BSCI 1510

DNA polymerase

catalyzes the addition of nucleotides to the 3ʹ end of a growing strand of DNA using a parental DNA strand as a template

Helicase

uses the energy of ATP hydrolysis to unwind the DNA double helix ahead of the replication fork

Single-strand DNA binding protein

binds to single-stranded DNA exposed by DNA helicase, preventing base pairs from re-forming before the lagging strand can be replicated

DNA topoisomerase

produces transient nicks in the DNA backbone to relieve the tension built up by the unwinding of DNA ahead of the DNA helicase

Sliding clamp

keeps DNA polymerase attached to the template, allowing the enzyme to move along without falling off as it synthesizes new DNA

Clamp loader

uses the energy of ATP hydrolysis to lock the sliding clamp onto DNA

Primase

synthesizes RNA primers along the lagging-strand template

DNA ligase

uses the energy of ATP hydrolysis to join Okazaki fragments made on the lagging-strand template

purines

adenine, guanine 2 rings and 4 nitrogen molecules

pyrimidines

thymine, cytosine- 1 ring and 2 nittogens

10 base pairs per turn

34 nm/turn

semiconservative (most right)

2 strands of DNA unwind and each acts as a template for synthesis for a new strand.

results in one original strand and one new one

conservative

one molecule that consists of both original DNA and another molecule that counts for two new strands

dispersive

two DNA molecules are mixtures of parental and daughter DNA, each individual is a patchwork of old and new DNA

initator proteins

disrupt hydrogen bonding at replication orgins mostly at A and T since they have two hydrogen bonds while G and C have three hydrogen bonds

requirements of polymerase

template strand, primer has to have an hydroxyl or 3 OH, and dNTPs

polymerase synthesis and reading

synthesized 5’ to 3’ but reads from 3’ to 5’

Primase

makes a short stretch of nucleic acid complementary to the template that provides a 3’ for the DNA polymerase to work on

leading strand

constantly synthesized since it runs from 5’ to 3’, only one RNA primer

lagging strand

discontinuous since it runs from 3’ to 5’ and polymerase synthesizes from 5’ to 3’, makes okazaki fragments, needs a lot of RNA primers for polymerase to latch onto

topoisomerase

prevents DNA from getting to winded up after the DNA is opened up, follows after the replication fork

DNA polymerase III

extends the primers, adding to the 3’ end to make the bulk of new DNA, also a exonuclease since it can add dNTP’s(polymerizing) as well as edit at different active sites

DNA polymerase I

RNA Primers are removed

eukaryotes and prokaryotes in leading strand synthesis

polymerase II in prokaryotes and polymerase in eukaryotes

lagging strands closing

prokaryotes- circular DNA so problem solved

eukaryotes- needs teleormases

telomerases

makes its own RNA template which it adds multiple copies of the same repetitive DNA so that the chromosome will not get shorter

1. RNA primer transcript through reverse transcriptase( DNA to RNA)

2. primase adds RNA primer

3. DNA polymerase fills it in

4. RNA primer is removed

nucleotide triphosphate importance

make beta and gamma phosphodiester bonds used to drive covalent bond formation

histones

positively charged, surface made up mostly lysines and arginines,

heterchromatin

highly condensed, few genes transcribed, constitutive (always compacted), facultative(differes between cells), centromeres and telomeres, CLOSED

euchromatin

less condensed, contains genes, active: genes are expressed, quiescent: genes are silenced, OPEN

Bps on histone

147 on bead and 200 on string

octomer

2 copies of each histone

methylation of histones

tails can be modified post transitionally, makes more heterochromatin

acetylation of histones

more euchromatin because the histones lose their positive charge just a bit so it makes the DNA bind looser

Histone H1

helps further condense the DNA through H1-H1 interaction

mitosis

cytokinesis, splitting chromosomes

G1

cell rest and growth, is the cell ready to replicate DNA, if not go into G0, humans have 46 centromeres, nonhomologous end joining

S phase

DNA replication, only if the environment is favorable will a cell enter here

G2

is the DNA replicated and is it damaged?

homologous recombination

if a diploid organism has 6 pairs of homologous chromosomes how many centromeres

24

before mitosis

chromosomes are duplicated, centromeres are duplicated, nuclear envelope is entact

kintechore

forms at the centromere and is the site of microtubule attachment

prophase

condensing duplicated chromosomes, intact nuclear enevelope, miotic spindle starts to form, nucleous dissapears

prometaphase

more movement and condensing, nuclear enevlope breaks down into fragments, some mitoic spindle catches chromosomes while others move

metaphase

chromosomes align in da center, 2 kintechores at each chromosome, spindle checkpoint occurs

anaphase

becomes its own chromosome, shortneing kintechore, spindle pole moving outward, microtuble not attached elongate cell

telophase

set of chromosomes at spindle pole at each side, contractile ring starts to form, nuclear envelope starts to reassemble, mitoic spindle broken down, chromosomes start to decondense

cytokinesis

completed nuclear enevlope surrounds chromosomes, reformation of interphase microtubles, contractile ring creates cleavage furrow,

cytoskeletons throughout the cell

• centromeres replicated in G1

• duplicated centromeres move apart in mitosis,

• chromosomes are attached to the cytoskeleton at kinetchore,

• contractile ring needed for cytokinesis which is made up of actin and filament

deamination

removes amine group from a base (cytosine to uracil)

daughter cells with difference in genomic sequence

depurination

removes purines from deoxyribose sugar(1200 a day)

guanine or adenine

deletion in replicated chromosomes

thymine dimer

caused by ultraviolet radiation

covalent linkage between to pyrimadines

uses NER

NER in thymine dimer repair

1. dimer recognized by endonuclease

2. endonuclease excises the nucleotides

3. helicase unzips single stranded dna

4. dna polymerase synthesizes new dna

transversion

purines to pyramidines

transitions

purines to purines or pyramidines to pyramidines

BER

damage nitrogenous base is removed and endonuclease nicks backbone, polymerase adds new nucleotides