Why does methylation turn dna into heterochromatin?
Why does methylation turn dna into heterochromatin?
Description
School: Ohio State University
Department: Biology
Course: Biological Sciences: Energy Transfer and Development
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
Reviews
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' We also discuss several other topics like What are the improvements needed in society?
Termination
5' end gets a cap
3' end gets a poly-A tail
Split genes and RNA splicing
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 Don't forget about the age old question of One of the major issues that divided the middle eastern arab states was the future of what?
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
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 If you want to learn more check out What is true about habituation?
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
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 If you want to learn more check out What is cultural transmission?
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
nucleotide sequence
Histone acetylation- opens up the chromatin structure If you want to learn more check out What is the law of diminishing returns?
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 We also discuss several other topics like How do you want the relationship to fit into other areas of your life?
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
