DNA

DNA
DNA
• must carry information
• must be replicatable (inheritance)
• must be changeable (mutation)
DNA
DNA structure
deoxyribonucleic acid - two
directional polynucleotide strands
in a double helix
A brief digression for terminology:
Carbon molecules
in rings are numbered….
5C
O
4
C1
C
C
3
C
2
two directional polynucleotide strands in double helix
start with a ribose
sugar…
two directional polynucleotide strands in double helix
start with a ribose
sugar…
remove an oxygen at
carbon 2’….
two directional polynucleotide strands in double helix
start with a ribose
sugar…
remove an oxygen at
carbon 2’….
add a phosphate group at 5’ side
add a nitrogenous base at 1’ side
= a nucleotide
two directional polynucleotide strands in double helix
A nucleotide, or base
Bases = purines (adenine, guanine) and pyrimidines (cytosine, thymine)
two directional polynucleotide strands in double helix
nucleotides are linked in chains with a phosphodiester bond
free ends of chain will have 5’ phosphate at one end,
3’ hydroxyl at the other end
5’ end
phosphodiester
bond
3’ end
two directional polynucleotide strands in double helix
nucleotides are linked in chains with a phosphodiester bond
free ends of chain will have 5’ phosphate at one end,
3’ hydroxyl at the other end
5’ end
3’ end
two directional polynucleotide strands in double helix
Hydrogen bonds
two directional polynucleotide strands in double helix
Two strands pair up, nucleotides linked with hydrogen bonds
adenosine pairs with thymine
cytosine pairs with guanine
two directional polynucleotide strands in double helix
Two strands pair up, nucleotides linked with hydrogen bonds
adenosine pairs with thymine
cytosine pairs with guanine
- abbreviated as “base pairs”
two directional polynucleotide strands in double helix
Strands have polarity
- 5'-hydroxyl group of first nucleotide at
one end, 3'-hydroxyl group at other end
(5’ to 3’ strand)
Strands run antiparallel:
(5' -> 3') ATGGAATTCTCGCTC
(3' <- 5') TACCTTAAGAGCGAG
DNA replication:
two strands are both available as templates for new strand
result is doubling (2 complete new double helices)
DNA replication:
is semiconservative
always occurs in 5’ to 3’ direction
DNA replication:
occurs at multiple replication forks (bubbles)
along the DNA strand
Important:
there are several DNA polymerases involved in replication
DNA polymerases have a proof-reading and editing function
(exonuclease activity)
TRANSCRIPTION
Consider:
if all DNA was actively used:
- most mutations would be lethal
- there would be no ‘raw material’ for evolutionary change
- what would happen to genes de-activated by mutation?
In fact, many errors and duplications leave ‘extra’ DNA
Consider:
If there is excess DNA, it may be
- only between genes
- also interspersed within genes
Consider:
If there is excess DNA, it may be
- only between genes
- also interspersed within genes
Consider:
Not all gene products are required simultaneously; needs for
proteins change or differ
- during development (e.g., milk digesting enzymes)
- over time (e.g., digestive enzymes)
- among organs (e.g., liver enzymes not used in muscle)
- in response to stimuli (e.g., melanin, adrenalin)
therefore regulation of gene activity is needed
Transcription:
Uses RNA as an intermediary
- to assemble genes
- to transmit the right information when/where it is needed
(regulation)
Transcription:
Uses RNA as an intermediary
- to assemble genes
- to transmit the right information when/where it is needed
(regulation)
RNA is ribonucleic acid
- has uracil instead of thymine
- sugar is ribose instead of deoxyribose
There are three types of RNA:
mRNA: messenger RNA – carries the code for a gene
rRNA: ribosomal RNA – used to construct ribosomes
tRNA: transfer RNA – short adapters to carry amino
acid and its anti-codon
DNA strand (double, helical) - permanent
(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
DNA strand (double, helical) - permanent
(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
mRNA strand (single, linear) – temporary, as needed
(5' -> 3') AUGGAAUUCUCGCUC (from template strand)
DNA strand (double, helical) - permanent
(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
mRNA strand (single, linear) – temporary, as needed
(5' -> 3') AUGGAAUUCUCGCUC (from template strand)
note: by taking information from the template (antisense) strand
of DNA, mRNA becomes the coding sequence
DNA strand (double, helical) - permanent
(5' -> 3') ATGGAATTCTCGCTC (coding, sense strand)
(3' <- 5') TACCTTAAGAGCGAG (template, antisense strand)
mRNA strand (single, linear) – temporary, as needed
(5' -> 3') AUGGAAUUCUCGCUC (from template strand)
protein sequence (single, with 1, 2, 3, 4 structure)
Met-Glu-Phe-Ser-Leu...
