dna

Hydrogen bond

Basepair

Ribbon model Partial chemical structure Computer model

G C

T A

A T

TA

C

C

G

G

GC

T

T

T

T

A

A

A

A

G C

A T

A

C

T

G

CG

AT

DNA

What does the cell use DNA for?

• Gives you traits

What IS a trait?

• Physical structure produced by a protein!• DNA controls the production of proteins.

What do we know about making proteins?

DNA is in the NUCLEUS

RIBOSOMES, ER, and GOLGI are in the CYTOPLASM

How does that work?

• RNA acts as a messenger to carry information from the DNA in the nucleus to the ribosomes in the cytoplasm

What’s RNA?

• Nucleic Acid• Similar to DNA• Some differences

Phosphategroup

Nitrogenous base(A, G, C, or U)

Sugar(ribose)

Uracil (U)

What’s RNA?

FEATURE DNA RNA

Subunits Nucleotide Nucleotide

Strands 2 – double helix 1 (mostly)

Sugar Deoxyribose Ribose

Bases A = T; C = G A = U; C = G

Protein Synthesis Overview

DNA is located in the NUCLEUS


A messenger RNA (mRNA) copy is made of DNA.


mRNA leaves the nucleus and goes to the ribosome


Ribosome uses mRNA to assemble amino acids in the correct order to make a specific protein

Genes to Polypeptides

• Polypeptides = chains of AA = proteins

• 20 different AA exist• specific polypeptide has

specific AA sequence• Sequence of AA

determines the shape and function of a protein

Genes to Polypeptides

• Sequence of bases in DNA determine AA sequence

• “Genes” store order of AA in a code in DNA

• One specific gene will yield one* specific polypeptide – polypeptide = protein

that does a job!

DNA & Genetic Code

• There are 20 amino acids, and a stop

• How can DNA specify 21 things with only four bases?

Genetic Code

• IF: 1 base = 1 amino acid

• THEN: how many amino acid possibilities are there?

GATC

4

Genetic Code

• IF: 2 bases = 1 amino acid


GATC

4 x 4 = 16

GATC

Genetic Code

• IF: 3 bases = 1 amino acid


GATC

4 x 4 x 4 = 64

GATC

GATC

DNA & Genetic Code

• In a gene, every three bases code for a specific amino acid (one of the 20)

• 4 x 4 x 4 = 64 total possiblities

• One amino acid can be coded for by more than one triplet

DNA & Genetic CodeGenetic code is composed of codons made up of of base triplets

DNA & Genetic Code

• The genetic code is both universal and degenerate. – Universal = found in all living organisms– Degenerate = having more than one base triplet

(codon) to code for one amino acid


• DNA is located in the nucleus


• Ribosomes are located in the cytoplasm


• Messenger RNA carries “message” from DNA to ribosomes

Transcription

• Genes are made of DNA• DNA cannot leave the

nucleus• A copy must be

“transcribed” into RNA• RNA exits nucleus

http://www.fed.cuhk.edu.hk/~johnson/teaching/genetics/animations/transcription.htm

Transcription

1. INITIATION: RNA polymerase uncoils DNA double helix

2. ELONGATION: RNA polymerase creates a new mRNA strand using free RNA nucleotides; a single DNA template strand is used

Transcription

3. RNA nucleotides attached together (type of reaction?) via RNA polymerase

4. TERMINATION: New mRNA strands separates from DNA

5. DNA reforms

Animation: Campbell Ch 10 – 10_9 TranscriptionAnimation: Campbell Ch 10 – 10_9 Transcription

GENE Contains the instructions to assemble one protein

TRANSCRIPTION The process by which an mRNA copy is made of a DNA sequence

RNA POLYMERASE Enzyme that catalyzes synthesis of mRNA strand

PROMOTER REGION Sequence of DNA bases within gene where RNA polymerase binds

CODING REGION Sequence of DNA bases that codes for the actual structure of the protein

TERMINATOR REGION

Sequence of DNA were RNA polymerase stops transcribing.

CODON 3 bases of DNA or RNA; specifies 1 amino acid

What’s it look like?

So, the new mRNA strand was just made, now what?

Final Steps – Eukaryotes ONLY

1. mRNA Splicing – INTRONS: non-coding

regions of the mRNA strand

– EXONS: coding regions of the mRNA strand

– Introns are spliced out of final mRNA

Final Steps – Eukaryotes ONLY

2. 5’ Cap– Modification to 5’ end

of mRNA– Ensures stability of

mRNA

Final Steps – Eukaryotes ONLY3. 3’ poly-A tail

– Addition of poly-A to 3’ end of mRNA– Protects RNA from nucleases

ExonExon ExonIntronIntron

Cap

DNA

RNAtranscriptwith cap and tail

mRNA

Coding sequenceNucleus

Cytoplasm

Exons spliced together

TailIntrons removed

TranscriptionAddition of cap and tail

Animation: Cain Ch13a03 - TranscriptionAnimation: Cain Ch13a03 - Transcription

Transcription in a cell

• Multiple genes can be transcribed at the same time

• The same gene can be transcribed at the same time

Translation

DNA mRNA ProteinTranscription Translation

Where we are now.

