Genomics: evolution of genes and change

for quiz 2 of bio

what are the first 3 ways the genome can evolve and change?

1. mutation in a gene

2. mutation in regulatory dna

3. gene duplication and divergence

what are the next 3 ways the genome can evolve and change?

4. exon shuffling

5. transposition 

6. horizontal transfer

how does the mutation within a gene change the genome

we have genes in the genome --> and we can get a mutation in the gene.

what’s one thing a mutation can do in a gene inside the genome

it can add a stop codon,

what’s another thing a mutation can do in a gene inside a genome

it can cause a change in the amino acids (can be rly bad depending where the change is and what it is.)

what can a mutation do in a gene inside a genome 3.

You can add a base/ delete a base

why is it bad to just add 1 base to a genome

its rly bad to add 1 base bc it alters frameshift since we read the code in groups of 3.

what is the regulatory DNA in a gene

the non-coding section of DNA that controls gene expression [cis elements]

how does regulatory DNA control gene expression

by acting as binding sites for transcription factors that control the rate of transcription. .(complimentary proteins) ex. TATA BOX, TFIIH, promoters, enhancer, silencer)

what do regulatory genes consist of

activator proteins and repressor proteins that act like switches to turn genes "on" or "off,

what do regulatory genes determine when they turn genes on and off

," determining which proteins are made and when, and at what level

what do the regulatory genes allow for cells

This allows different cells in the body to have distinct functions, even though they contain the same set of genes.)

how does a mutation occur in a regulatory dna area in the genome

A gene can have a regulatory area before the gene mutation can occur in the regulatory DNA area.

in what ways can the regulatory dna be mutated .1

• you can mutate the RNA site where polymerase binds).

in what ways can the regulatory dna be mutated 2.

• We could mutate the TATA boxes where those enhancers and silencers are

what are cis elements

(cis elements) [cis elements= elements on the dna strand)

what are examples of cis elements

tata box, promoters, enhancers, silencers,

in what ways can the regulatory dna be mutated 3.

• You can have a mutation that adds a stop codon, or a mutation that changes the amino acid

what can occur when you change the amino acid

1. you can add 1 base compared to 3 bases (very bad)

2. you can mutate the regulatory area

3. or mutate the cis elements

what does a stop codon do

a three-nucleotide sequence in messenger RNA at the end of protein synthesis.

what causes BIG changes in the genome out of the 6?

gene duplication and divergence (BIG PAPAAAA)

What occurs in Gene duplication and divergence

We can have a single gene—> and the gene duplicates with one copy being mutated and the other copy being normal.

is the change caused by gene duplication big?

yes its Huge, it allows for flexibility in genes and the mutations in them

what does it mean for there to be lots of flexibility from a gene duplication

if a mutation occurs in 1 gene it wont be Lethal because we have a spare copy untouched (yay)

are all mutations bad in a gene

no, some mutations are good (ex. hemoglobin oxygen one), they can cause evolution. but some can be bad and lethal.

how big is gene duplication in evolution

big, because it allows for the cell to experiment with a variation in one gene, to see if we can get something better through variations.

what occurred in the Hemoglobin example

we originally had 1 but as we evolved we created 2

what are the 2 forms of hemoglobin called 

1. alpha globin-

2. beta globin

how many copies of the forms of hemoglobin do we have now

1. alpha hemoglobin; has 2 copies called alpha version

2. beta hemoglobin: has 2 copies called beta version

so we have complex 4 chain of hemoglobin what

what do the copies in our hemoglobin useful for

since we have 2 copies of both alpha and beta hemoglobin, one can be experimented on while the other does its job. (one of the genes create the alpha one and one creates the beta)

what are the most important part of genes

exons

what is useful about EXON SHUFFLING

Instead of starting from scratch, you can take an exon and duplicate it and let it evolve.

what often occurs in the grand scheme of evolution

Exons are be moved around to create new combinations with slightly new functions.

what is the context of the image

Each of the shapes represents an exon (you can have one shape that has one type of exon and another with another type and when you put them together you create a new gene with a different function.)

