Genetics (Bio And Biochem)

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B-DNA

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Regular DNA double helix. Right handed

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Z-DNA

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Left handed inactive DNA

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Probe DNA

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process where DNA is denatured with certain complementary sequences. If those sequences bind you may have a certain gene of interest

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Nucleoproteins

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Proteins associated with DNA

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Nucleosome

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Histone/DNA complex.

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What are the histones?

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H1(seals off DNA at entry exit of nucleosome)

H2A

H2B

H3

H4

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Heterochromatin

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Dark compact chromatin that is transcriptionally silent

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Euchromatin

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Light, dispersed, active DNA

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Replisome

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The whole DNA replication complex

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Replication forks

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Start at origin of replication and proceed in both directions

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Prokaryotes have _____ set of chromosome forks and eukaryotes have______

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One

Multiple

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Helicase

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Enzyme that unwinds DNA

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ssDNA binding proteins

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Bind to unwinded DNA during replication to prevent DNA reassociation and degradation by nucleases

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Supercoiling

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Wrapping of DNA on itself

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DNA topoisomerase

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Introducing negative supercoils by working ahead of helicase to nick strands and relieve torsional pressure then resealing

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Semiconservative replication

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Each new strand is made of one parent and one daughter strand

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DNA polymerase

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Reads in 3-5 direction and synthesizes DNA in 5-3 direction

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Primase

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Lays down RNA primer for DNA polymerase

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DNA polymerase III

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Prokaryote polymerase for leading strand

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DNA alpha (charge thing) and epsilon

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Leading strand eukaryote

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DNA polymerase I

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Prokaryote removed RNA primers and replaces with DNA

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RNase H

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Eukaryotes removes RNA primer

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DNA (charge symbol one)

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Eukaryote places DNA in place of removed RNA primers

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Ligase

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Seals DNA ends and joins Okazaki fragments

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Oncogenes

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Mutated genes that cause cancer

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Proto-oncogenes

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Genes that when mutated cause cancer. They are usually cell cycle related “gas pedal” genes

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Antioncogenes

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Tumor suppressor genes that when mutated promote cancer by “releasing the brakes”

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Proofreading

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During synthesis polymerase proofreads and corrects the new strand

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Mismatch repair

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G2 phase enzymes coded by MSH1 and MSH2 genes which correct gene errors missed during S phase

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Nucleotide excision repair

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UV light forms causes thymine dimers. These are repaired by excision endonuclease which nicks phosphodiester bonds and excises bad gene allowing polymerase to fix

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Base excision repair

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Heat can change cytosine to uracil through deamination. Such small non helix distortions fixed by the named phenomenon. Glycolyase enzyme removed base leaving AP site recognized by AP endonuclease which removes damaged sequence allowing polymerase repair

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Recombinant DNA tech

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Multiply DNA via gene cloning or PCR

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DNA Cloning process

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Ligate desired DNA to form a recombinant vector. Usually a plasmid. The plasmid is transferred to host bacterium along with an antibiotic resistant gene so they multiply and then you kill off all the non mutated bacteria. Now you can either Lyse the new DNA to recombinant vectors from bacteria or have the bacteria express the gene

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Restriction enzyme (restriction endonuclease)

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Enzymes that recognize a specific dsDNA sequence. They recognize palindromic sequences. Get from bacteria where they are used to protect bacteria from infection. Recombinant DNA is made with sequences recognized by restriction enzymes so that that they can cut and produce “sticky ends”

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What do recombinant plasmids need?

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Antibiotic resistance strand. Strand recognized by restriction enzyme. And origin of replication

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Genomic library

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Contains coding and non coding regions of genes in a large library

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cDNA (expression library)

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Contains only expressed portion of genes in a large library

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Hybridization

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Joining of complementary DNA-DNA or DNA-RNA sequences

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PCR

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Knowing the flanking sequences of desired sequence allows to replicate genes in between. Uses primers which compliment flanks, nucleotides, and DNA polymerase from bacteria from hot springs . Primer has high GC content. DNA is denatured, copied and allowed to reanneal. Repeat

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Gel electrophoresis

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Separates genes by size and charge. All dna neg charged so migrate to positives uses agarose gel

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Southern blot

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Conducted during gel electrophoresis. Detects presence and quantity of various DNA strands in sample. DNA cut by restriction enzymes then allowed to do gel electrophoresis. DNA saved in membrane. Membrane probed with isotope or indicator protein labeled complementary strands to form full DNA and indicate presence of desired DNA

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DNA sequencing

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Uses dideoxyribonucleic acid during dna replication which terminates polymerase. Samples put through gel electrophoresis. End base read in order by size

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What vectors are used in gene therapy usually?

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Viruses

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Transgenic mice

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Transgene introduces to mice. If gene is disease related then the diseased mice can be researched

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Knockout mice

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Gene deleted in mice

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Complete dominance

Codominance

Incomplete dominance

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One dominant trait masks recessive

Both traits expressed equally (ab blood)

An intermediate phenotype (red and white makes pink flower)

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Penetrance

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Proportion of individuals with genotype that actually express phenotype

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Expressivity

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Varying phenotypes despite distinct genotype.

