene

insertion mutation

When a deletion or insertion is not a multiple of 3

frameshift mutation

the phenotype for a character most commonly observed in natural populations

wild type

mutant type

the uncommon phenotype

neutral mutations

bitter taster/ nontaster

beneficial mutations

CCR5 and HIV infection

why are polyps removed during a colonoscopy?

to prevent them from mutating and becoming cancerous

Genetic element that has the ability to move (transpose) from one site on a chromosome to another.

transposable elements

how genetic differences are passed down through generations

transmission genetics