The Central Dogma and Transcription Chapter 17: Sections

Today’s Exit Ticket The bonds creating the primary structure of a protein are called 1) peptide bonds and form between a 2) C atom in one amino acid and a 3) N atom in another amino acid. The bonds creating the secondary structure of a protein are called 4) hydrogen bonds and form between 5) the backbone molecules of amino acids (NOT R-groups). The bonds creating the tertiary structure of a protein can be covalent, ionic, or hydrogen bonds, and form between 6) R-groups. 7) Describe the quaternary structure of a protein. Quaternary structure is the interaction of different polypeptide subunits to make a larger molecule. 2

Unit 4 Proteins Transcription (DNA to mRNA) Translation (mRNA to tRNA to proteins) Gene expression/regulation (turning genes on and off) Viruses 3

The Central Dogma and Transcription Chapter 17: Sections

How do we get from DNA to traits? Gene expression = DNA directs the synthesis of proteins TWO STEPS: (1) transcription (2) translation All organisms do this!

Outline 1.Basic principles of transcription & translation 2.Transcription in detail 3.RNA processing in Eukaryotes 4.The genetic code

Fig Information flow from genetic information encoded as DNA blueprint (genes) to RNA copies mRNA Synthesis of mRNA in the nucleus DNA NUCLEUS mRNA CYTOPLASM Movement of mRNA into cytoplasm via nuclear pore 1 2

What’s the difference between DNA and RNA?? 3 Major Differences:DNARNA – Different sugars:deoxyriboseribose – Different bases:C & G, A & TC & G, A & U – Structure:double-strandedsingle-stranded (usually) DNA & RNA provide information to make proteins DNA and RNA = both nucleic acids Both are made of nucleotide monomers

and on to synthesis of proteins. Fig Information flow from genetic information encoded as DNA blueprint (genes) to RNA copies mRNA Synthesis of mRNA in the nucleus DNA NUCLEUS mRNA CYTOPLASM Movement of mRNA into cytoplasm via nuclear pore Ribosome Amino acids Polypeptide Synthesis of protein 1 2 3

Transcription vs. Translation DNA RNAProteins Transcription: Like copying info from a book in the reserved section of the library Using the same language Translation: Literally translating between two different languages Take the copied info from the library and translate it into French/Spanish/Mandarin สวัสดีเพื่อน Hello, friend Hullo, mate

Videos of Gene Expression: Hank’s Transcription and Translation Crash Course From DNA to Protein

1. Overview of transcription and translation Genes are nucleotide sequences, hundreds or thousands of nucleotides long

THE CENTRAL DOGMA: DNA  RNA  PROTEIN 1. Overview of transcription and translation

PROTEIN

1. Overview of transcription and translation

Outline 1.Easing in: basic principles of transcription and translation 2.Transcription in detail 3.RNA processing in Eukaryotes 4.The genetic “code”

Transcription vs. Translation DNA RNAProteins Transcription: Like copying info from a book in the reserved section of the library Using the same language Translation: Literally translating between two different languages Take the copied info from the library and translate it into French/Spanish/Mandarin สวัสดีครับ Hello

Fig Transcription in detail Successful transcription requires 3 basic processes: 1. Initiation 2. Elongation 3. Termination

Fig Transcription in detail Successful transcription requires 3 basic processes: 1. Initiation Find the location where we start reading DNA Actually begin making mRNA  To achieve this, we need some kind of signal on or in the DNA that says “START TRANSCRIBING HERE”

2. Transcription in detail a) Initiation “Upstream” of the gene is a promoter whole promoter = several dozen nucleotides  example of DNA that is essential but is not transcribed where the gene is the “start here” signal Now we know WHERE to initiate, but HOW do we initiate? Transcription Unit:

2. Transcription in detail a) Initiation HOW: With an enzyme, as usual! RNA polymerase Reads one strand of DNA and builds the mRNA Can’t bind to the promoter on its own (in eukaryotes) Only binds when specific transcription factors are present Promoter sequence

Once RNA polymerase binds, it can only synthesize RNA in a 5’ to 3’ direction. Which of the two DNA strands shown here will it “read” as it makes RNA? a) Top one b) Bottom one c) Both strands Promoter sequence

2. Transcription in detail a) Initiation With transcription factors in place, RNA polymerase can now bind DNA at the right place to begin transcription of the gene

Fig Transcription in detail Successful transcription requires 3 basic processes: Initiation Bind transcription factors, then RNA polymerase to promoter region 2) Elongation Make the full length mRNA transcript

