DNA

Saturday, October 24, 2015

1:52 PM

Talked about genes, talked about fact that genes are located on chromosomes
Talk about genes actually are
At molecular level
Chromosomes are made up of DNA
Dioxide neucleic acid and proteins
For a long time people know that chromosomes responsible for genetic information
but unsure what part of chromosomes carried
Dna or proteins
Leading candidate was proteins
Proteins came in a bunch of varieties
Convey information
But alphabet fairly complex
Our alphabet 26 letters
Need alphabet extensive
Proteins have that
Dna no varieties so didn't think it was
Major question

Protein or DNA
Elegent experiment
Hersehy and chase decided matter
Hershey and chase
Viruses are very simple and we don't know if we want to call them organisms
Not a lot of characteristics
Reporoduce simple
Look like funny looking spider
Bacteriaphogue
Attack bacteria
Attach to outside
Virus attached itself to outsie
The virus - inserts some genetic material into cell and that genetic material takes
over and causes the bacterium to make virus particles or tihngs that bacterium
would do

Hershey and chaes knew that this particular virus had inside of it DNA - plain DNA
Outside of it was protein
Both protein and DNA question was when it inserts genetic information is it inserting
protein or DNA
Now ho can you tell difference
Use some radiioactive lables
Protein has chemical consituents - sulfer
Make radioactive suilfer do something where virus gets made protein part made
with radioactive sulfer
Than do Bacteriaphogue
All of protein radiactively labeled
That virus inserts genetic information into cell
If genetic information protein
Label inside the cell
Hershey and chase no radioactive sulfer lable inside cell
None of protein gotten inside
Protein not genetic information
To prove DNA was
Dna has phosphorus in it that protein doesn't
Constructed virus particles
Radioactive phosphorous have label
Virus to effect bacterium
Looked inside for radioactive label it was there
Genetic information inserted into cell

Cell do virus's bidding was dna

DNA structure Determined that DNA is genetic material

People very interested in what it was, what does it look like, what is it composed of
Knew it is chemically but not what structure it was
Structure held key to how it functioned
How does someone find out what it is
Can't put molecule under microscope and see where they are
Indirect methods
One of methods called xray defraction
Shine xrays through it
Xrays reflected in different direction
Takes interpretiation to figure out what structure is
Watson and crick in 1953 took information that others have produced
Xray information and so on
And thought quite a bit of what kind of molecule can produce some of patterns
Come up with structure of dna

What we know about dna - polymer of neucleoties

Neucleotide - phosphate group, sugar, and something called nitrogogen base
Dna consists of 4 different nucleotides
All have same phosphate and sugar group
Differ in base they have
4 kinds of neucleotides we have
Upper left hand adenine
Upper right guanene
Lower left thymine
Lower right cytosine
Blue part of molecule - bases
Some similarties
Adeninie and guanine - look fairly similar
Two hexagon shaped
Thymine and cytosine bases somewhat similar one hexagon shaped things
Are two classes of bases

One which includes adenine and guanine

And the other incluses thyneme and cytosine

Dna structure contains 2 strands of nucleotides

Structure of dna
And this is where watson and crick amazing insights
Contains 2 strands of nucleotides
Not single stranded
Two strands ropes
Side by side
Not only that - they are coiled - double helix - helical shape
Like a twisted rope ladder
Two strands are connected by base
Rungs of ladder
By bases part of nucleotide
Each has base part of it
Two strands are connected by the base on one strand connecting with base on other
strand
Bases are paired up in very specific way
A base always pairs with t
G base always pairs with c base
See in picture
An example of two strands
Layed them out
Ladder

See one strand has string of nucleotides

Carrying basses gcaccaata
And that strand is then paired up with cgtggttat
Complenmentary base pair

Two strands connected by these nitrogogen base portions

Bottom see there the t on the left is connected with the a on the right
Moving up we see g connected with c
In fact see the shapes of those nucleotides
See that a one hexagon shape connects with a two hexagon shape complementary
base pairs

Things dna must do

Make copies of itself - replication - everytime it replicates

Cell producing gametes meiosis or just duplicating mitosis
Dna making copy of itself
Mitosis, meiosis
Give directions on running the cell carries genetic information
Directions on running cell
Things cell should do
Genes for making proteins
How that happens
DNA molecule with nucleotides and instructions for making proteins
Genes have instructions for making proteins