Constant then all individuals with genotype express the phenotype

Variable same genotype may have different phenotypes

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Expressivity vs penetrance

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Penetrance more population based and expressivity more individual based (one disease genotype with varying conditions)

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Mendel first law

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Law of segregation

Two alleles for each gene, one from each parent

Expressed dominant other is recessive

Key associated step is metaphase 1

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Mendel first law

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Law of segregation

Two alleles for each gene, one from each parent

Expressed dominant other is recessive

Key associated step is metaphase 1

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Mendels second law

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Independent assortment

Inheritance of one gene doesn’t affect inheritance of others

Explained by crossover (recombination)

Some linked genes conflict this law

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Mutation and wild type

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Changed dna and “normal” dna

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Mutation and wild type

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Changed dna and “normal” dna

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Gene pool

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All alleles in a population

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Nutagen

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Causes mutation

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Nutagen

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Causes mutation

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Transposon

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Inserts and takes itself out of genome

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Some mutations are ______ which is good and others are _____ which is bad

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Advantageous

Deleterious

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Some mutations are ______ which is good and others are _____ which is bad

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Advantageous

Deleterious

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Inborn errors of metabolism

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Gene defects in metabolism genes

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Gene leakage

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Flow of genes between species. Can produce hybrids

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Founder effect

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Small part of species in reproductive isolation or bottlenecks. Inbreeding happens which increases bad stuff

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Founder effect

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Small part of species in reproductive isolation or bottlenecks. Inbreeding happens which increases bad stuff

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Outbreeding (outcrossing)

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Opposite of inbreeding. Bringing in new genes

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P and F generation

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Parent

Filial (offspring)

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Dihybrid cross

Ratio of two parents with two sets of complete dominant heterozygous genes

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Doing four traits. 4 by 4 square

9:3:3:1

Both dominant, 3 for one dominant one recessive of each type. One for completely recessive

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Crossing two heterozygotes results in a _____ phenotype and _____ genotype ratio

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3:1 dominant to recessive

1:2:1 homozygous dominant, heterozygous, homozygous recessive

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Recombination frequency (theta) problems

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Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Recombination frequency (theta) problems

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Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

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Modern synthesis model

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Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Recombination frequency (theta) problems

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Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

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Modern synthesis model

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Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

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Inclusive fitness

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Organism success in population. Explains altruism

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Recombination frequency (theta) problems

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Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

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Modern synthesis model

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Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

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Inclusive fitness

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Organism success in population. Explains altruism

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Punctuated equilibrium

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Evolution in rapid bursts

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Recombination frequency (theta) problems

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Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

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Modern synthesis model

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Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

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Inclusive fitness

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Organism success in population. Explains altruism

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Punctuated equilibrium

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Evolution in rapid bursts

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Types of selecion

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Stabilizing: graph narrows down middle eliminating extremes

Directional: graph shifts one direction. Bacterial resistant ca non

Disruptive: extreme favored over norm. Boob graph

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

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Recombination frequency (theta) problems

Back 91

Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

Front 92

Modern synthesis model

Back 92

Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

Front 93

Inclusive fitness

Back 93

Organism success in population. Explains altruism

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Punctuated equilibrium

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Evolution in rapid bursts

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Types of selecion

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Stabilizing: graph narrows down middle eliminating extremes

Directional: graph shifts one direction. Bacterial resistant ca non

Disruptive: extreme favored over norm. Boob graph

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Polymorphism

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Different forms of same species such as color of butterfly

Facilitated disruptive selection

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

Front 98

Recombination frequency (theta) problems

Back 98

Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

Front 99

Modern synthesis model

Back 99

Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

Front 100

Inclusive fitness

Back 100

Organism success in population. Explains altruism

Front 101

Punctuated equilibrium

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Evolution in rapid bursts

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Types of selecion

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Stabilizing: graph narrows down middle eliminating extremes

Directional: graph shifts one direction. Bacterial resistant ca non

Disruptive: extreme favored over norm. Boob graph

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Polymorphism

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Different forms of same species such as color of butterfly

Facilitated disruptive selection

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Adaptive radiation

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Rise in species from one ancestor

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Test cross

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Determine unknown genotype with a known homozygous recessive

If all are dominant offspring unkown likely homozygous dominant

1:1 heterozygous

Sometimes called back cross

Front 106

Recombination frequency (theta) problems

Back 106

Proportional to distance between alleles on chromosome

One centimorgan equals one percent chance

Front 107

Modern synthesis model

Back 107

Neo Darwinism

Combined natural selection with knowledge of mutation and crossover

Front 108

Inclusive fitness

Back 108

Organism success in population. Explains altruism

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Punctuated equilibrium

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Evolution in rapid bursts

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Types of selecion

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Stabilizing: graph narrows down middle eliminating extremes

Directional: graph shifts one direction. Bacterial resistant ca non

Disruptive: extreme favored over norm. Boob graph

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Polymorphism

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Different forms of same species such as color of butterfly

Facilitated disruptive selection

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Adaptive radiation

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Rise in species from one ancestor

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Niche

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Specific habitat. Adaptive radiation favors by isolation or change of niche

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Evolution patterns

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Divergent: developing dissimilar stuff overtime

Parallel: related species evolve in similar ways similar environments

Convergent: species not sharing common ancestor getting similar traits dolphins and fish

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Evolution patterns

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Divergent: developing dissimilar stuff overtime

Parallel: related species evolve in similar ways similar environments

Convergent: species not sharing common ancestor getting similar traits dolphins and fish

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Greater change of environment results in _____ evolution

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More

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Genome similarity correlated with amount of time species split off this model is called

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Molecular clock model