Download DNA powerpoint

DNA
Deoxyribonucleic Acid
What is DNA?
•
•
•
•
DeoxyriboNucleic Acid (DNA)
genetic information for all forms of life
found in all living cells
responsible for the production of inherited
traits
• encodes, stores, & transmits instructions
for making proteins
The Structure of DNA
Large and complex, easy to understand due
to orderly, recurring structure.
The Basic Structure
• DNA is a polymer .
• made of just 4 simple compounds
– nucleotides.
• Each nucleotide has a phosphate
group, deoxyribose (a sugar), and
a nitrogenous base.
S=sugar, P=phosphate group,
A=Adenine, G=Guanine,
C=Cytosine, T=Thymine
Nucleotide Bases
There are only four different kinds of bases,
which make up the complex genetic code.
• Adenine,
Guanine, Cytosine, &
Thymine.
•Complementary base-pairing rules:
1. Adenine always pairs with Thymine.
2. Cytosine always pairs with Guanine.
• Adenine & Guanine are purines (two
C/N rings).
•Cytosine & Thymine are pyrimidines,
(one C/N ring).
• approx. 3 billion base pairs in each
somatic cell.
- a spiral shape used to describe the
form of DNA.
•Resembles a twisted ladder wound around a cylinder - two
nucleotide chains connected by hydrogen bonds between the
nucleotides.
•Sugar-phosphate backbone - deoxyribose sugars covalently
bonded to an adjacent phosphate group.
•Complementary bases are perpendicular to the “backbone” and
form the rungs of the ladder.
Replication
DNA replication is the synthesis of two
new DNA molecules from one that
already exists.
st
1
step: Separation
Replication Fork
• Initiator protein binds at
replication origin , separates the
2 strands & opens a replication
bubble.
• Happens simultaneously at many
points along molecule so
replication occurs faster.
• DNA helicase attaches at the
replication fork & unzips DNA
molecule by breaking the
hydrogen bonds between
complementary bases.
• Each of the separated strands
serve as templates. The templates
make it possible to synthesize two
daughter molecules of DNA
identical to the original.
• RNA Primase binds to the
separated strands of DNA,
makes RNA “primer”.
• DNA Polymerase III binds
at primer, “reads” each
nucleotide of old strand.
• Adds complementary
nucleotides from those
floating free in nucleoplasm.
• Joins adjacent nucleotides to
form the sugar-phosphate
backbone.
• Creates two identical copies of
original molecule. Each copy
has one chain from original
DNA molecule and one new
chain of nucleotides.
2nd Step:
Polymerization
3’ and 5’ Ends
• Each DNA strand begins with the 5’ end of a
phosphate group on the first nucleotide and
ends with the 3’ end phosphate group on the
final nucleotide.
•The strands run
antiparallel to each
other. Therefore one
strand runs 5’ to 3’
and the other runs 3’
to 5’.
• DNA Polymerase III reads the strand in the 3’ to
5’ direction only and builds the new strand
from 5’ to 3’ direction only.
Leading and Lagging Strands
On each side of the
replication fork there is a
different type of strand used
for replication.
•DNA polymerase III reads 3’5’.
•One side is the leading strand,
which DNA polymerase reads
continuously & synthesizes toward the
replication fork.
•The opposite side is the lagging
strand, which runs in the opposite
direction, 5’3’.
•RNA primase reads the DNA, adding
RNA in short segments. This is more
complicated because DNA can not be
read in the 5’ to 3’ direction.
•DNA Polymerase III lengthens these
segments, forming Okazaki
fragments.
•DNA Polymerase I then removes the
RNA and adds its own nucleotides.
•DNA ligase joins the fragments
together.
Putting It All Together
• http://www.bioteach.ubc.ca/TeachingResources/Molecul
arBiology/DNAReplication.swf
• http://www.johnkyrk.com/DNAreplication.html
• http://video.google.com/videosearch?hl=en&q=replicatio
n+animation&um=1&ie=UTF8&ei=jCScSeSbHOH8tge0mITqBA&sa=X&oi=video_res
ult_group&resnum=5&ct=title#
Troubleshooting
•
•
•
As replication bubbles open, DNA
twists begin to bind up.
An enzyme called topoisomerase
cuts one or both strands of coiled
DNA, making replication and
transcription easier.
http://video.google.com/videosear
ch?hl=en&q=replication+animation
&um=1&ie=UTF8&ei=jCScSeSbHOH8tge0mITqB
A&sa=X&oi=video_result_group&r
esnum=5&ct=title#
Error and Mutation
•Incorrectly paired nucleotides are a Mutation. (addition, deletion,
substitution)
•DNA polymerase III proofreads its work and usually
removes & replaces incorrect nucleotides, and
continues building the new strand.
•Repair enzymes fix damage to the DNA molecule
directly or with the help of DNA polymerase III &
ligase.
•Hundreds of mutations are
inherited from parents, but
most mutations have little or
no effect.