Gene structure
promoter region: immediately upstream (5’ end) of its gene
Steps in transcription:
1. initiation
RNA polymerase recognizes and binds to promoter sequence
- these contain TATAAA and TTGACA or CCAAT codes
Steps in transcription:
1. initiation
RNA polymerase recognizes and binds to promoter sequence
- these contain TATAAA and TTGACA or CCAAT codes
2. elongation
- similar to DNA replication
- only one strand (template) is used
Steps in transcription:
1. initiation
RNA polymerase recognizes and binds to promoter sequence
- these contain TATAAA and TTGACA or CCAAT codes
2. elongation
- similar to DNA replication
- only one strand (template) is used
3. termination
- transcription keeps going for 1000-2000 bases beyond
end of ‘gene’
After transcription: RNA processing
capping
polyadenylation
intron removal
promoter
elements
UTR= untranslated
region
TRANSLATION:
The Genetic Code
The genetic code
DNA and RNA have 4 types of bases
proteins are composed of amino acids, of which there are 20
- so how do 4 bases encode 20 amino acids?
The genetic code
“words” with a single base allow no combinations (4 words)
“words” with two bases allow 16 combinations (42)
“words” with three bases allow 64 combinations (43)
= more than enough combinations for 20 amino acids
The genetic code
• composed of nucleotide triplets (codons)
mRNA
protein sequence
AUG GAA UUC UCG CUC
Met
Glu
Phe
Ser
Leu
The genetic code
• composed of nucleotide triplets (codons)
• non-overlapping
mRNA
protein sequence
NOT
AUG GAA UUC UCG CUC
Met
Glu
Phe
Ser
Leu
AUGGAAUUCUCGCUC
The genetic code
• composed of nucleotide triplets (codons)
• non-overlapping
• unambiguous – each codon only specifies one amino acid
• degenerate – most amino acids specified by several codons
third position
first position
second position
Reading frame must be uniquely specified:
theredfoxatethehotdog
t her edf oxa tet heh otd og
th ere dfo xat eth eho tdo g
the red fox ate the hot dog
start
codon
Reading frame must be uniquely specified:
mRNA code begins with start codon (AUG)
protein is constructed along open reading frame
translation stops at stop codon (UAA, UAG, or UGA)
(only in frame: sequence out of frame does not work)
Reading frame must be uniquely specified:
mRNA code begins with start codon (AUG)
protein is constructed along open reading frame
translation stops at stop codon (UAA, UAG, or UGA)
(only in frame: sequence out of frame does not work)
5’
3’
GUCCCGUGAUGCCGAGUUGGAGUAAGUAACCU
met
pro
ser
trp
ser
lys
stop
The genetic code
• composed of nucleotide triplets (codons)
• non-overlapping
• unambiguous
• degenerate
• nearly universal – except for portions of mitochondrial
DNA and a few procaryotes
TRANSLATION:
assembling proteins
Three types of RNA:
mRNA: messenger RNA – carries the code for a gene
5’
3’
GUCCCGUGAUGCCGAGUUGGAGUAGAUAACCU
Three types of RNA:
mRNA: messenger RNA – carries the code for a gene
rRNA: ribosomal RNA – used to construct ribosomes
- four types, used to make two-unit ribsome
(30 S)
(60 S)
Three types of RNA:
mRNA: messenger RNA – carries the code for a gene
rRNA: ribosomal RNA – used to construct ribosomes
tRNA: transfer RNA – short adapters to carry amino acid
and its anti-codon
anticodon
Steps in translation:
1. initiation
ribosomal subunits recognize, bind to 5’ cap on mRNA
initiator tRNA (with UAC anticodon) binds to AUG start codon
Steps in translation:
1. initiation
2. elongation
next tRNA pairs with its codon
peptidyl transferase
1. catalyzes formation of peptide bond between amino acids
Steps in translation:
1. initiation
2. elongation
next tRNA pairs with its codon
peptidyl transferase
1. catalyzes formation of peptide bond between amino acids
2. breaks amino acid bond with previous tRNA
ribosome shifts over one codon
Steps in translation:
1. initiation
2. elongation
3. termination
stop codon is recognized, bound to by release factor, polypeptide
is freed
Protein structure
primary: amino acid sequence
secondary: helix or pleated sheet, held with hydrogen bonds
tertiary: collapsed molecule with internal bonds
quaternary: protein subunits combine to form functional protein
Protein structure
quaternary: protein subunits combine to form functional protein
subunits may be from same gene, or different
may need two (dimers), three (trimers), or more
Protein function
enzymes – catalyze chemical reactions; most common proteins
usually have active sites (tertiary structure) that mediate function
structural proteins
collagen, keratin
transporters
hemoglobin
contractile – tissue and muscle movement
actin, myosin
intercellular communication
insulin, other hormones
Fig. 9-20