Nucleus Ribosome (cytoplasm)

Translation Summary

• Instructions in the mRNA are used by a ribosome to assemble amino acids in the correct order

• Order of amino acids gives the protein its shape

• Shape gives protein its function

Translation Summary

The Key Players• mRNA• tRNA• rRNA

The Stages of Translation• Initiation• Elongation• termination

Animation: Cain Ch13a07 - TranslationAnimation: Cain Ch13a07 - Translation

mRNA (messenger RNA)

• copy of the directions to make the product (protein)

• tells the ribosome the correct sequence of Amino Acids while putting together the protein

• each codon (3 bases) directs a specific amino acid to be added to the growing protein

tRNA (transfer RNA)

• the delivery RNA; delivers specific Amino Acids to the ribosome

• composed of RNA• anticodon binds to a

corresponding codon on mRNA

• Carries one specific amino

Translation6.4.1

rRNA (ribosomal RNA)

• ribosomes are made of RNA and protein

• composed of two subunits: the 30s and 50s subunits

• two tRNA binding sites; one mRNA binding site

Translation INITIATION

• small (30S) ribosome subunit binds to mRNA at the 5’ end of the mRNA

• 30S moves along mRNA 5’ to 3’ until it hits the start codon AUG


• large subunit binds• Methionine tRNA moves into ribosome


• another tRNA, with the anticodon complementary to the next codon binds to the ribosome

Translation ELONGATION

• first amino acid added• ribosome moves down

mRNA to next codon• next tRNA comes in• its amino acid is bound

to the polypeptide chain

• ribosome moves down mRNA to next codon

Translation TERMINATION

• the ribosome encounters a stop codon• no tRNA molecule has an anticodon for this

codon

Translation TERMINATION

• polypeptide is released and ribosome disassociates

Animation: Campbell Ch 10 – 10_14 TranslationAnimation: Campbell Ch 10 – 10_14 Translation

Where does translation happen?

• Cytoplasmic (free) Ribosomes proteins for use in cytoplasm

• Rough ER (attached) Ribosomes proteins secreted or used in lysosomes

• DNA– TRANSCRIPTION

• RNA– TRANSLATION

• PROTEIN

DNA molecule

Gene 1

Gene 2

Gene 3

AAAAA C C GG C

CCGG G U U U UUUU

AADNA strand

Transcription

RNA

Translation

Polypeptide

Amino acid

Codon

Interpreting the Genetic CodeSecond base

Firs

t bas

e

Thir

d ba

se

UUUU C A G

GAA

C

U

U

U

C

AC

A

G

G

UCAG

U

C

A

G

UUC

UUA

UUG

CUU

CUC

CUA

CUG

AUU

AUC

AUA

Leu

lle

AUG Met orstart

GUU

GUC

GUA

GUG

Val Ala

Thr

GCG

GCA

GCC

GCU

ACG

ACA

ACC

ACU

Pro

CCG

CCA

CCC

CCU

UCG

UCA

UCC

UCU

Ser

Tyr CysUAU

UAC

UAA

UAG

CAU

CAC

CAA

CAG

His

Gln

Stop

Stop

UGU

UGC

UGA

UGG Trp

Stop

Arg

CGU

CGU

CGA

CGG

Asn

Lys

Asp

Glu

Gly

Arg

SerAAU AGU

AAC

AAA

AAG

GAU

GAG

AGC

AGA

AGG

GGU

GGC

GGG

Phe

Leu

GAC

GAA

GAG

GGA

Strand to be transcribed

Transcription

DNAT

A GT

A C T T

T T

A A

AA G

C

G

C

T T

TA A

A

A GURNA

Translation

Startcodon

A A U UG U U A G

Stopcodon

PheLysMetPolypeptideAnimation: Starr Ch 14 – Genetic codeAnimation: Starr Ch 14 – Genetic code

Changes in the Genetic Code

• MUTATION = change in the nucleotide sequence of DNA

Normal hemoglobin DNA

mRNA

C T T

AAG

Normal hemoglobin

Glu

mRNA

C

G

A

Sickle-cell hemoglobin

Val

Mutant hemoglobin DNA

A

T

U

What causes mutations?

• Spontaneous mutations: uncorrected errors in replication



• Harmful environmental agents: UV light, radiation, chemicals

Radiation damages DNA

Radiation as a cancer treatment

Why would radiation be a treatment for cancer?

