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9/19/11 Human Gene,cs 06: Gene Expression 20110920 Diversity of cell types neuron
How do cells become different? A.  Each type of cell has different DNA in its nucleus
B.  Each cell has different genes
C.  Each type of cell has the same DNA, but can turn different genes
on or off
D.  Each type has all genes turned on at the same levels, but some
of these gene products are degraded
1 9/19/11 Gene Expression •  Each cell type contains the same genes, but expresses a different set of genes •  What does it mean when a gene is ‘switched on’ or ‘switched off’ or expressed? •  What controls the ways in which genes are expressed at the right /mes and in the right places? Central Dogma (again!) DNA (genes)
RNA
PROTEIN (enzymes)
A Gene is expressed when RNA is made
Central Dogma (again!) DNA (genes)
transcription
RNA
PROTEIN (enzymes)
A Gene is expressed when RNA is made
This process is called transcription
Transcription = the formation of Messenger
RNA (mRNA) from a DNA template
2 9/19/11 DNA is the template for transcrip,on • DNA is made of a strings of nucleotides
• Each nucleotide pair interacts via hydrogen bonds
• Each strand is directional (5’ to 3’)
phosphates at 5’ of ribose
P
base
5
4
3
2
1
1 nucleotide
P
• Strands are antiparallel (opposite direction)
hydrogen bonds
Transcrip,on Transcrip,on DNA has two strands; genes can be on either strand
3 9/19/11 Transcrip,on Transcription is controlled by RNA Polymerase
Transcrip,on 3’
5’
5’
3’
Genes always go in the 5’ to 3’ direction
The strand encoding the gene is called the SENSE strand
mRNA sequence = SENSE sequence
Transcrip,on 3’
5’
5’
3’
The antisense strand is used as the template
RNA polymerase ‘reads’ it in the 3’ to 5’ direction
mRNA is made in 5’ to 3’ direction
4 9/19/11 Transcrip,on The mRNA has the same* sequence as the sense strand
Standard basepairing rules apply between DNA and mRNA
G = C, C = G, T = A, A = U
Transcrip,on Movie •  Movie #1 DNA (genes)
transcription
RNA
PROTEIN (enzymes)
What is the sequence of RNA that would be transcribed from the following DNA template sequence: TTACACTTGCTTGAGAGTC a-­‐AATGTGAACGAACTCTCAG b-­‐AAUGUGAACGAACUCUCAG c-­‐UUACACUUGCUUGAGAGUC 5 9/19/11 What determines when and where a gene is expressed? •  Anatomy of a Gene: enhancer
promoter
Coding Region
Termination
For clarity, only one strand is shown
The Coding Region •  Anatomy of a Gene: Coding Region
Coding region: area of DNA that is actively transcribed
This DNA ‘codes’ for a protein (more soon)
Splicing Not all DNA in the ‘coding region’ codes for protein
Exons code for protein, introns need to be spliced out
•  Anatomy of a Gene: Coding Region
Transcription
Pre-mRNA
Splicing
Mature mRNA
6 9/19/11 The Promoter promoter marks the DNA that is recognized by
The promoter
RNA polymerase at the beginning of the gene
•  Anatomy of a Gene: promoter
Coding Region
RNA
Polymerase
Promoter
RNA polymerase binds to DNA at the Promoter
Elonga,on RNA polymerase moves along the DNA,
copying the DNA template to make mRNA
•  Anatomy of a Gene: enhancer
promoter
Coding Region
Termination
RNA
Polymerase
mRNA is transcribed from the DNA template
Termina,on of Transcrip,on The Termination Sequence marks the DNA that is recognized by
RNA polymerase at the end of the gene
•  Anatomy of a Gene: enhancer
promoter
Coding Region
Termination
RNA
Polymerase
RNA polymerase releases from
DNA at the Termination Sequence
7 9/19/11 Enhancers determine when and where a gene is expressed Enhancer elements are regions of DNA that are recognized by Transcription Factors
•  Anatomy of a Gene: enhancer
promoter
Coding Region
Termination
Transcription
Factor
Transcription Factor: a protein that binds to DNA and activates or reduces
gene expression
Transcription factors bind to enhancer regions that can be quite distant from
the gene that they regulate
Transcrip,on Movie •  Movie #2 DNA (genes)
transcription
RNA
PROTEIN (enzymes)
DNA
Nucleus
Cytoplasm
8 9/19/11 Replication
DNA
Nucleus
Cytoplasm
Replication
DNA
Transcription
Nucleus
Cytoplasm
Replication
DNA
Transcription
RNA
Nucleus
Cytoplasm
9 9/19/11 Replication
DNA
Transcription
RNA
Nucleus