what occurs with a lot of evolution in the genome

moving things around (creating new combinations) and letting them evolve.

what’s the difference between exon shuffling and splicing 

splicing is taking away introns, shuffling is duplicating exons inside of another gene. adding another domain

how big is exon shuffling compared to gene duplication

Similar to gene duplication it’s just a smaller scale

what consists in HORIZONTAL GENE TRANSFER

we transfer genes between speciescan you 

can you do horizontal gene transfer in eukaryotes?

no, only in bacteria because It forms structures between them that pulls cells together ti exchange genes. 

what’s the danger of sharing genes between bacteria?

they can create resistance genes for antibiotics. making it harder to create antibiotics to combat bacteria viruses

If you take the whole genome how do we make sense of it?

This is known as genomic annotation where we label the beginnings and the ends of everything, size etc..

what doe the chart show

the size of genomes in organisms:

what doe the genome size chart reveal

There is not a correlation between size of the genome and complexity

how many protein coding genes are in human genome

20,000

how many pseudo genes do humans have 

more than 20,000

what’s a pseudo gene

a DNA sequence that resembles a functional gene but has a lot of mutations that prevent proper expression

how do most pseudo genes arise

from the duplication of a functional gene with an accumulation of damaging mutations in one of the two copies.

what happens when a mutation is bad and causes the gene to be non-functional

the non functioning bad mutation in one of the genes copies is known as the PSEUDO GENEEEE.

do pseudo gene get expressed

no… 

what is half our dna made up of that is a high copy and repetitive

transposons (junk) and 1% is exons 

what are the 4 types of genetic testing 

1. single gene testing

2. gene panel

3. whole exam sequencing 

4. whole genome sequencing 

how common is single gene testing

very common especially if there’s one genome in your family that causes a condition

example of single genome testing

1.     A single gene test can be done. (Ex. Cancer runs in the family so we test a single gene of the grandson to see if he has the condition.)

what is Gene Panel often done for

often done for cancer

what is the process for gene panel in cancer

they will look at the top 2 dozen cancer genes to see if you have any of the top 2 dozen. (does not test for all genes, only the most common ones [more limited]).

what occurs in Whole Exome Sequencing

last 5 years is has become popular. They sequence the exons, which is only 1% of the genome (so it’s doable).

Whole genome Sequencing 

very expensive, debate if it’s worth it,

how much of a difference is there with genome of chimps and humans

1.2% difference, You don’t need a huge change in genome to get a drastic change in the gene

What do Restriction Enzymes do

They cut dna at a specific site to open it up to study, They cut a specific site In a specific way

where do the restriction enzyme cut and how

cuts at cleavage site, just cutting up and down ‘straight line’ is called a BLUNT END, if not straight down its called a STICKY END

PLASMIDSSS AGHHH. what are plasmids used for

(they are extra separate from chromosome) they’re used to change things up.        Ex. If we want bacteria to grow faster or change its shape we would add this

what do you work with plasmids in 

in a tube where we add cells to see how they react 

what are the 3 important areas to the plasmid

1. polylinker

2. orgin of replication

3. anti-biotic resistance

what’s the polylinker

its the multiple cloning sites (where you add the gene you want to study)

what’s origin of replication

once the plasmid enters the cell you can make copies of it 

what is anti-biotic resistance 

it works as a tracker to weed out the cells that have the plasmid insertion to study those genes 

how do you begin cloning in a plasmid

you add the restriction enzyme to cut open the gene

what do we hope to achieve by cutting open the plasmid with the restriction enzyme

that our gene is inserted into the plasmid through its sticky ends and they line up in the circle and are bonded by ligase.

what is the new plasmid dna with the new dna fragment inside called

recombinant dna

what could be the next step after cloning the plasmid 

to insert the plasmid into cells where the ells with divide and the plasmid will replicate on its own. 

The DNA fragments that are cloned in the plasmid can be: 

1. a normal version of the gene

2. a mutated version (to see how the mutated gene would affect the nucleus )

3. a gene tagged with a GFP

4. ETC.

what is something you can do to the gene that is being cloned

you can add a GFP tag to it to monitor movement