• What type of cells would radiation affect most: rapidly dividing or rarely dividing cells?

• Cancer cells are very rapidly dividing cells

• Radiation targets ALL rapidly dividing cells, not just cancer cells



• Harmful environmental agents: UV light, radiation, chemicals

• Transposable elements: “jumping genes”

Mutations

• Sickle Cell Anemia– Single-base substitution

Sickle Cell Anemia

Missense mutation = single base substitution

Changes one amino acid

Variable effect on protein depending on how much structure is changed

Missense Mutations

• Tay Sachs Disease– Single-base substitution

in HexA gene

Missense Mutations

• Cystic Fibrosis– Single-base substitution

in CFTR gene

Nonsense mutation = single base substitution that introduces a STOP

Truncates proteinOften more severe

Nonsense Mutations

• Cystic Fibrosis– More severe form

• Duchenne Muscular Dystrophy– Dystrophin – connects

cytoskeleton to extracellular matrix

Silent mutation = single base substitution that doesn’t change an

amino acidSecond base

Firs

t bas

e

Thir

d ba

se

UUUU C A G

GAA

C

U

U

U

C

AC

A

G

G

UCAG

U

C

A

G

UUC

UUA

UUG

CUU

CUC

CUA

CUG

AUU

AUC

AUA

Leu

lle

AUG Met orstart

GUU

GUC

GUA

GUG

Val Ala

Thr

GCG

GCA

GCC

GCU

ACG

ACA

ACC

ACU

Pro

CCG

CCA

CCC

CCU

UCG

UCA

UCC

UCU

Ser

Tyr CysUAU

UAC

UAA

UAG

CAU

CAC

CAA

CAG

His

Gln

Stop

Stop

UGU

UGC

UGA

UGG Trp

Stop

Arg

CGU

CGU

CGA

CGG

Asn

Lys

Asp

Glu

Gly

Arg

SerAAU AGU

AAC

AAA

AAG

GAU

GAG

AGC

AGA

AGG

GGU

GGC

GGG

Phe

Leu

GAC

GAA

GAG

GGA

Insertion mutation = addition of one or more nucleotides

Can change entire protein after mutation

Deletion mutation = deletion of one or more nucleotides


Frameshift mutation = Change of “reading frame” in DNA


Insertion or deletion

Cancer

• BRCA1 - increased risk of developing breast cancer

• Mutations due to mutagens

Summary of Mutations

• Base Substitution– Missense– Nonsense– Silent

• Frameshift– Insertion– Deletion

• Which kind would be most likely to cause disease?

Normal gene

Base substitution

ProteinmRNA

Base deletion Missing

Met

Met

Met Lys

Lys

Lys Phe Gly Ala

AlaPhe

Ala

Ser

Leu His

A

A A A A

A A A

A

AAAAA U U U U

UUUU

U U U U G G GGG

G G G G

C C

C C

G G G G G CC

U

Good information about genes and mutations

• http://ghr.nlm.nih.gov/handbook/basics

Effect of Mutation on Protein Structure

Transcription Assembly of RNA on unwound regions of DNA molecule

mRNA rRNA tRNAmRNA processing

mature mRNA transcripts ribosomal

subunitsmature tRNA

Convergence of RNAsTranslation cytoplasmic

pools of amino acids,

ribosomal subunits, and

tRNAsAt an intact ribosome, synthesis of a polypeptide chain at the binding sites for mRNA and tRNAs

Protein

Animation: Starr Ch 14 - Protein Synthesis in Prokaryotes vs Eukaryotes

Animation: Starr Ch 14 - Protein Synthesis in Prokaryotes vs Eukaryotes

In-class assignment – Protein Synthesis

• Complete the classwork assignment

Gene Expression

• Every cell in your body came from 1 original egg and sperm

• Every cell has the same DNA and the same genes

76

Gene Expression

• Every cell in your body came from 1 original egg and sperm

• Every cell has the same DNA and the same genes

• Each cell is different, specialized• Differences due to gene expression

– Which genes are turned on– When the genes are turned on– How much product they make

77

Genetic Potential

• Embryonic Stem Cells– Can differentiate to

become any type of cell in the body

• Adult Stem Cells– Can differentiate to

become several types of cell

Root ofcarrot plant

Root cells culturedin nutrient medium

Cell divisionin culture Plantlet Adult plant

Single cell

Genetic Potential

• Plants in Cell Culture• Plants creating roots

Genome Size

• Genome: total amount of DNA

• Prokaryotes– 0.6 to 30 million base pairs– Approximately 2,000 genes

• Eukaryotes– 12 million to 1 trillion base

pairs– Humans have ~25,000

genes

80

Organization of DNA

• Prokaryotes– Several million base pairs -

one circular piece– Related genes grouped

together– Mostly coding DNA

81

Organization of DNA

• Eukaryotes– Billions of base pairs –

several linear chromosomes

– Genes not grouped– Mostly non-coding DNA

82

83

Noncoding DNA

• Spacer DNA• Transposons – “selfish DNA”

