Download DNA Structure and Protein Synthesis notes-2008

The Molecular Biology
of the Gene
Identifying the Genetic Material
• Mendel’s experiments—inherit
chromosomes that contain genes
• The Question now:
– What are genes made of?
• Scientists searching for the answer:
– Griffith and Avery
– Hershey and Chase
Griffith-Avery Experiment:
Transformation of Bacteria
Controls
THE STRUCTURE OF THE
GENETIC MATERIAL
•Experiments showed that DNA is the genetic material
– The Hershey-Chase experiment showed that certain
viruses reprogram host cells
• To produce more viruses by injecting their DNA
Head
DNA
Tail fiber
300,000
Tail
Bacteriophage-virus that infects only bacteria
Hershey-Chase Experiment:
DNA, the Hereditary Material in Viruses
Phage
Radioactive
protein
Bacterium
Empty
protein shell
Radioactivity
in liquid
Phage
DNA
DNA
Batch 1
Radioactive
protein
Centrifuge
Pellet
1 Mix radioactively
labeled phages with
bacteria. The phages
infect the bacterial
cells.
2 Agitate in a blender to
separate phages outside
the bacteria from the cells
and their contents.
3 Centrifuge the mixture
so bacteria form a pellet
at the bottom of the test
tube.
4 Measure the
radioactivity in
the pellet and
the liquid.
Radioactive
DNA
Batch 2
Radioactive
DNA
Centrifuge
Pellet
Figure 10.1B
Radioactivity
in pellet
DNA and RNA are polymers of
nucleotides
•DNA is a nucleic acid
– Made of long chains of nucleotide monomers
Nucleotides of DNA
• Nucleotides are the monomeric units that
make up DNA
3 main parts:
5 carbon sugar—deoxyribose
Phosphate group
Nitrogenous base
Nitrogenous bases of DNA
• Pyrimidines: singlering structures
 Thymine (T)
 Cytosine (C)
• Purines: larger,
double-ring structures
 Adenine (A)
 Guanine (G)
http://www.phschool.com/science/biology_place/biocoach/images/transcription/chembase.gif
RNA
• RNA is also a nucleic
acid
– But has a slightly
different sugar
– And has the
pyrimidine, Uracil (U),
instead of T
http://www.phschool.com/science/biology_place/biocoach/images/transcription/chembase.gif
Discovery of the Double Helix
• 1953—James Watson
and Francis Crick
determined the
structure of the DNA
molecule to be a
double helix
– 2 strands of
nucleotides
twisted around
each other
Discovery of the Double Helix
• Rosalind Franklin contributed to this discovery by
producing an X-ray crystallographic picture of
DNA
– Determined helix was a uniform diameter and
composed of 2 strands of stacked nucleotides
– The structure of DNA
• Consists of two polynucleotide strands wrapped
around each other in a double helix
Figure 10.3C
Twist
Double Helix Structure
•Hydrogen bonds
between bases
– Hold the strands
together
•Each base pairs with
a complementary
partner
– A base pairs with T
– G base pairs with C
Structure of DNA relates to its
Function
G C
A
T
G
C
C
G
A
T
T
C
A
A
G
T
C
G
C
C
T
A
T
A
A
G
T
G
C
G
C
G
T
A
G
C
G
C
T
A
A
A
G
T
T
C
T
A
T
A A
T
Structure of DNA is related to 2 primary functions:
1. Copy itself exactly for new cells that are created
2. Store and use information to direct cell activities
DNA Complementary Strands
• Strands run in
opposite directions
– Anti-parallel
Complementary Strands of DNA
• If one strand is known, the other strand can be
determined
3’
5’
A
C
G
G
T
A
T
C
C
5’
=T
G
C
C
=A
=T
=A
G
G
3’
DNA Replication
•DNA replication depends on specific base pairing
– DNA replication
• Starts with the separation of DNA strands
– Then enzymes use each strand as a template
• To assemble new nucleotides into complementary
strands
A
T
A
T
A
T
A
T
A
T
C
G
C
G
C
G
C
G
C
G
G
C
G
C
G
C
G
C
T
A
T
A
T
A
T
A
T
A
A
T
A
T
A
T
Parental molecule
of DNA
C
A
Nucleotides
Both parental strands serve
as templates
Two identical daughter
molecules of DNA
DNA Replication
• Replication occurs
simultaneously at
many sites (replication
bubbles) on a double
helix
 Allows DNA
replication to occur in
a shorter period of time
DNA Replication Process
1. Helicase unwinds the
double helix to