2. Transcription in detail b) Elongation RNA Polymerase untwists DNA, makes mRNA RNA Polymerase untwists DNA, makes mRNA

2. Transcription in detail b) Elongation Summary of elongation in transcription: 1.RNA polymerase untwists and separates base pairs of DNA at a time 2.RNA nucleotides enter and pair with the DNA template (U, not T, pairs with A) 3.RNA polymerase bonds nucleotides onto the 3’ end of the RNA molecule 4.RNA polymerase moves along, the new RNA molecule peels away from the DNA, and the helix re-twists

Fig Transcription in detail Successful transcription requires 3 basic processes: Initiation Elongation  make the full length mRNA transcript Termination  stop transcribing; mRNA completed

2. Transcription in detail c) Termination But how does it stop? Bacteria: termination sequence in the DNA Eukaryotes: a bit more complicated enzymes cut the transcript free…among other things!

Outline 1.Easing in: basic principles of transcription and translation 2.Transcription in detail 3.RNA processing in Eukaryotes 4.The genetic code

3. RNA processing in eukaryotes Observations: Average human pre-mRNA transcript length: 27,000 nucleotides Each amino acid is coded by 3 nucleotides Average human protein: 400 amino acids  requires only 1200 nucleotides How does that work?

3. RNA processing in eukaryotes Before RNA transcripts leave the nucleus, they are modified.

3. RNA processing in eukaryotes Before RNA transcripts leave the nucleus, they are modified. Modified how? 1.Alteration of ends 2.Cutting out some of the middle  offers cell a way of controlling when and where proteins are produced

3. RNA processing in eukaryotes 1. Alteration of ends

3. RNA processing in eukaryotes 2. Cutting out some of the middle: RNA splicing

3. RNA processing in eukaryotes The sequence of DNA that codes for a eukaryotic protein is NOT a continuous sequence Some introns are “self-splicing”  catalyze their own excision!

Ribozymes! Thomas Cech CU Professor 1989 Nobel Prize winner, along with Sidney Altman Discovered that RNA can sometimes splice itself!

3. RNA processing in eukaryotes 1.Cutting out some of the middle: RNA splicing Why do introns exist? Alternative splicing  alternative mRNA  multiple proteins from a single DNA sequence

Outline 1.Easing in: basic principles of transcription and translation 2.Transcription in detail 3.RNA processing in Eukaryotes 4.The genetic code

Nucleotides: A, T, G, and C in DNA (A, U, G, and C in RNA) Amino Acids  20 are commonly used by most organisms The genetic code consists of 3-letter codons: Sequence of 3 nucleotides = specification of amino acid Each triplet of mRNA nucleotides is called a codon The genetic code consists of 3-letter codons: Sequence of 3 nucleotides = specification of amino acid Each triplet of mRNA nucleotides is called a codon

Fig DNA molecule Gene 1 Gene 2 Gene 3 DNA template strand TRANSCRIPTION TRANSLATION mRNA Codons Protein Amino acid 4. The genetic code note: either strand may serve as the template depending upon the particular gene U U U UUG G G G C C A

Math check: WAIT a second! 4 nucleotides...in sets of 3... Shouldn’t there be 4 3 codons?? YES! Using just 4 nucleotides, DNA can make 64 different codons BUT... You just said there are only 20 amino acids!?! Yes, friends, there are only 20.

C C C C C C U U U U U U A A A A A A G G G G G G

Fig The genetic code Some notes on codons: 1.When we say “codon”, we are referring to RNA triplets 2.Codons are read in the 5’ to 3’ direction, because that is how they are read by the translation machinery 1.Codons don’t overlap (300 nucleotides encode 100 codons) ACUUCCAAG 1 2 3

Today’s Exit Ticket The final product of transcription is _(1)_. The template used for transcription is _(2)_. The first step of the process is called _(3)_ and involves the _(4)_ binding to the _(5)_ region. This allows _(6)_ to bind to the DNA and begin transcribing, in a process called _(7)_. During that process, the enzyme reads from the _(8)_’ to _(9)_’ direction and builds the new strand from _(10)_’ to _(11)_’. The last step of transcription is called _(12)_. In _(13)_, there is another step before translation. This is called _(14)_, and involves removing _(15)_ and adding a 5’ cap and 3’ poly-A tail. WORD BANK (not all will be used, some are used more than once): 35DNAelongation eukaryotes exonsinitiationintrons mRNAprokaryotes promoterRNA polymerase RNA processingterminationtranscription factors