Does in elegant way

Two strands
Smallerp icture on right
What happens when dna replicates
Two strands separate and one strands then serves as template to make new strand
in yellow and other starnd serves as template to make new strand
Picture on left unzips
Complementary bases separaed and nucleotides brought in - in yellow
Strand built pu as template
Strand on left
Original strand in blue
New nucleotide
G nucleotide brought in to compliment c one
Another g brought in to another c
T to compliment a nad so on
As unzipping occurs nucleotides brought in added to each of strands to produce new
strand
Original strand on right same thing happening
Unzipped completely two new strands
Each new strands one of original strands and one completely new strand

Replication another view

Base pairing htem

Separated
New neucleotides brougth in
And matched up with complementary pairs
Complementary strand to each of the two original strands
Panel at bottom done with process
See we now have two new dna molecules each composed of origian and new strand

Dna replication summary

Making copies mitosis and meiosis
Two nucleotide strands
Unzip like zipper
Each serves as template to build new strand
Mentioned before
Many processes involve dna polymerase
Involved in replication process
Brings in new nucleotides
Joins with complementary base and connects it with previous nucleotides
Stiches all new nucleotides to original strands
Mutations
Mistakes in dna replication
1 in a billion times the wrong nucleotide is inserted
Proofreading enzyme
Checks for mismatches in base pairs
3 billion nucleotides
When dna replicates
Bring in over 3 billion nucleotides
Sometimes something can go wrong
1 in a billion times wrong thing inserted
Isn't correct
Other enzymes called proofreading enzyme - check if things done properly
Bases paired with each other

Pair in specific way

A with t and g with c
If you put wrong one in there
Shape of molecules dna you get from that has bump in it
Not quite semetrical it should be
Proofreading enzyme can catch and snip those out and make sure rihgt one gets in
Proofreading enzyme isn't perfect and proofreading enzyme doesn't catch it
Dna molecule misinformation
When misinformation is there - refered to as mutation

Dna acts as gene or genetic information

What do genes really do
What is the information used for by cell
Gene for blue or brown eyes
Gene is a message about how to make a particular protein
Blue eyes and brown eyes protein responsible for melenene deposited in eye
Gene responsible for making particular protein
What we need to know is how we go from dna to protein being made
Protein synthesis to occur based on genetic information in dna
Whatever genetic message is - gets out of nucleus
Gets to ribosomes where proteins are made
Use a messenger molecule, process is called transcription
Take it out of nucleus into cycoplamsa where it is located
Transcription

Once we get genetic message from nucleus to ribosome - read dna message and
translate that into protein
We know that dna molecule composed of sequence of nucleotides - differ in
nitronogous bases
Genetic information series of nitrogogen bases
Protein - series of amino acids
Translate series of bases to series of amino bases
Translation
Two step process
First transcription - getting message from dna in nucleus
Transcriped message taken from nucleus to cytoplasma translated into protein

Dna inside nucleus

Ribosomes outside nucleus

Responsible for protein production
Transcription
Take dna message and write it out on molecule
Comes out of nucleus and gets to ribosomes
Messenger rna
Talk about shortly
Messenger rna molecule
Comes out of nucleus
Second part of process occurs - translation
Translate messenger rna message into protein

Encountering rna several times

Talking about messenger rna
Transfer rna
Ribosomal rna
Rna sounds like dna
In fact very similar molecule
Sugar part of nucleartide - bit different
single stranded as opposied to dna
Other differences
4 bases in dna agtc
Instead of having t has different called u for uracil
Talk about process of transcription transcribing dna message on rna molecule

Molecule called as messenger rna

Carrying message
One other thing we see here
Dna message has some things inserted into it that doesn't make a lot of sense
Portions of the dna that is the gene that is non coding
Doesn't contain relative information for making protein
Nonsene information that got stuck in there
One of things that has to happen is to snip out noncoding sections called introns)

Dna molecule huge thing

Only small portion constitutes gene
If gene has to be activated to do something
We don't need to use entire dna molecule
Only use portion with particular genetic information we want
Molecule opens up at that point
Doublly stranded two strands come apart

