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OSU / Biology / BIOLOGY 1113 / Why does methylation turn dna into heterochromatin?

Why does methylation turn dna into heterochromatin?

Why does methylation turn dna into heterochromatin?

Description

School: Ohio State University
Department: Biology
Course: BIOLOGY 1113
Professor: Ball and dr. weinstein
Term: Summer 2015
Tags: Biology, Biotechnology, Genome, and human genome project
Cost: 50
Name: Bio 1113 Final Study Guide
Description: These notes cover our final section of the class! I used Dr. Weinstein's study guide as a tool to find important information to know and highlighter of bolded the most relevant sections.
Uploaded: 12/11/2016
7 Pages 21 Views 7 Unlocks
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Beadle and Tatum 


Why does methylation turn dna into heterochromatin?



One gene one enzyme

Early hypothesis by Beadle and Tatum

Later changed to one gene one polypeptide (protein)  

The central dogma 

DNA to RNA to protein

Violation

RNA to DNA back to RNA (HIV)

The triplet code

Problem: we have 4 nucleotides to specify 20 amino acids  

3 nucleotides in one codon

1 codon makes 1 amino acid (64 possible combinations)

Template strand- provides a template for ordering the sequence of transcribed DNA Made 5' to 3'

Codons

Read 5' to 3'

Stop codon- codon sequence that causes transcription to stop

One amino acid can have several codons that code for it


What is the effect on the life cycle if there is a mutation in the env gene?



AUG always starts proteins

Stop codons = UAA UAG UGA

3 stages of transcription

Initiation

DNA unwinds

Synthesis starts at start codon

Promoter- DNA sequence where RNA polymerase attaches

Transcription unit- a stretch of DNA that is transcribed

Start point- extend several dozen nucleotide pairs

Elongation

RNA elongates the RNA transcript from 5' to 3'

Termination

5' end gets a cap

3' end gets a poly-A tail

Split genes and RNA splicing If you want to learn more check out How to measure overall economy?

Introns- non-coding regions on an RNA

Importance of introns


What is the use of bioinformatics?



Some may code for gene expression

Alternative splicing- can encode for more than one polypeptide

RNA splicing- removes introns and joins exons

Takes out the immature codons and joins together mature codons to make a mature mRNA Spliceosomes- carries out the splicing reaction

Translation

Cell translates an mRNA message into protein with the help of transfer RNA

Transfer amino acids to the growing polypeptide in a ribosome

Important parts of tRNA

Anticodon- how the tRNA attaches to the mRNA

Amino acid attachment site- where the amino acid attaches

2 major steps

Aminoacyl-tRNA synthase- matches tRNA and amino acids

Correct match between tRNA anticodon and mRNA codon

Wobble- flexible pairing at the third base of a codon

Allows some tRNA to bind to more than one codon

Ribosomal subunits

All of this happens in the ribosomes

Ribosomal subunits are made of proteins and ribosomal RNA We also discuss several other topics like What is fascism?

3 binding sites

P- holds tRNA with growing polypeptide chain

A- holds tRNA that carries the next amino acid to be added to the chain E- exit site We also discuss several other topics like What is true about habituation?

Translation

3 stages of translation

Initiation

Brings together mRNA and 2 ribosomal subunits

Elongation

Amino acids are added in the 5' to 3' direction

Termination  

Occurs when they hit stop codons

Release factor

Adds water to the end

Hydrolyzes bond

Mutations 

If shown in phenotype of an individual, it is considered a genetic disease Mutation- any change in the DNA sequence

Substitutions

Nucleotide-pair

Replaces a pair with another pair

Silent

No effect

Missense

Still code for an amino acid, but not the right amino acid

Nonsense

Changes a normal codon to a stop codon

Makes the protein non-functional

Insertions and deletions

Disastrous effect

May alter reading frame

Frameshift mutation

Add or delete one nucleotide

Mutagen- causes mutation

Ames test- assay to asses if a compound is a mutagen

Uses bacterial growth

A carcinogen is not always a mutagen

Regulation of Gene Expression

Operons If you want to learn more check out What is cultural transmission?

Operon- consists of the operator, the promoter, and the genes they control

Promoter- a site where RNA polymerase binds to DNA and starts transcription

Transcription makes one long mRNA molecule  

Grouping genes of similar function allows for one on/off switch

Means they are coordinately controlled  

Operator- controls the access of RNA polymerase to the genes

Located on the promoter or between the promoter and the genes

Repressor- binds to the operator and blocks attachment of RNA polymerase to the  promoter

Product of a regulatory gene

Corepressor- small molecule that works with a repressor to turn an operon off

Negative gene regulation

Negative regulation is when the transcription is turned off

Repressible operon- transcription is usually on but can be turned off

Inducible operon- usually off but can be turned on

Inducer- inactivates the repressor

Positive gene regulation

Activator- a protein that binds to the DNA and stimulates transcription

Stages of gene expression

Differential gene expression- the expression of different genes by cells with the same genome Makes differences between cell types

Stages

Signal is received

Chromatin is unpacked into DNA

Epigenetic inheritance- traits transmitted through mechanisms not involving  If you want to learn more check out What is the law of diminishing returns?

nucleotide sequence

Histone acetylation- opens up the chromatin structure If you want to learn more check out How do you want the relationship to fit into other areas of your life?

