Cell Bio Lectures 2-1 to 2-4

chromosomal regions in the nuclease

Where are interphase chromosomes located?

attached to nuclear lamina or nuclear envelope

Where chromosomal regions are located within the nucleus

nuclear lamina

a network of intermediate filaments made from nuclear lamins

nucleolus

A structure in the nucleus that is the site of ribosomal RNA transcription and ribosomal unit assembly

Histones and nonhistone proteins

proteins that coil and fold DNA

Chromatin

a complex of DNA and proteins that make up the chromosomes in a eukaryotic cell

nucleosome

a bead like structural unit of eukaryotic chromosome

Watson crick model

double helix has 10 nucleotide pairs per complete turn

knob and hole end

chemically distinct ends of nucleotides

nucleotide

5’ carbon of sugar has phosphate group

• 3’ carbon of sugar has OH

• 5’ and 3’ ends of molecule

ester bond

bond that forms between an oxygen atom and carbon atom

major grooves minor grooves

form as DNA strands twist around each other

genome

The total genetic information carried by all the chromosomes of a cell or organism

replication origin

Site where DNA replication begins

telomeres

ends of chromosomes, act as protective caps, TTAGGG

centromere

allows chromosomes to be separated

chromatid

identical duplicated DNA

molecule, Associated with proteins

core particle of nucleosomes

histone octamers

linker DNA

links nucleosome beads together

histones

high proportion od positively charged amino acids, binds to negatively charged DNA

H2A, H2B, H3, H4

make up bead of nucleosome

H1

pulls adjacent nucleosomes together making DNA more compact

nucleosome formation, chromatin fiber formation, nucleosomes pulled together by H1

steps in packaging of nuclear DNA

chromatin loops

made up of a ring of nonhistone protein

SMC ring complex

forms chromatin loops, made of SMC (structural maintenance of chromatin) proteins, additional proteins.

cohesin

a specific type of SMC complex that enlarges chromatin loops

clamp proteins

what regulates the size of chromatin loops

DNA looping in mitotic chromosomes

cohesins replaced by condensins (SMC proteins). Condensins form loops within loops

ATP hydrolysis

what fuels loop formation in DNA

chromosome that is 10,000 fold shorter

net result of DNA packaging

transcriptionally active DNA

is less tightly packed than inactive DNA

chromatin remodeling complexes

ATP dependent enzymes that change the position of DNA wrapped around nucleosomes

active chromatin

“open”

inactive chromatin

“closed”

Histone modifications

regulate transcriptional activity

methyl, acetyl, phosphate etc

Histone tail can be modified by the addition or removal of:

acetylation

addition of an acetyl group, activation

methylation

addition of methyl group, repression

heterochromatin

highly compacted chromatin

euchromatin

loosely packed chromatin

highly compacted

during cell division all chromatin becomes ____

constitutive heterochromatin

type of heterochromatin that becomes permanently compacted

telomers, centromeres

types of constitutive heterochromatin. Do not contain genes

facultative heterochromatin

type of heterochromatin that can be converted to euchromatin and vice versa

Heterochromatin-specific histone modifications

allow heterochromatin to form and to spread

reader

detects modifications

writer

makes additional modifications on near by histones

barrier DNA sequence

stops the histone modifications

Epigenetic Inheritance

Heterochromatin can be inherited by generations. H3 and H4 histone proteins are directly passed to daughter helices

kinetochore

complex of proteins that binds centromere

base pairing

____enbales precise copying of DNA during replication

semiconservative replication

Each daughter DNA double helix is composed of one old strand and one new strand

replication origin

the nucleotide sequence at which DNA replication is initiated, AT rich

replication forks

Y shaped sites where parental DNA unwinds

initiator proteins

attract replication machine to origin of replication

opposite directions

what direction do replication machines move in

DNA polymerase

synthesizes DNA replication by using a parental strand as template , elongation occurs in 5 to 3 direction

what DNA polymerase needs

1. template DNA

2. primer

3. dNTP bases

phosphodiester bonds

Formed between phosphate group on 5’-carbon of incoming

dNTP and hydroxyl group 3’-carbon of nucleotide in growing chain

leading strand

continuous strand

lagging strand

discontinuous fragments

Okazaki fragments

name for the discontinuous fragments

DNA ligase

“glues” fragments together

proof reading

The process by which DNA polymerase corrects its own mistakes as it moves along DNA template. Mismatched nucleotide is cut from new strand and replaced with correct match

the correct base pair

what allows DNA polymerase to catalyze its reaction?

RNA primers

synthesized by primase

primase

RNA polymerase, uses ribonucleotide TP

3 prime end

where incoming nucleotides are added by DNA polymerase

multiple primers

lagging strand synthesis needs

nuclease

removes RNA primers

repair polymerase (DNA pol I)

replaces primers with DNA

sliding clamp proteins

keep the polymerase attached to template DNA

clamp loaders

hydrolyze ATP to get calm around DNA

DNA helicase

unwinds DNA by breaking hydrogen bonds. NEEDS ATP

single stranded binding proteins

Bind to the single stranded DNA to keep it unwound

topoisomerase

relaxes DNA supercoiling

telomerase

an enzyme that replicates the ends of eukaryotic chromosomes

protein and RNA

What is telomerase composed of

8 proteins involved in DNA replication

accurate replication

without this, the genetic material of resulting cells would be riddled with error

Depurination and deamination

types of spontaneous damage in DNA

Depurination

loss of purine base A or G, if uncorrected it can lead to the loss of a nucleotide pair

Deamination

moving an amine group from adenine, cytosine, and guanine. if uncorrected, leads to wrong base pairing

converts cytosine to uracil

the major type of deamination

UV radiation

causes two adjacent thymine bases to become covalently attached

chemicals in tabacco smoke

add bulky side groups to bases

Xeroderma pigmentosum

genetic disease that effects DNA repair. Thymine dimers cannot be repaired

Three basic steps of DNA repair

1. Excision

2. Resynthesis

3. Ligation

Excision

the damage is cut out by one of a series of nucleases

Resynthesis

a repair DNA polymerase restores the original DNA sequence

Ligation

DNA ligase seals the nick left in the sugar phosphate backbone of the repaired strand

mutation

a random permanent change in the nucleotide sequence of DNA

mismatch repair system

removes replication errors that escape proofreading

Mismatch repair

an enzyme recognizes the mismatched bases and initiates the repair process. One enzyme cuts the DNA backbone and another removes the successive nucleotides including the faulty one, Then DNA polymerase fills in the gap. Finally, DNA ligase completes the repair

base excision repair

corrects single damaged bases.

Steps of base excision repair

nuclease removes the base by cleaving the sugar-base bond. DNA polymerase synthesizes the correct new base.

DNA ligase seals the nicks.

uracil DNA glycoylase

detects uracil in DNA (Not supposed to be there!!!!)

Nonhomologous end joining, homologous recombination

Strategies for repairing breaks in both strands of DNA

Nonhomologous end joining

proteins (KU70/KU80) bind to the ends of broken DNA fragments and join them together. Nucleases trim the ends and the break is sealed by DNA ligase. some loss of nucleotides :(

homologous recombination

flawless! Nuclease chews back on the 5 prime ends on both broken strands. One of the broken ends invades the unbroken homologue with help of enzymes. DNA polymerase elongates the broken strand. the elongated strand is released from the homologue and joins the original partner.