84

DNA Packaging

• Eukaryotic chromosomes are very large• Must be packaged to fit inside nucleus• Unavailable for transcription• Unpacking must occur before transcription

85

Levels of Packaging

• Chromosome – fully condensed

• Tightly packed loops• 30 nm fibers• Histone spool• Double helix

86

Patterns of Gene Expression

• Bacteria directly exposed to environment• Respond to changes in nutrient availability

directly– Make enzymes for nutrients when they are

present– Turn genes off when they are not

87

Patterns of Gene Expression

• Eukaryotic cells• Tissue specific expression• Housekeeping

genes

Gene Expression: Development

• Embryo development depends on gene expression

• Timing of expression vital

• Controlled by cascades of gene expression

88

89

Levels of Gene Control

1. Packaging2. Transcription3. mRNA maturation4. mRNA breakdown5. Translation 6. Protein Regulation 7. Protein Degradation

1. Packaging

• If the DNA isn’t unwrapped from the histones, it can’t be transcribed

• DNA Methylation• HistoneMethylation

Animation: Campbell Ch 11 – DNA PackingAnimation: Campbell Ch 11 – DNA Packing

1. Packaging

Methylation

• DNA marked with a methyl group can be identified by an enzyme

1. Packaging

• X chromosome Inactivation– Females have 2 X

chromosomes– One gets methylated

and inactivated during development

1. Packaging

• “Copycat” – first cloned cat

1. Packaging

• Agouti, mottled and yellow mice

1. Packaging

• Methylation is required for development– Lethal to eliminate methylation in animals– Not lethal in plants, but profound effects on

development

1. Packaging

• Imprinting – methylate and silence genes on one parent’s chromosome specifically– About 1% of total human genes (about 300 genes)

1. Packaging

• Parental DNA contributions to embryo are marked

1. Packaging

• Normal = maternal expressed, paternal silenced

• Prader-Willi = paternal allele lost, maternal allele present

• Angelman = maternal allele lost, paternal allele present

1. Packaging

• Cancer cells are often aberrantly methylated

2. Transcription

• Control when and how much a gene is transcribed

2. Example of Transcriptional Control: The Lac Operon in Bacteria

• E. coli lactose sugar utilization genes

• When lactose is present, bacteria needs to have the proteins coded for by these genes– Lactase Enzymes

Lac Operon Animation (online)Lac Operon Animation (online)

2. Example of Transcriptional Control: The Lac Operon in Bacteria

• Operon: group of nucleotide sequences including an operator, a promoter, and one or more genes that are controlled as a unit to produce messenger RNA (mRNA)

*The Operon model is one example of gene expression regulation

Lac Repressor Protein

• NO LACTOSE: repressor binds to the DNA and prevents RNA pol from binding (no transcription)

• No lactase is produced

6.3.2

Lac Repressor Protein

• LACTOSE: repressor binds lactose and changes shape. Now repressor can’t bind DNA

• Lactase is produced; lactose is metabolized

6.3.2

107

2. Example of Transcriptional Control: The Trp Operon

Tryptophan AA genes

ANIMATION (Ch14a03)

2. Transcriptional Control - Eukaryotic Gene Expression

• No operons• More complex than prokaryotic• Many different types of regulatory proteins• Many DNA elements controlling each gene

108

2. Transcriptional Control - Eukaryotic Gene Expression

• OFF: proteins are produced that bind to gene preventing RNA polymerase from binding

3. mRNA Maturation

• If 3’ cap, 5’ poly-A tail are not added, mRNA cannot be transported out of the nucleus and used

• mRNA can be “alternatively spliced” to generate different transcripts

Exons

orRNA splicing

mRNA

RNAtranscript

DNA

4. mRNA Breakdown

• If mRNA is broken down more quickly, it can be used fewer times

5. Translational Regulation

• Inhibit any of the steps of translation and the mRNA can’t be used

6. Protein Regulation

• Activate or inactivate the newly made protein– Phosphorylation– Acetylation

6. Protein Regulation

• Activate or inactivate the newly made protein– Phosphorylation– Acetylation– Cleavage

INSULIN

7. Protein Degradation

• If the protein is broken down, obviously it can’t work anymore

dna

Documents

dna genetic codethere

specific amino acid

amino acidthen

amino acids

amino acid possibilities

bases code

dna double helixelongation

cytoplasmwhats rna