Human Gene,cs 06: Gene Expression. Diversity of cell types. How do cells become different? 9/19/11. neuron

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1 Human Gene,cs 06: Gene Expression 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

2 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!) transcription DNA (genes) RNA PROTEIN (enzymes) A Gene is expressed when RNA is made This process is called transcription Transcription = the formation of Messenger RNA () from a DNA template 2

3 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 P 2 base 1 1 nucleotide Strands are antiparallel (opposite direction) hydrogen bonds Transcrip,on Transcrip,on DNA has two strands; genes can be on either strand 3

4 Transcrip,on Transcription is controlled by RNA Polymerase Transcrip,on 3 5 Genes always go in the 5 to 3 direction The strand encoding the gene is called the SENSE strand sequence = SENSE sequence Transcrip,on 3 5 The antisense strand is used as the template RNA polymerase reads it in the 3 to 5 direction is made in 5 to 3 direction 4

5 Transcrip,on The has the same* sequence as the sense strand Standard basepairing rules apply between DNA and G = C, C = G, T = A, A = U Movie #1 Transcrip,on Movie transcription DNA (genes) 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

6 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) Anatomy of a Gene: Splicing Not all DNA in the coding region codes for protein Exons code for protein, introns need to be spliced out Coding Region Transcription Pre- Splicing Mature 6

7 The Promoter The promoter marks the DNA that is recognized by RNA polymerase at the beginning of the gene Anatomy of a Gene: promoter Coding Region RNA Polymerase RNA polymerase binds to DNA at the Promoter Elonga,on RNA polymerase moves along the DNA, copying the DNA template to make Anatomy of a Gene: enhancer promoter Coding Region Termination RNA Polymerase 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

8 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 Movie #2 Transcrip,on Movie transcription DNA (genes) RNA PROTEIN (enzymes) DNA Nucleus Cytoplasm 8

9 Replication DNA Nucleus Cytoplasm Replication DNA Transcription Nucleus Cytoplasm Replication DNA Transcription RNA Nucleus Cytoplasm 9

10 Replication DNA Transcription RNA Translation Nucleus Cytoplasm Replication DNA Transcription RNA Translation Nucleus 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 RNA Protein Transcrip,on Nucleus Transla,on Cytoplasm 10

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 Codons of two nucleo/des: AA GA CA UA AG GG CG UG AC GC CC UC AU GU CU UU Can only encode 4 amino acids 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

12 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. hionine 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

13 What do you need for transla,on? A Ribosome directs protein synthesis the template coding the protein Transfer RNA bring the individual amino acids to the ribosome Transla,on Machinery Small Ribosomal Subunit 5 Start codon 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 Transfer RNA (trna) Large Ribosomal Subunit Transla,on ini,a,on Assembling to begin transla/on Small ribosomal subunit 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 13

14 Transla,on Elonga,on Ribosome A U G G G A U G U A A G C G A U A C C C U Amino acid Gly Transla,on Elonga,on Ribosome A U G G G A U G U A A G C G A U A C C C U Amino acid Gly Transla,on Elonga,on A U G G G A U G U A A G C G A U A C C C U A C A Gly Cys 14

15 Transla,on Elonga,on U A C A U G G G A U G U A A G C G A C C U A C A Gly Cys Transla,on Elonga,on U A 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 Gly Cys Lys Transla,on Elonga,on A U G G G A U G U A A G C G A A C A U U C C C U Lengthening polypeptide (amino acid chain) Gly Cys Lys 15

16 Transla,on Elonga,on A U G G G A U G U A A G C G A A C A U U C C C U G C U Gly Cys Lys Arg Transla,on Elonga,on 5 A U G G G A U G U A A G C G A U A A A C A U U C G C U Stop Codon Gly Cys Lys Arg Transla,on Termina,on Stop codon 5 A U G G G A U G U A A G C G A U A A A C A U U C G C U Gly Cys Lys Arg Release factor 16

17 Transla,on Termina,on Ribosome reaches stop codon Stop codon 5 A U G G G A U G U A A G C G A U A A Gly U U C Cys Lys G C U Arg Release factor 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 Gly Cys Lys Arg Release factor Transla,on (3 steps) Ini/a/on Elonga/on transla,on begins at start codon (AUG=methionine) 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

18 Mul,ple copies of a protein are made simultaneously Transla,on Movie transcription translation DNA (genes) RNA PROTEIN (enzymes) Why are cells different? neuron Because they express different genes 18