expose DNA
nucleotides
http://www.nature.com/nature/journal/v439/n7076/images/439542a-f1.2.jpg
DNA Replication Process
2. Primase lays down
an RNA primer to
provide a 3’ OH
group
http://www.nature.com/nature/journal/v439/n7076/images/439542a-f1.2.jpg
•
•
Can only add bases to
the exposed 3’-OH
group
Therefore, DNA
Replication always
occurs in the 5’→ 3’
direction
http://www.mun.ca/biochem/courses/3107/images/S
tryer/Stryer_F31-23.jpg
3. DNA polymerase
attaches complementary
DNA nucleotides to the
3’ end of a growing
daughter strand
http://www.nature.com/nature/jour
nal/v439/n7076/images/439542af1.2.jpg
DNA Replication Process
DNA Replication Process
http://www.nature.com/nature/jour
nal/v439/n7076/images/439542af1.2.jpg
4. DNA polymerase
then removes the
RNA primer and
replaces it with
complementary DNA
nucleotides
5. DNA Ligase creates
a covalent bond
between the DNA
fragments
http://porpax.bio.miami.edu/~cmallery/150/chemistry/sf3x14a.jpg
DNA Replication “Problem”
• DNA Polymerase can only replicate in the 5’→ 3’
direction
• One of the template strands would require replication
in the 3’→ 5’ direction (WON’T WORK)
• So, one daughter strand is made continuously while
the other strand is made in short pieces called Okazaki
fragments
Overall Direction of Replication-toward the replication fork
DNA Replication
DNA Replication
• Assures that daughter cells
will carry the same genetic
information as each other
and as the parent cell.
 Each daughter DNA has one
old strand of DNA and one
new strand of DNA
Semiconservative
Replication
Checking for Errors
• 1/1,000,000,000 chance of an error in DNA
replication
– Can lead to mutations
• DNA polymerases have a “proofreading” role
– Can only add nucleotide to a growing strand if the
previous nucleotide is correctly paired to its
complementary base
• If mistake happens, DNA polymerase backtracks,
removes the incorrect nucleotide, and replaces it
with the correct base
Flow of Genetic Information
• Flow of genetic information from DNA to
RNA to protein
• The DNA genetic code (genotype) is
expressed as proteins which provide the
physical traits (phenotype) of an
organism
GCTGCTAACGTCAGCTAGCTCGTAGC
GCTAGCGCTTGCGTAGCTAAAGTCGA
GCTCGCTTGCGTAGCTAAAGTCGAGC
TGCTGCTAACGTCAGCTAGCTCGTAG
AGCGCTTGCGTAGCTAAAGTCGAGCT
AGCGCTTGCGTAGCTAAAGTCGAGCT
GCTGCTAACGTCAGCTAGCTCGTAGC
AGCGCTTGCGTAGCTAAAGTCGAGCT
AGCGCTTGCGTAGCTAAAGTCGAGCT
GCTGCTAACGTCAGCTAGCTCGTAGC
AGCGCTTGCGTAGCTAAAGTCGAGCT
AGCGCTTGCGTAGCTAAAGTCGAGCT
GCTGCTAACGTCAGCTAGCTCGTAGC
AGCGCTTGCGTAGCTAAAGTCGAGCT
GCTGCTAACGTCAGCTAGCTCGTAGC
AGCGCTTGCGTAGCTAAAGTCGAGC,
cont.
RNA
Proteins
Protein Synthesis
• Transcription
 Process in which a
molecule of DNA is
copied into a
complementary strand
of RNA
• Translation
 Process in which the
message in RNA is
made into a protein
Forms of RNA
3 Main Types of RNA
1) mRNA (messenger RNA) – RNA that decodes
DNA in nucleusbrings DNA message out of
nucleus to the cytoplasm
Each 3 bases on mRNA is a “codon”
2) tRNA (transfer RNA) – RNA that has the
“anticodon” for mRNA’s codon The anticodon
matches with the codon from mRNA to
determine which amino acid joins the protein
chain
3) rRNA (ribosomal RNA) – make up the
ribosomes—RNA that lines up tRNA molecules
with mRNA molecules
Transcription produces genetic
messages in the form of RNA
RNA
polymerase
RNA nucleotide
Direction of
transcription
Template
strand of DNA
Newly made RNA
Figure 10.9A
Copyright © 2003 Pearson Education, Inc. publishing Benjamin Cummings
Transcription
1. Initiation:
• RNA polymerase (enzyme)
attaches to DNA at the
promoter and “unzips” the
two strands of DNA
2. Elongation:
• RNA polymerase then
“reads” the bases of DNA
and builds a single strand
of complementary RNA
called messenger RNA
(mRNA)
3. Termination:
• When the enzyme reaches
the terminator sequence,
the RNA polymerase
detaches from the RNA
molecule and the gene
Transcription
The code on DNA tells how mRNA is put together.
