Bio - Exam 4 - DNA Replication

Nucleic acids store and transmit

hereditary information

The amino acid sequence of a polypeptide is programmed by

a unit of inheritance called a gene

Genes are made of

DNA, which is a nucleic acid

Two types of nucleic acids

Deoxyribonucleic acid (DNA)

Ribonucleic acid (RNA)

DNA provides directions for

its own replication

DNA directs synthesis of

Messenger RNA (mRNA) and, through mRNA, controls protein synthesis

mRNA is synthesized in the

nucleus

after mRNA is synthesized in the nucleus, it

is moved into the cytoplasm via nuclear pore

Once mRNA reaches the cytoplasm, it 

synthesizes protein

Nucleic acids are polymers called

polynucleotides

Each polynucleotide is made of monomers called

nucleotides

Each nucleotide consists of

a nitrogenous base, a pentose sugar, and a phosphate group

Where is the phosphate group bonded to on the pentose sugar 

the 5’

Where is the nitrogenous base bonded to on the pentose sugar

the 1’

DNA or RNA polymers have a

directionality

Directionality affects what part of DNA and RNA

the 3’ and 5’ ends

What happens on the 3’ end of a nucleotide

more nucleic acids are polymerized

the H2O breaks to OH, forms bonds

What is the 5’ end of a nucleotide

where the phosphate attaches

The two types of nitrogenous bases

pyrimidines, purines

Pyrimidines include

cytosine, thymine, uracil

pyrimidines are

nitrogenous bases that have a single six-membered ring

Purines include

adenine and guanine

Purines are

nitrogenous bases that have a six-membered ring fused to a five-membered ring 

Sugar backbone: In DNA the sugar is

deoxyribose

Sugar backbone: In RNA the sugar is

ribose

Ribose in RNA causes the 2’ to have a

OH group

Deoxyribose in DNA causes the 2’ to have a 

H 

The OH functional group in RNA is

polar, which means it’s more reactive

More functional groups means

more reactive, which is why RNA are messengers and DNA are more stable

Nucleotide polymers are linked together to

build a polynucleotide

Adjacent nucleotides are joined by 

covalent bonds that form between the -OH group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon on the next

phosphodiester linkage

a covalent bond that links the 5' carbon of one nucleotide's sugar to the 3' carbon of another nucleotide's sugar via a phosphate group

phosphodiester links create a backbone of

sugar-phosphate units with nitrogenous bases as appendages

The sequence of bases along a DNA or mRNA polymer is

unique for each gene

Base Pairing

purines pair with pyrimidines 

A with T

G with C 

Erwin Chargaff

reported that DNA composition varies from one species to the next

Chargaff’s Rule uncovered the fact that

The percentages of bases in organisms will always be the same for A and T and the same for G and C

Watson and Crick found that

only purine-pyrimidine pairs fit inside the double helix

purine-purine, not enough space

pyrimidine-pyrimidine, too much space

How to purines and pyrimidines stick together

hydrogen bonds form between G and C and A and T

G triple bond C

A double bond T

Transcription occurs at high concentrations of

A’s and T’s, because it is easier to pull apart a double bond than a triple bond

DNA contains thymine, whereas RNA 

contains Uracil

Antiparallel

5’ and 3’ ends of one strand will always be opposite to the strand it connects with

arrow always faces 3’

Deoxyribonucleotides are joined by

phosphodiester linkages

Phosphodiester linkages make up

DNA’s primary structure (one strand)

DNA’s primary structures are arranged in pairs as 

antiparallel strands

Antiparallel strands are held together by

complementary base pairing and hydrophobic interactions

Complementary base pairing make up

DNA’s secondary structure

Deoxyribonucleotides include

purines and pyrimidines

Purines and pyrimidines are held together by 

complementary base pairing (AT, GC)

T.H. Morgan’s group showed that

genes are located on chromosomes, the two components of chromosomes (DNA and Protein) became candidates for the genetic material

