Segregation

Independent Assortment

Seperation of alleles in meosis

Two alleles seperate and are inherited independently from alleles at other loci

Coupling 

Repulsion

For linked genes!

M----D

m----d

M----d

m----D

Interchromosomal recombination

Intrachromosomal recombintion

unlinked genes on different chromosomes from independant assortment

between genes on the same chromosomes from crossing over

Chromosomal rearrangments 

Aneuploidy 

Polyploidy

alter the structure of chromosomes (duplication, deletion, inversion, translocations)

alter the number of individual chromosomes

alter the number of chromosomal sets

Tandem is when the copied section is right next to the old one.

Displaced is when the copied section is away from the original section.

Reverse is when it is next to it but inverted.

In meosis, one of the chromosome has to loop on itself to make the pairing up possible. 

Allows for novel function of proteins

Removal of a chromosome 

if it involves a centromere, then chromosome is usually lost

can cause pseudodominance- has hetero genotype, but loses the dominant trait in del so recessive shows up

can cause haploinsufficiency-2 copies of the wild type gene to express trait.

Inversions

Position Effect

paracentric-ones that dont involve the centromere

pericentric-involve the centromere

genes expressed at inappropriate times or in inappropriate tissues due to inversion

lead to inversion loops in meosis. Have reduced recombination and have a lot of unviable gametes

Occur if only one of the chromosomes has an inversion

These inverted chromosomes also exhibit less recomb

If peracentric cross over one will have 2 centromeres (dicentric) and the other will have none (acentric). not viable offspring. dicentric bridge.

Pericentric will also not have any viable offspring. no dicentric bridges.

translocations

Robertsonian translocation

movement of genetic material between non homologous chromosomes or within the same chromosome. Reciprocal is when 2 sides exchange, and nonreciprocal gives only one chromosome DNA.

2 chromosomes combine to form one. the other little bit is lost

Form crosses if hetero for translocation

Change in the number of individual chromosomes (nullisomy, monosomy, trisomy, tetrasomy)

Usually lethal because of abnormal protein concentration.only exception is the X chromosome.

Normal DS is caused by trisomy 21

Familial DS is caused by part of extra chromosome 21 fused on 14. So they have norma number of chromosomes (46)

Normal carriers have 45 chromosomes

More than one set of chromosomes

autopolyploidy- all chromosme sets from a single species

allopolyploidy-from more than one species

tetraploidy-occurs from nondisjunction in mitosis

triploidy-non disjunction in meosis

Usually sterile

Relaxed State of DNA

Supercoiling

Beta form and has 10 BP per turn 

Over or underrotating a molecule in order to stuff it into tiny space. Happens because the tortional strain cannot be relieved (most negatively supercoiled-underrotation. Requires less energy to seperate strands during replication)

Caused by topoisomerase

Euchromatin- undergoes condensation and ucondensation during the cell cycle

Heterochromatin-remains in condensed state even in interphase

Histones

Non Histone Proteins

Positively charged proteins that help bind and fold DNA

Chromosomal scaffolding proteins that are responsible for higher order folding. Make up kinetochore and telomeres

Chromatin Structure: 

nucleosome

chromatosome

30 nm fiber

nucleosome-beads. DNA wrapped around 8 histone proteins. Little nuclease cuts beads into ~200 bp. More nuclease ~147 bp

chromatosome-nucleosome and histone H1. the h1 acts as a clamp and binds the DNA to the histone (20 bp).

30 nm fiber-this stucture is formed by histones folding on themselves 

300 nm fiber

250 nm wide fiber

700 nm wide fiber

More structures, each composed of the previous one. 700 nm wide fiber is what u can see on microscopes

Chromosomal puffs

DNAse I Hypersensitivity

Acetylation

Occur because of relaxed DNA where transcription is occuring.

DNAse I is less likely to cut DNA when it is bound to histones. Correlated with gene transcription.

acetylation destablaizes nucleosome so it holds DNA less tightly. Makes em sensitive to DNAse

Centromere

Telomere

Tandem repeats of specific DNA structures. has its own type of chromatin structure and histone. 

Caps that prevent the degredation of the ends of the molecules. 