Transcription
Transcription is the process in which genetic information is
copied from DNA to RNA.
The Need
• Cells are like little factories that make
proteins.
• DNA codes for proteins.
• DNA remains in the cell’s nucleus, but
proteins are made in the cytoplasm.
• mRNA is a copy of a gene that is sent into
the cytoplasm to be “translated” into a
protein.
The Process
• Transcription is very similar to the
process of DNA replication.
• RNA polymerase initiates
transcription by binding to the
promoter region, (TATA box or
CAAT box) just “upstream” of
gene to be copied.
• Separates one twist (10 bp) of the
DNA molecule.
• Reads 3’5’, builds mRNA 5’3’
• Only reads the sense strand
(other one is the nonsense
strand.)
RNA Polymerase
Template
The Process, Continued
•RNA polymerase adds complementary RNA nucleotides to the newly
forming RNA molecule one at a time.
•This continues until the polymerase reaches the termination signal, (a
specific nucleotide sequence or a protein).
•RNA polymerase then releases the DNA molecule and the new RNA
molecule.
•DNA retwists.
Try it!
Transcribe the following sense strand:
TAC/GGA/CGT/GTT/CCC/GCG/ATG/ACC/CTA/GAT/TGA
AUG/CCU/GCA/CAA/GGG/CGC/UAC/UGG/GAU/CUA/ACU
Post-processing
•In raw mRNA, sequences that
do not code for anything, are
called introns. They will be
removed.
•Sequences that do code for
something, exons, are now
next to each other and will be
expressed as proteins.
•A cap is added to the 5’ end necessary for mRNA to bind to
ribosome.
•A poly-A tail is added to the 3’
end – helps mRNA move from
nucleus to cytoplasm
•Both prevent degradation of
the molecule.
Structure of RNA
• RNA is a single-stranded nucleic acid
that has a similar structure to that of
DNA (chain of nucleotides attached by
the sugar and phosphate groups).
However, RNA’s sugar is ribose.
• The four nucleotide bases are
adenine, guanine, cytosine, and
uracil. In RNA, uracil replaces
thymine (a DNA nucleotide).
• The same base pairing rules apply for
RNA, except now uracil pairs with
adenine.
A=Adenine U=Uracil
C=Cytosine G=Guanine
RNA Molecules
There are three different types of RNA
molecules that are created during
transcription
•Messenger RNA (mRNA): copy of a gene, carries the
genetic information out of the nucleus into the cytoplasm
for protein syntheses. It is a straight, uncoiled strand.
•Transfer RNA (tRNA): picks up amino acids in the
cytoplasm & transfers them to the correct location in the
growing peptide chain. It has a hairpin structure.
•Ribosomal RNA (rRNA): combines with proteins in the
cytoplasm to create ribosomes. It has a globular
structure.
Accuracy of Transcription
• The RNA polymerase proofreads its work to
ensure accuracy.
• As the enzyme is adding nucleotides it can also
remove them if a pair forms that is not
complementary.
• RNA polymerase stays around the mismatched
nucleotides longer, allowing time to remove the
incorrect nucleotide.
• Error rate is just 1 in10,000 nucleotides added.
Translation
Translation is the process of putting together polypeptides from
information encoded in mRNA.
Codons
• Codon – 3-base sequence on mRNA that codes
for an amino acid
• start codon: AUG, also codes for methionine. (It
tells ribosome where to begin translation, but that
initial methionine is often removed later on in the
process)
• stop codon (UAA, UAG, or UGA) - tell ribosome
to stop translating the mRNA molecule.
• only 20 amino acids, so some amino acid have
more than one codon.
tRNA
• Transports amino acids to the
ribosomes.
• The structure of tRNA is very
important to its job in translation.
Each tRNA has an anticodon, a
region which is complimentary to
its corresponding codon on the
mRNA molecule.
• A specific amino acid attaches on
the opposite side of the molecule
from the anticodon.
• This structure ensures that the
amino acids placed precisely to be
added to the polypeptide chain
(protein).
Step One – Initiation
• The ribosome recognizes the start codon and
attaches to it, holding the mRNA in place for
easier translation.
• A special initiator tRNA molecule, carrying
methionine and with anticodon UAC
(complimentary to AUG) bonds to the start codon
mRNA.
• A ribosome covers two codons simultaneously.
Once the first two sites are filled, protein
synthesis can continue.
Step Two - Elongation
• The amino acid on the next tRNA attaches to the
previous amino acid by a peptide bond (covalent),
forming a polypeptide chain, one amino acid at a time.
• As the ribosome moves on the mRNA, the first tRNA is
released from the ribosome. However, the amino acid
stays attached to the polypeptide chain, attached to the
next tRNA.
• The movement of the ribosome is called Translocation.
The ribosome moves (reads) in the 5’ to 3’ direction.
• As the ribosome moves it exposes new codons that
attract the corresponding tRNA molecule with its amino
acid.
