1. Alpha - catalytic core (pol. activity).

2.Tau - dimer that links the 2 catalytic cores together.

3.Beta - clamp (2 homodimers)

4.Gamma-delta - clamp loader complex

5. Epsilon - 3'-5' proofreading exocuclease

A tagging technique in which DNA Pol. 1 is used to replace some nucleotides of a DNA sequence with their labeled analogs, creating a tagged DNA sequence that can be used in FISH (Fluorescent in situ hybridization).

A large protein fragment with 5'-3' polymerase activity and 3'-5' exonuclease activity for removing precoded nucleotides and proofreading.

Has lost 5' → 3' exonuclease activity because the other fragment has it.

Critical players in recognizing repaired replication forks and reloading the replisome onto the template to reinitiate DNA replication.

Restarts replication after it stalls.

A bacterial primase which synthesizes short RNA oligonucleotides during DNA replication which serve as primers for DNA synthesis by bacterial DNA polymerase Pol III.

Associates with DnaB

An enzyme in bacteria which opens the replication fork during DNA replication. Initially when DnaB binds to DnaA, it is associated with DnaC, a negative regulator. After DnaC dissociates, DnaB binds DnaG.

Product of DnaB gene.

Mitochondrial DNA Replication

and the D loop (displacement loop)

1. Alpha - cytoplasmic DNA Polymerase.

2. Delta -extend DNA synthesis from the primer.

3. Gamma - enhances DNA binding.

Proteins that are essential in detecting mismatches and directing repair machinery.

(methyl directed)

Removes T from mismatch.

Involved in base mismatch repair.

Codes for Adenosine glycosylase.

Removes A from mismatch.

Coded by MutY

Creates an apurinic site.

This is removed by an excision repair system.

DNA adenine methylase.

Adds a methyl group to the A and the 5'-GATC-3' in newly synthesized DNA.

Insertion sequences.

Group of transposable elements that constist of 800 to 2000 bp and carry inverted repeats at their ends. Central part codes for Transposase responible for transposition.

Simple transposons - similar to IS elements, contain DNA segments flanked by short inverted repeat sequences, usually code for a number of gene products and also code for a resolvase or antibiotic resistance genes.

Composite transposons -  DNA segments that are flanked by an IS element at either end, they now act in concert and move together along with the intervening DNA that often carries the genetic determinants for a number of antibiotic or other toxin resistances

Topoisomerase I - solves the problem caused by tension generated by winding/unwinding of DNA. It wraps around DNA and makes a cut permitting the helix to spin. Once DNA is relaxed, topoisomerase reconnects broken strands.

Topoisomerase IV - able to pass one double-strand of DNA through another double-strand of DNA, thereby changing the linking number of DNA by two in each enzymatic step. Responsible for unlinking DNA following replication and relaxes positive supercoils.

Occur during the diplotene stage of meiosis I and indicate that the transcription of mRNA is taking place.

Appear as large puffs, looks like Christmas tree garland.

Diffuse uncoiled regions of the polytene chromosome that are sites of RNA transcription.

Cells undergo repeated rounds of DNA replication without cell division, extra DNA stays in same cell

Highly conserved.

Chromatin assembly factor.

Guanine-rich DNA and RNA have the ability to form inter- and intramolecular four-stranded structures, referred to as G-quartets.

Account for the stability properties of chromosome ends.

Repressor Activator Protein

Involved in transcriptional activation of genes encoding ribosomal proteins and glycolytic enzymes.

hairpin or hairpin loop

Intramolecular base pairing is a pattern that can occur in single-stranded DNA or RNA It occurs when two regions of the same molecule, usually palindromic in nucleotide sequence, ends in an unpaired loop. The resulting lollipop-shaped structure is a key building block of many RNA secondary structures.

Binds to 5’ end of the top strand of adenovirus DNA between 9 & 18 nucleotide.

Silent Information Regulatory proteins.

Telomeric repeat-binding protein.

Required for the chromatin- mediated gene repression observed at yeast telomeric regions.

Histones H3, H4, H2A, H2B[image]

[image]

Packing ratio = 6

"Beads on a string"

DNA organization.

Packing ratio = 40

Futher DNA organization dependent on the H1 histone.

Bacterial RNA Polymerase

[image]

Wall -Bends the hybrid about 90°.

Rudder - prevents extension of the DNA-RNA hybrid beyond 9 base pairs.

Bridge - acts as a ratchet, allowing the release of the DNA and RNA strands for translocation but maintaining its grip on the growing end of the hybrid, thus enabling the next step in the elongation cycle to take place.

1.1 - N terminus that prevents binding

2.3 -Interacts with -10 region

3.2 -Blocks path for RNA exit

4.2 - Interacts with -35 region

Forms a closed complex with the promoter and is incapable of proceeding to an open form on in the absence of the activator protein.

Binds 1st.

Lac Repressor

[image]

Has amino acid Leucine.

Heptad repeat.

Creates adhesion forces between parallel alpha helices.

When arabinose is absent, there is no need to express the structural genes.

The ara operon demonstrates both negative and positive control. It shows a different function for CRP. It also shows how a protein can act as a switch with its activity being radically altered upon the binding of a small molecule.

Class 1 - lac, 1 CAP binds upstream of alpha CTD

Class 2 - gal, 1 CAP binds downstream of alpha CTD

Class 3 - ara, malK, needs 2 or more CAP

Refers to a specific regulatory sequence that, when transcribed into RNA, forms hairpin structures to stop translation when certain conditions are not met.

Trp operon.

2-3 = antiterminator

1-2 = pause so 3-4 can bind = attenuation

Nucleate the assembly of basal transcription complexes, components of which interact with activators.

Tells where to start.

Basal = constitutive

An increased rate of gene expression triggered either by biological processes or by artificial means.

A protein that increases gene expression by binding to an activator (or transcription factor) which contains a DNA binding domain.

HAT - histone acetyltransferases, closely linked to gene transcription.

p160 - recruits HAT and contains HAT

Leave when mediator attaches.

TATA Binding Protein.

The molecular saddle.

Transcription factor that binds specifically to a DNA sequence called the TATA box.

Recognizes core promoter, target for recruitment by transactivator proteins, binds other basal factors, and has enzymatic activity.

Contain TBP and TAFs.

Head = Srb4

Middle = Med9/10

Tail = Gal11 module

Srb10/Srb11

Inhibits TFIIH

Remember 7-Heaven!!

THIIH

Nuclear Receptors

(Steroids and related hormones)

TATAA

BRE

inr

DPE