C value paradox

Renaturing

Bacterial DNA

Just because you have more DNA doesnt mean that you are more complex

the lower the concentration of DNA the slower it will renature.

Methylated and have a lot fewer repeats than eukaryotes

Meselson-Stahl Experiment

Replicon

Showed that DNA rep is semi conservative

origin+DNA made from that origin

Theta replication

Rolling circle replication

Linear replication

circular DNA. happens from a single replicon. Replication bubble (uni or bidirectiona). Semidiscontinuous

circular DNA (viruses and some E coli)-break in nucleotide strands and as nuclotides are added complementary to the 3' and the 5' end spools outward (unidirectional). cont

linear replication for eukaryotic chromosomes-many replicons and bidirectional replication. sdc

leading strand made constantly and lagging made in fragments (Okazaki fragments)

Helicase

Single stranded binding proteins

Gyrase

Primase

breaks the H bonds between two nucleotides

After strands are seperated, then these are used to bind single strands and keep em seperated

nicking and sealing topoisomerase to relieve stress

makes a small primer (RNA) to get polymerase started

DNA Polymerase III

DNA Polymerase I

Ligase

DNA pol III 5-3' polymerase ability and 3-5' exonuclease ability. Main function is DNA synthesis (less than 1 error/ billion BP)

DNA pol I- has the 2 abilities of pol III but also has 5-3' exonuclease ability in order to remove primers. Main function is primer removal. 

Connect the free end of the 3'OH and 5' by pde bond. 

Helicase unwinds DNA

SS binding proteins need to stabalize the single stands of DNA

Topoisomerase DNA gyrase relieves stress ahead of the rep fork

Primase adds an RNA primer

DNA polymerase adds complementary BP for the leading and laggin strand

Termination of Replication

Licencing factor

Could happen once 2 forks meet, some have termination sequences (Tus in Ecoli)

Attaches to origin and approves replication

DNA pol alpha

DNA pol delta and epsilon

Nucleosomes on new strands or old?

primase activity, initiates DNA synthesis by making a primer RNA and short DNA segments. 

complete synthesis of DNA strands of lagging and leading respectively

old nucleosomes are found on both old and new strands of DNA, so are not conserved with only the old response

Restriction Enzymes

Type I, II, III types of RE

Cut DNA at certain palindromes

I and III cut around the recognition sequence

II cuts at the recognition sequence

Avery, MacLeod, McCarthy

Hershey Chase

DNA is transforming substance

DNA, not protein is inherited not protein

Ribose v Deoxiribose

Purines vs Pyrimidines

Adenine and Guanine

Cytosine,Thymine,Uracil

2 OH's v 1 OH

2 rings (6 and 5C rings) vs 1 6 C ring

Adenine has NH2 instead of C=O (Guanine)

Cytosine only has one C=O, thymine has a methyl with 2 C=O, uracil has 2 C=O. 

Southern blotting

Cloning genes

DNA is seperated by gel electrophoresis. This is then copied over to a membrane which is hybridized to a probe.

Amplify the isolated gene in a bacteria. needs to have an origin of replication, selectable markers, and a unique restriction site. All of this done with a plasmid

Need to first ligate plasmid, then insert trait, then get bacteria to uptake and transform, and select for the colonies which have uptaken trait. 

PCR

What does it do?

What does it need?

What are the steps?

How is it limited?

amplify genes many times over. 

Needs a DNA template. 2 primers complementary to the target sequence, DNA polymerase, bases, and other salts. 

Steps are denaturing, primer annealing, and primer elongation. 

Need to know what the target protein's sequence is. Risk of contamination, not as accurate (1/20k bp), and doesnt work too well for 2k bp size sequences.

uses TaqMan chemistry to see how many times the DNA has replicated as a measure of light. the probe has a reporter and quencher. If the probe is broken then more light is emitted. 

Can be used to see if a sample has viral DNA in it or not. 

use dideoxiribonucleosidetriphosphates (ddNTP's). Dont have a 3' OH, so when these are added they prevent the addition of any more nucleotides. Done by first having a lot of DNA copies via PCR.This is done 4 seperate time, each time with a different nucleotide. Incubate. Run on gel and then under x ray can see pieces and compare for size. THIS SEQUENCE IS OF THE COMPLEMENT TO THE ACTUAL STRAND!