Sort of thing happening in dna replication

Each strand serves as template to make new strands
Little bit like it but somewhat different
Two strands opening up
One strand on top odesn't do anything
Lower strand serves as template to make rna
So just as we saw dna replication
This strand of dna serves as template and nucleotides brought in to compliment
bases of nucleutides that are already there
Only difference
We are makign single stranded molecule
Thats a molecule of rna
Other tihng thats different
Complimentary nucleotide
Instead of bringing in t
We bring in u instead
Nitrogogous base - part of rna

Two upper strands open up

Lower template as rna molecule
Only difference here
See dna molecule
Serves as template has the bases cgta
And when we build a messaenger rna molecule
Its base sequence gcau
C and g go together t and a go toegher
Instead of a pairing with t
It has a u instead

On top dna strand - gene here

Portions of it called introns which don't contain information
Just nonsense sequence of nitrogogen bases
But they exist
That misinformation has to be snipped out before we complete transcription process
Make messenger rna
Some point in process snip out those introns
On bottom you see genetic information
Introns removed

Translation
Taken dna message and dna message is - a sequence of bases - taken dna
messages transcribed it into rna languages - 4 bases one being uracel
Translate message into sequence of amino acids
What amino acids should be

About 20 different amino acids that can exist

Protein - fair sized protein
100 amino acids in it
Somehow information has to come from messenger rna
And to make translation to make switch from something written in nitrogonous
bases
Know genetic code
Know how to translate sequence of bases to sequence of amino acids
Look at three of bases at time
Tell you particular amino acid
3 bases called codon - every codon particular amino acids it codes for
Codons where protein starts and stops

Look at all possible sequences of three bases

What that sequence codes for
Amino acids
If you look at brown column on left
First base of the three
If you look along top - second base in this triplet is
If you look at right hand column - third base might be

Top here - first base is a u

U and not t because translating something from messenger rna
Codon a u, an a, and another a
u-a-a
What does that mean?
What amino acid does it code for
Follow in chart
Find uaa means stop
Codon which is agc - serine - produces or has information make amino acid called
serine
Genetic code - thing you'll notice
Some cases same amino acid made in several different ways by several different
codons
64 different combinations of 3 bases
Redundancy in genetic code
Same amino acid coded for in several different ways
Any particular code codes for one and only one

We now know how to translate it

See how it is physcially done
Rna messenger
How to use genetic code to translate it
Reader - molecules caled ribosomes - take message and read it three bases at a
time
Every 3 bases they read

They say okay these three bases amino acid called serine and put it in this
particular position
Another rna called trna - transfer rna
Responsible for bringing in amino acids to link up to other amino acids to grow in
this chain
On its end 3 bases as anticodon
Compliment 3 bases of codon
This shows specificity
Transfer rna molecules out there
Carrying speccific amino acids
And each one can only hook up to particular codon exactly complementary to it

Transfer rna might look like

One end have three bases
Refered to anticodon
If it recognizes three bases that re in codon in messenger rna
Than it can attach at that point

See at other end carrying amino acid

Dna and nucleus and messenger rna has been made

Moved out to clunky looking thing robosome
Fed through ribosome
Ribosome reader of message
Reads message
Is looking at two codons at a time
Top part of middle - see these are two little places where transfer rna molecules can
come in
Messenger rna molecule
Two codons next to each other
Place in ribosome where transfer rnas can come in
First codon
Codes for serine

Trasnfer rna carrying serine having anti codon hooks up

And second slot taken up by different transfer rna molecule
Anticodon matches codon of rna
Follow arrows second transfer rna coming in
Middle of bottom
Two in the slot
First one that came in breaks away but leaves behind its amino acid
Connected to the animo acid of the second transfer rna

New transfer molecule comes in carrying an amino acid

Amino acid hooked up to previous ones
Another transfer rna leaves
Reader shifts down one more slot
And keeps going until we get this growing sequence of amino acids linked together
Eventually we come to stop codon

Thats the end and protein made

Amino acids constitutes protein

Think about what happens here

Transcription
Takes dna message
Dna can't get out - stuck there
Take information dna has and takes it to ribosomes
Transcribe dna message to rna message
Molecule meseger rna
Snip out introns