Example: DNAACCGTAACG
mRNAUGGCAUUGC
• Each set of 3 bases is called a triplet or codon
(in mRNA)
UGG CAU UGC
•
Eukaryotic RNA is processed before
leaving
the
nucleus
Noncoding
segments called
introns are spliced
out
• Coding segments
called exons are
bonded together
• A 5’cap and a
3’ poly-A tail are
added to the ends
Exon Intron
Exon
Intron
Exon
DNA
Cap
RNA
transcript
with cap
and tail
Transcription
Addition of cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
NUCLEUS
CYTOPLASM
Figure 10.10
Copyright © 2003 Pearson Education, Inc. publishing Benjamin Cummings
Protein Synthesis
• Transcription
• Translation
Process in which RNA is used to make a
protein
Transfer RNA molecules serve as
interpreters during translation
Amino acid attachment site
• In the cytoplasm, a
ribosome attaches to
the mRNA and
translates its
message into a
polypeptide
• The process is aided
by tRNAs
Hydrogen bond
RNA polynucleotide chain
Anticodon
Copyright © 2003 Pearson Education, Inc. publishing Benjamin Cummings
Figure 10.11A
Ribosomes build polypeptides
Copyright © 2003 Pearson Education, Inc. publishing Benjamin Cummings
Elongation adds amino acids to the
polypeptide chain until a stop
codon terminates translation
• The mRNA moves a codon at a time relative to
the ribosome
– A tRNA pairs with each codon, adding an amino
acid to the growing polypeptide
1. Initiation:
–
–
–
Translation
mRNA molecule binds to the small ribosomal subunit
Initiator tRNA binds to the start codon (AUG—
Methionine) in the P-site of the ribosome
The large ribosomal subunit binds to the small one so
that the initiator tRNA is in the P-site to create a
functional ribosome
2.
Elongation:
–
–
–
Codon recognition: anticodon
of incoming tRNA molecule,
carrying its amino acid, pairs
with the mRNA codon in the
A-site of the ribosome
Peptide formation: polypeptide
separates from the tRNA in the
P site and attaches by a peptide
bond to the amino acid carried
by the tRNA in the A site
Translocation:
the tRNA in the P-site now
leaves the ribosome, and the
ribosome moves along the
mRNA so that the tRNA in the
A-site, carrying the growing
polypeptide, is now in the Psite. Another tRNA is brought
into the A-site
Translation
Translation
3.
Termination:
–
–
Elongation continues until a
stop codon is reached—
UAA, UAG, or UGA
The completed polypeptide is
released, the ribosome splits
into its subunits
• An exercise in translating the genetic code
DNA
RNA
Start
codon
Polypeptide
Stop
codon
Mutations
•
•
Mutagenesis—creation of mutations
Can result from Spontaneous Mutations
•
•
Errors in DNA replication or recombination
Mutagens—physical or chemical agents
– High-energy radiation (X-rays, UV light)
Types of Mutations
• Mutations within a gene
– Can be divided into two general categories.
• Base substitution
• Base deletion (or insertion)
– Can result in changes in the amino acids in proteins.
Normal hemoglobin DNA
mRNA
Mutant hemoglobin DNA
Sickle-Cell
Disease
mRNA
Normal hemoglobin
Glu
Sickle-cell hemoglobin
Val
Substitution Mutations
• Missense mutation:
altered codon still codes
for an amino acid,
although maybe not the
right one
• Nonsense mutation:
altered codon is a stop
codon and translation is
terminated prematurely
– Leads to nonfunctional
proteins
Insertions and Deletions
• Frameshift mutation:
addition or loss of one
or more nucleotide
pairs in a gene shifts
the reading frame for
translation and
incorrect protein is
made
Are all Mutations Bad?
• Although mutations are often harmful,
– They are the source of the rich diversity of
genes in the living world.
– They contribute to the process of evolution by
natural selection.