DNA methylation- adding methyl groups to DNA bases in order to condense the  chromatin and reduce transcription  

Transcription

Control elements- segments of non-coding DNA that serve as binding sites for  

transcription factors

Regulate gene expression through transcription factors

Enhancers- distal control elements  

RNA processing

Alternative RNA splicing  

Different mRNA molecules are produced from the same primary transcript

Transport to cytoplasm

mRNA translation

Protein processing

Transport of active protein to cellular destination

Charges

DNA is a negative molecule

Histone proteins are positive

Need to have opposite charges to have the DNA wrap around the histones for chromatin packing

Acetyl groups are negative

If acetyl groups are added, DNA is repelled more and allows for space in transcription DNA is more easily read when it is not as tightly associated with Histones

HATs- add acetyl groups

Increases transcription

HDACs- remove acetyl groups

Decreases transcription

Methylation 

Heavily methylated DNA is heterochromatin

Heterochromatin is silent

Sparsely methylated DNA is euchromatin

Euchromatin is silent

Why does methylation turn DNA into heterochromatin?

Heterochromatin is packed more tightly than euchromatin

Represses transcription

Viruses

Lysogenic life cycle

Does not kill the host cell after it reproduces

Virus remains in the host cell's genome

Repressor acts in prophage

Does not synthesize proteins

Keeps genes off

Membrane fusion protein

Enveloped RNA virus binds to the host cell

Replicates inside of the cell

Envelope makes it able to fuse and infect the host cell

Takes part of the envelope with it as it leaves

What does the E6 protein do for the p53 protein?

When the cell detects DNA damage, the p53 protein shuts down replication until the  damage is repaired

Viral life cycle 

Virus binds to a receptor of the cell membrane

By non-covalent chemical bonds

Viruses break through the membrane and move toward the nucleus

DNA is inserted into the nucleus  

DNA is replicated

Infected cells replicate

Go on to infect other genes

Examples and questions

If there is a disabling mutation in the pol gene (reverse transcriptase), will the virus bind to  its host?

Yes, it will bind

But, the viral DNA will not be produced  

There will be no viral cells produced

What is the effect on the life cycle if there is a mutation in the env gene?

The viron will not bind

Nothing will be produced

HIV can only get into cells if your cell has 2 co-receptors so if you don't have one you can't be  infected

Viruses are originated from animals

Thought to originate from chimpanzees  

Viral host range

Some viruses are able to mutate and cover a different range of receptors

Can be limited to a group of species

Can pass human to chimp, but not human to dog

How viruses spread

Have to have a living host

Need a type of fluid  

Do best in a densely populated area

Vaccines

Mumps and measles  

Huge outbreaks in Europe, even where they have vaccines

Why??

Misconceptions about vaccines caused children to get autism WRONG

Measles vaccine

There is about a .00004% chance that people will die

There is about a .0007692% chance you will have side effects

Without the vaccine, there is a .3% chance you will die

Lesson: Vaccinate your children!!

Prions

Put holes in your brain

Both spongiform encephalopathy and Alzheimer's are caused by protein misfolding

Biotechnology

Biotechnology can make miracles happen

Allows us to make new drugs to cure previously deadly diseases

We can grow crops where we never before could

Plasmids

Circular, extrachromosomal DNA has an origin of DNA replication

Carries genes beneficial to bacteria

Resistance plasmids

Contains genes for antibiotic resistance

Easy to get  

Restriction enzymes

Cut DNA at restriction sites

Hundreds of different enzymes

Used by bacteria as a defense mechanism

Bacteria is methylated  

Viruses are non-methylated  

Get digested  

Restriction sites are palindromic

Same backwards as forwards

Gel Electrophoresis  

Gel is basically a maze the DNA has to go through to get to the positively charged in Separates DNA by size

Smaller DNA molecules travel to the bottom

Genomic library 

Collection of DNA fragments

Each fragment is on its own plasmid in a bacterium

To create a genomic library

Start with genomic DNA

Digest it with restriction enzymes

Insert into a vector

Plasmid or phage

Insert vector into bacteria and isolate clones

Each clone contains only one type of plasmids

You can make DNA from copies of mRNAs

Starts with the purification of mRNA from cells and tissues

Purify by using the polyA tail to bind with a polyT tail

Couple the polyT tail with an insoluble bead and use it as a primer

Reverse transcriptase

Has to be primed

Once the first strand is synthesized, a second strand is synthesized

The completed copy is called a cDNA

Does not have introns or promoter sequences

Clone into a plasmid

DNA sequencing 

Dideoxyribonucleotide triphosphate

Missing the second Oxygen at the 3' position

Prevents the chain from elongating

Done in gel electrophoresis  

Read from bottom up

Amplification of DNA sequences

PCR- polymerase chain reaction

Exponential amplification of specific DNA

Cloning

DNA from a mature organism is inserted into an egg  

New DNA replaces egg's DNA

First done successfully on a sheep

Problems with cloning

Most injected eggs don't develop

Clones have health issues

Methylation can interfere with gene expression

Cloning cells can be used to treat different diseases

Donor egg + sick person's DNA

Forms an embryo

Stem cells from embryo can be used as therapeutic treatment

Stem cells are not fully differentiated

Totipotent- can become anything

Genomes and their Evolution

Bioinformatics- uses computational methods to analyze biological data

Genomics- the study of whole sets of genes and their interactions

Proteomics- the study of whole sets of proteins

The Human Genome Project

Started in 1990, ended in 2003

Sequenced the human genome

Chromosomal maps can be used to determine the location of genes

Using fluorescent in situ hybridization (FISH)

Genome sequencing 

Linkage map

AKA genetic map

Determines the location of several thousand genetic markers on each chromosome  Recombination frequencies are used to determine the distance between each one Physical mapping

Distinguishes the difference between each marker

DNA sequencing

Whole Genome Shotgun Approach

Developed in 1992 by J Craig Venter

Skips mapping and goes straight into sequencing

Done with computers

Puts DNA fragments into bacterial or viral vectors

Clones vectors

Sequence the fragments

Combine and order the fragments with computer software

Identifying protein coding genes in these sequences

Computer can find likely genes

"New" genes are compared with genes from other species

If they are similar, it is likely that they are important

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