• Ribosomes translate mRNA constantly, with one right
after another.
http://bioweb.uwlax.edu/GenWeb/Molecula
r/Theory/Translation/translation.htm
http://www.youtube.com/watch?v=41_Ne5
mS2ls
translation
Step Three - Termination
• Elongation continues until the ribosome is
at the site of the stop codon.
• The tRNA molecule and the polypeptide
are released.
• The polypeptide will be used and
processed in different parts of the cell
depending on what it is suppose to do and
its destination. Its function depends on the
polypeptide sequence.
What’s the story?
• Only 10% of human genome codes for proteins (mRNA).
• Remaining 90%:
•
•
•
•
Introns
Code for making rRNA & tRNA
Regulatory or control sequences (enhancers, promoters)
Repetitive sequences – function unknown (leftovers from
evolution?)
Proteins, a.k.a. Polypeptides
Protein diversity: variation in proteins is due to:
1. length of peptide chain (# of AA).
2. sequence of AA within the chain (order of AA).
3. 3-D configurations (shapes) due to folding of molecule.
4. protein may contain a single chain or multiple chains.
Amino Acids
• 20 Different AA’s (we make 12, must get 8 in diet).
Structure:
• “Backbone” is the same for each:
(amino group) R (carboxyl group)
H2N – C – COOH
H
• Sidechain (R-group) differs for each AA, determines its
characteristics.
Protein Structure
• Bonding of AA’s – peptide (covalent) bonds form between
carboxyl group of one AA and amino group of another.
R
R
R
H2N – C – COOH H2N – C – COOH H2N – C – COOH
H
H
H
• “Backbone” consists of the repeating sequence :
-N-C-C-N-C-C-N-C-C-N-C-C- plus all other atoms EXCEPT
the R groups.
Proteins have four different
levels of organization:
• Primary (original): A long,
linear sequence of amino
acids (string of beads).
• Secondary: results from
hydrogen bonding involving
the backbone (N of amino
group with O of carboxyl
group).
1. Can form alpha-helix or betapleated sheet.
2. Like the coils of a telephone
cord.
• Tertiary: Folded coiled
(secondary) amino acid
chains.
• Quaternary: Multiple amino
acid chains.
Proteins
Sidechain Interactions
• Hydrophobic (non-polar) – orient themselves
toward the interior of the protein molecule.
• Hydrophilic (polar) – orient toward the outside,
hydrogen-bond with water in cytoplasm.
• Acidic (negative charge) attracted to basic
(positive charge), +/- pairing stabilizes protein.
• Cysteine sidechains pair inside the molecule
to form a covalent disulfide bond (also
stabilizes protein).
• Proteins assume the shape that gives them
their maximum stability (lowest energy state).
Gene
Expression
• Activation of a gene
results in the
expression of that gene
by production of the
protein(s) for which it
codes.
• Repression ceases the
production of proteins
coded in a gene.
• Regulating gene
expression saves
resources and controls
all cellular activity.
Gene Expression in Prokaryotes
• Operon – series of
genes that code for
specific products
AND regulatory
elements that
control these genes.
Elements of an Operon
• Structural genes – code for particular
polypeptides.
• Promoter – DNA segment that recognizes RNA
polymerase & promotes transcription.
• Operator – DNA segment, serves as a binding site
for an inhibitory protein blocking transcription.
lac operon turned OFF
• When lactose is
absent, a repressor
protein (coded for
by regulator gene)
binds to operator &
blocks attachment
of RNA polymerase
to structural genes.
lac operon turned ON
• When lactose is
present, it acts as an
inducer (binds to
repressor proteins,
preventing them from
attaching to the
operator, & RNA
polymerase transcribes
the structural genes).
• This is feedback
inhibition.
Gene Expression in Eukaryotes
• Enhancer – noncoding
control sequence on
DNA.
• Transcription factors
– proteins that bind to
both enhancer & RNA
polymerase to facilitate
transcription.
Cell Differentiation
• Homeotic genes –
regulatory genes
determine WHERE
certain structures will
develop.
• Homeobox –
sequences within
homeotic gene for
specific body regions.
Bibliography
http://www.rcsb.org/pdb/molecules/pdb40_1.html
http://www.dnaftb.org/dnaftb/
http://en.wikipedia.org/wiki/DNA
http://www.answers.com/main/reference.jsp
http://www.mansfield.ohio-state.edu/~sabedon/biol1060.htm
www.andrew.cmu.edu/.../DNA_Replication.html
http://www.alumni.ca/~mcgo4s0/t3/RNA.html
http://www.rothamsted.ac.uk/notebook/index.html
http://ull.chemistry.uakron.edu/biochem/12/
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translati
on.html
http://www.johnkyrk.com/DNAtranslation.html
http://www.medterms.com/script/main/art.asp?articlekey=32631
Travers, Bridget. The Gale Encyclopedia of Science. Volume 2.
Encyclopedia of Life Sciences. Second Edition. Volume 4.