Translation
Cytoplasm
Replication
DNA
Transcription
RNA
Nucleus
Translation
Protein
Cytoplasm
Central Dogma: another view DNA is the gene,c material within the nucleus. The process of replica/on creates new copies of DNA. The process of transcrip/on creates an RNA using DNA informa,on. The process of transla/on creates a protein using RNA informa,on. Replica,on DNA Transcrip,on RNA Transla,on Nucleus Protein Cytoplasm 10 9/19/11 The Gene,c Code •  How does the DNA sequence code for proteins? •  How to turn 4 nucleo/des into 20 amino acids? How does coding work? •  Proteins are formed from 20 amino acids in humans. Codons of one nucleo/de: A G C U Can only encode 4 amino acids Codons of two nucleo/des: AA GA CA UA AG GG CG UG AC GC CC UC AU GU CU UU Can only encode 16 amino acids Codons of three nucleo,des are sufficient to form 20 amino acids •  Proteins are formed from 20 amino acids in humans. Codons of three nucleo,des: AAA AGA ACA AUA AAG AGG ACG AUG AAC AGC ACC AUC AAU AGU ACU AUU GAA GGA GCA GUA GAG GGG GCG GUG GAC GGC GCC GUC GAU GGU GCU GUU CAA CGA CCA CUA CAG CGG CCG CUG CAC CGC CCC CUC CAU CGU CCU CUU UAA UGA UCA UUA UAG UGG UCG UUG UAC UGC UCC UUC UAU UGU UCU UUU Allows for 64 poten/al codons => sufficient! 11 9/19/11 The gene,c code The gene,c code is non-­‐overlapping The gene,c code is universal -­‐All known organisms use the same gene/c code. (Rare organisms use one codon for an addi,onal amino acid.) The gene,c code is degenerate -­‐Some codons encode the same amino acid. e.g. GGU, GGC, GGA, and GGG all encode glycine -­‐Degeneracy is mostly at the third base of the codon. Some codons have addi/onal func/ons -­‐AUG encodes methionine. Methionine usually cues the beginning of transla/on -­‐UAA, UAG, and UGA do not encode amino acids These codons signal termina/on of the protein. 12 9/19/11 What do you need for transla,on? • A Ribosome – directs protein synthesis
• mRNA – the template coding the protein
• Transfer RNA – bring the individual amino acids to the ribosome
Transla,on Machinery Small Ribosomal Subunit
Start codon
5’
3’
U U C G U C A U G G G A U G U A A G C G A A U A C
Met Large Ribosomal Subunit
Transfer RNA (tRNA)
Transla,on ini,a,on Assembling to begin transla/on mRNA Small ribosomal subunit 5’ 3’ mRNA U U C G U C A U G G G A U G U A A G C G A A U A C Ini/ator tRNA Met 13 9/19/11 Transla,on Elonga,on Ribosome
5’
mRNA
3’
A U G G G A U G U A A G C G A
U A C
C
C
U
Amino acid
Met
Gly
Transla,on Elonga,on Ribosome
5’
mRNA
3’
A U G G G A U G U A A G C G A
U A C C C U
Amino acid
Met
Gly
Transla,on Elonga,on 5’
mRNA
3’
A U G G G A U G U A A G C G A
U A C C C U
A C
Met
A
Gly
Cys
14 9/19/11 Transla,on Elonga,on 5’
mRNA
3’
A U G G G A U G U A A G C G A
C C U A C A
U
A
C
Me
t
Gly
Cys
Transla,on Elonga,on 5’
mRNA
U
A
3’
C
A U G G G A U G U A A G C G A
C C U A C A
U
U
C
Me
t
Gly
Cys
Lys
Transla,on Elonga,on 5’
mRNA
3’
C
C
U
A U G G G A U G U A A G C G A
A C A U U C
Gly
Lengthening
polypeptide
(amino acid chain)
Cys
Lys
t
Me
15 9/19/11 Transla,on Elonga,on 5’
mRNA
3’
C
C
U
A U G G G A U G U A A G C G A
A C A U U C
G C
U
Cys
Gly
Me
Lys
Arg
t
Transla,on Elonga,on 5’
mRNA
A U G G G A U G U A A G C G A U A A
A
C
Gly
M
Stop Codon
U U C G C U
A
Cys
Lys
Arg
et
Transla,on Termina,on Stop codon
5’
mRNA
A U G G G A U G U A A G C G A U A A
A
C
Gly
M
et
U U C G C U
A
Cys
Lys
Arg
Release
factor
16 9/19/11 Transla,on Termina,on Stop codon
Ribosome reaches stop codon
5’
mRNA
A U G G G A U G U A A G C G A U A A
U
G C U
C
Release
factor
Lys
Cys
Gly
Met
U
Arg
Ribosome disassembly Once stop codon is reached,
elements disassemble.
A U G G
G A U
G U A A
G C G
A U A
A
G
C
U
Release
factor
Arg
Lys
Met
Gly
Cy
s
Transla,on (3 steps) Ini/a/on transla,on begins at start codon (AUG=methionine) Elonga/on the ribosome uses the tRNA to match codons to amino acids adds those amino acids to the growing pep,de chain Termina/on transla,on ends at a stop codon UAA, UAG or UGA 17 9/19/11 Mul,ple copies of a protein are made simultaneously Transla,on Movie DNA (genes)
transcription
RNA
translation
PROTEIN (enzymes)
Why are cells different? neuron
Because they express different genes
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