Messenger rna leave nucleus

Goes out to clunky structure ribosome
Ribosome takes message
Looks at 2 codons at a time
Each codon it finds transfer rna that has proper anticodon
Hooks it in place
And ribosome then goes down that message one codon at time
Looking at 2 simultanously
Each time it goes down
Another transfer brings amino acid up to previous one, moves to another notch
Goes to propper anticodon
Linking up proper amino acids
Messenger rna
Sequence of bases
Turns into proteins sequence of amino acids

About protein synthesis

Talk about mutations
Talk first about simplest type - point mutation
Situation where genetic message
Sequence of nucleutides or bases
Point mutation
One of nucleotides is changed
Whatever was supposed to be there isn't there

Codon that nucleotide is a part of

Codon is different
When we translate that odon using the genetic code
Amino acid thats made in that spot in protein is different
This is the basis for all these genetic diseases we refered to before
Sickle cell anemia
Hemoglobin molecule
Fairly big molecule more than 100 mutations
Point mutation
Hemoglobin thats made - one wrong amino acid - one wrong base means we got a
different codon than before, different amino acid than before

Ctt codon
What happens when you have sickle cell
That particular codon
Instead of ctt you have cat
One nucleotide with different base

When we make messenger rna

On the left hand side
See what happens normally
When we make messenger rna is complementary to ctt gaa and gaa codes for an
amino acid called glutamic acid
Consequence of point mutation instead of ctt we hae cat
Messenger rna based on that gua
Codon message gua
Look that up in genetic code
Codes for different amino acid called valene
Should be glutamic acid theres valene
Enzymes and proteins - molecules fold back on themselves amino acids interact
with others
Change one - folding of molecule isn't quite like its used to be
Enzyme molecule very important
Doesn't take a lot to change function in important ways

Other kinds of mutations - much more serious

Consider what happens if you change one nucleotide from g to c

What if we insert a nucleodtide where there isn't supposed to be one

We have a dna molecule (blue on bototm) and above that messenger rna made
from it
Names of amino acids that codons would refer to
What if in the middle we stick a nucleotide that doesn't belong
Don't replace, we add one
What's going to happen
Everything shifted over
Codon that was supposed to be uau in messenger is now uua
Code for something different lucine
Everything from thereon in off by one
Three nucleotides supposed to be reading
Two nucleotides of one and one of the other
Cause some major changes to protein not just one amino acid but whole thing
wrong
What kinds of genes are mutated
In general two kinds of genes
Structural genes and regulator genes
Genes aren't equal but some are intragally involved in developmental processes
Regulatory - orchestra conductors - tell instruments what they are supposed to play
and when - very important
Structural genes - orchestra members - one isn't playing exactly - may notice that
BUT the overal symphony may sound what its supposed to sound
If orchestra conductor different - whole symphanthy break down sound different
Regulator gene - consequences more severe on organisms
Structural gene - things talked about - eyes blue or brown

Hair is brown or blonde or black

Mutations in those genes effect how you look
Overall be okay
Regulatory much more serious
Mutations cont.
Mutations rare - once in a million due to DNA repair enzymes - chek out what
happens in dna replication process
Dna replication - separate two strands and bring in nucleotides - build
complementary strands
Human dna - over 3 billion nucleotides in properpalce
Mistakes can occur
Repair enzymes go along and check things
Base thats not where it should be
Physical demensions off and enzyme can recognize and attempt to fix it
Mutagens - materials that increase mutation carcinogens
Hemicals radiation viruses
All these things general category - increase mtation rates

Cells somatic cells in body

Cells producing gametes
Consequeces of muations in these kinds of cells is different body cells
Perhaps one of consequences
Cancer or tumor starts growing
That mutaiton cant be passed on to offspring of individual

Sematic cells can't make gametes

Replicated in process of meiosis - that mutation can be passed on to offspring
When gametes made - few mutations
Every parent gives child few mutations by way of gametes
Most of time - fact that there are some mutations in gamete - not really problem
Most mutations recessive
Other parent - normal alleles - you should be okay
Fairly rare in parents
Individuals related to each other - related to each other - inheretant some mutation
from grandfather
Increases chances of bad mutation
Individual inherited genetic disease