DNA can transform

bacteria

When you stress bacteria, they

shed plasmids, which have genes on them

incorporating genes means they were transferred

Viral DNA can program 

Cells

these are called bacteriophages (phages) and are widely used in molecular genetics research

Capsid

a protective protein coat on a virus that surrounds their genetic material

DNA are double stranded, so in order to replicate

they have to pry strands apart

in order to replicate DNA,

a nitrogenous base (AT, GC) comes in and reads one strand, then provides its compliment

DNA replication can only be continuously built with 

3’ ends

The three competing theories of DNA replication

Conservative, semiconservative, dispersive

DNA Replication: Conservative

Parent strands come back together

DNA Replication: Semiconservative

Parent strands serve as a template for the daughter strands

DNA Replication: Dispersive

New strands are a mix of parental and daughter strands

origins of replication

special sites where replication begins

where the two DNA strands are separated

opens up a replication “bubble”

origins of replication in eukaryotic chromosome

may have hundreds or even thousands

replication proceeds in both directions from each origin, until 

the entire molecule is copied

DNA will resist unwinding and separating the two strands, this new conformation is

very unstable

how does the cell keep the DNA in the new conformation after DNA replication

Proteins

replication fork

at the end of each replication bubble

Y-shaped region where new DNA strands are elongating

Helicases

enzymes that untwist the double helix at the replication forks

Single-strand binding protein

binds to and stabilizes single-stranded DNA until it can be used as a template

stabilizes N bases

Topoisomerase

corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

relieves supercoiling

DNA polymerase

enzymes that catalyze the elongation of new DNA at a replication fork

most DNA polymerases require 

a primer and a DNA template strand

Primase

an enzyme that can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template

The primer is

short (5-10 nucleotides long)

and the 3’ end serves as the starting point for the new DNA strand

the rate of elongation is about

500 nucleotides per second in bacteria

50 per second in human cells

along one template strand of DNA, the DNA polymerase 

synthesizes a leading strand continuously, moving toward the replication fork

Synthesis of leading strand: Step 1

DNA is opened, unwound, and primed

primase synthesizes RNA primer, topoisomerase relieves twisting forces, helicase opens double helix, SSBP stabilize single strands

Synthesis of leading strand: Step 2

synthesis of leading strand begins

sliding clamp holds DNA polymerase in place, DNA polymerase works in 5’ to 3’ direction, synthesizing leading strand

continuous strand =

leading strand

discontinuous strand = 

lagging strand

DNA ligase

only on lagging strand, joins together Okazaki fragments

to elongate the lagging strand, DNA polymerase must

work in the direction away from the replication fork

Okazaki fragments

the series of segments in the lagging strand

synthesis of the lagging strand: step 1

primer added 

synthesis of the lagging strand: step 2

first fragment synthesized

synthesis of the lagging strand: step 3

second fragment synthesized

synthesis of the lagging strand: step 4

primer replaced

synthesis of the lagging strand: step 5

gap closed 

Replisome

all the proteins required for DNA synthesis

telomeres

ends of linear chromosomes (the end of lagging strand)

don’t get fully replicated

telomerase

elongates telomeres, typically stem cells and gonads

made of protein and RNA

DNA mistakes: DNA polymerase

can make a mistake about 1 in every 100,000 base-pairs 

mismatching of bases

has the ability to proofread and fix the mistake

DNA polymerase does not catch all mistakes and some still

make it into the newly synthesized DNA (s phase)

Mismatch repair

slew of enzymes detects the mismatch and takes out a portion of the DNA and replaces it

in G2 phase

Damaged DNA - UV light

takes DNA and forms thymine dimers

Nucleotide excision repair 

for damage outside of cell cycle

similar to mismatch repair but nucleotide excision repair is not involved with DNA synthesis 

Single stranded binding proteins

stabilizes single-stranded DNA

Helicase def

catalyzes breaking of hydrogen bonds between base pairs to open the double helix

DNA polymerase does what

extends the leading strand

sliding clamp 

holds DNA polymerase in place during strand extension