Unit 6 AP Bio: Gene Expression

Central Dogma of Biology

DNA → RNA → Polypeptide

Transcription → translation

One gene codes for

one polypeptide

Retrovirusus

What do they do that violates the central dogma

they do reveerse transcripase

this is done to synthesize DNA from RNA to input host DNA

Where does replicaion occur in

Eurkayotes and Prokayotes

Prokayotes - nucleoid

Eukrayotes - Nucleus

DNA structure

Eurkayotes vs prokayotes

Virus Violations

Double Stranded, anti parrelel, negative charge

Eukryates have linear DNA and multiple chromosomes and have histones (nucleosomes)

Prokayotes have one chromosome and circule + Plasmid and is naked

Virus can violate the single-stranded or double stranded for both RNA and DNA

What makes up DNA

Base Pairs?

CHONP

Nitrogenous Base+ Sugar + phosphate

Purine (double G and A)

Pyrmadines (C and T) single ring

A T 2 bonds

C and G 3 Bonds

How is DNA read and how is it replicated or trasncribed

read 3-5

built 5-3

antiparrelel

Replication Enzymes

Helicase unwinds the DNA strands by breaking down the hydrogen bonds

• more bonds from C-G - higher melting point

Primase - it sets RNA primer

DNA polymerase - will go on the Primer, and then will build on the primer - has many other roles

Ligase - connects the okizaki fragments

Replication Fork

helicase finds the orgin of replication to binds to and start

is where the DNA polymerase bind and then there is like a fork

Semi-conservative

means that one parent strand and new strand are together.

Lagging Strand and Leading Stand

The Leading Strand is continoius

The lagging strand is going “backwards” and needs RNA polymerase to be build back wards and DNA builds foward

Where is transcription taking place

EUkrayotes and Prokeayotes

in eukraes- nucleus - monocintronic - one promoter one gene

in prokayoes - nucloid (cytosol) - polycistronic - one promoter (operon), many genes

What is different about RNA from DNA

Rna is singel stranded

has U instead of T

Has pentose sugar with hydroxl group

How does RNA poymerase read and build

read 3-5

build 5-3

Template Strand

Names

It is the strand being read.

non coding strand, minus strnad, antisense stand

RNA Polymerase

can pull aparts the DNA

goes onto the promoter and is helped by the Transcription factors

ends on the terminator

transcriptrion factors

can turn on or off the gene expression

Bacteria Transcription and Translation

as soon as it is transcribed, it will be translation

Coupling with Ribosomes

The RNA lasts way less because it is not processed

Eurkayaotic Transcription and RNA Processesing

• It is compartmentalized

• 3 Cap and 5 Cap are added.

  • makes it easier for the RNA to go out of the nuclear Pores

• Poly A 5’- increases the Lifespan of the RNA, makes RNA more stable

• Poly 3’ GTP

• Splicing - removal of introns (non coding) - done by spliceosomes (snRNA+Protein)

• The promoter is on the 5’

• 3’ was the end

Alternative Splicing

• done by spliceosomes

• different exons are used to use different domains or parts of the protein.

• this allows for more types of receptors or responses, etc

Translation and Ribosomes

Structure?

Ribosome = rRNA + Protein. 2 Subunits (top mRNA, Bottom transferRNA)

A site (added in) (P Site ATP NEED) (E Site Exit)

• takes place in the cytsol or ER

• synthesis of Proteins by the Ribosome

initiation at start Codon, the small subunit binds, Elongates, then terminates with stop codon (release factor comes in + water)

release factor protein will make the translation end

Point Mutations

Silent - no phenotypic change - usually on the third base -

Missense - one ammino acid to another

Nonsense - change the stop codon location

Frameshift - deletion or additrion changes all teh reading frame and changes everything

Chromosome Mutations

reareangment during egg and sperm formatio

• deletion - part of chromosome is removed

• duplication - part of the chromosome is duplicated

• inversion

• translocation - movemnt of a gene from one chromosome to another

• can lead to more expression of a certain protein or etc

CHanges in chromsome number

• nondisjuntion - failure to separate in meosis 1 or 2

• polyplodiody - from non disjuction, creating od hybrid, more than 2 sets of chromosomes etc

polyploid - more than 2 sets of chromosoems

Operons

Gene Regulation only found in Prokayotes

“bundle of related Genes”

Promoter

Operator is where the repressor binds

Repressible Operon

THe gene is on and will be turned off

The repressor is inactive at first

Lots of a supply → binds to allosteric site → activates the repressor and will go on the operator and not allow transcription because RNA polymerase cant bind

trp operon

Inducible Operon

The gene is off and the represosr is active - start

as there is more supply → binds to alosteric site → turns off repressor, turns on gene

lac operon

Gel Electrophoresis

DNA samples put into wells

The other side is positive charge

DNA is negative so it will be drawn

The longer heavier fragments will stay close to well, the lighter will get closer to charge

Used to compare

Thicker band more DNA

the DNA broken by endonucleases or restriction enzymes

PCR

makes copies of DNA artificially, mass productiuon

Using DNA polymerase and primers and free nucleotides

amplifies DNA

Heterochromatin

DNA which is tighly packed around histones and cannot be used

methylation

Eucrhomatin

DNA that is able to be used

Acytlation

RNA interfrerance

short RNA molecules silence the genes by

inhibiting the expression by degrading or by blocking their translation by preventing the Ribosome binding

some bind to the rna and precent transcription

ex: siRNA, miRNAr

Repressor Proteins

bind to the operator and prevent

what makes DNA good for genetic material

it is specific

many varieites

can be replicated because of specific base pairing and templates

the double base pair is very stable

some mutations can allow for mutations

What do UV Rays fo to DNA

it breaks the hydrogen bonds between the nuceleotides and cause mutuations

Advantage of compartemenzalizing transcription from translation

• ability to conttol gene expresssion

• metabolic efficiency

• genes can stay longer becuase of gene processing

How to use Codon Chart

nontemplate - is also called the coding strand, just switch the letters

template strand has to be switched lettetrs

tRNA anticodons are the opposite

Hershey Chase Experiment

Purpose and findings

what they did was put in differnt isotopes in virus and induce transduction and see what genetic information was transfered to the bacteria

what they found was the radioactive phosphorous transfered, meaning that it was DNA that was tranfeted

epignetics

is changes in DNA expression that involve reversible chemical modifications of DNA or modifications in DNA packaging but not actual changes in sequence of mucleotides

Cell Differentiation

same dna or not?

all cells have the same DNA and come from the same zygote, same geonome

they diffenciate because differnent genes are expressed

sickle cell disease mutation

there is a missense mutation

leads to a change in the shape of the RBC and less O2

mutation consequences

-positive- can cause evolution and will be passed

-negative- it can reduce fitness

-both- sicle disease can cause both postitive and negttive “resistance to malaria but less o2”

-neutral can be a silent mutation or a mutation in a noncoding part of the DNA

restriction enzymes

can be used to make recombined DNA

-finds sequences called restriction sites and then fragments are glued together with ligase

-type of endonucluase

Artificial Recombinant DNA

-dna which was artificially combined

-could be human + bacteria DNA

-tool with restriction enzymes

Activators and enhancers