honors bio ch13

Chapter 13: RNA and Protein Synthesis

April 3, 2014

13.1 RNA

• The Role of DNA– Comparing RNA and DNA– Functions of RNA

• RNA Synthesis– Transcription– Promoters– RNA Editing

Comparing RNA and DNA

• Ribonucleic acid

• Sugar is ribose

• Single-stranded

• Uracil (AU/GC)

• Deoxyribonucleic acid

• Sugar is deoxyribose

• Double-stranded

• Thymine (AT/GC)

Functions of RNA

• RNA is like a disposable copy of a DNA segment

• Protein synthesis (controls assembly of aa into proteins)

• 3 types of RNA:–Messenger RNA (mRNA)– Ribosomal RNA (rRNA)– Transfer RNA (tRNA)

So how does the cell make RNA?

Transcription

• Segments of DNA serve as templates to produce complementary RNA mole-cules

• Prokaryotes: RNA & Protein synthesis cytoplasm

• Eukaryotes: RNA synthesis nucleus cytoplasm Protein synthesis cytoplasm

Transcription

• RNA Polymerase: enzyme that links together the growing chain of RNA nucleotides during transcription us-ing a DNA strand as a template

• Promoters: specific region of a gene where RNA polymerase can bind and begin transcription

http://www.phschool.com/science/biology_place/biocoach/transcription/tcproc.html

RNA Editing

• RNA gets edited before becoming mRNA

• Introns: sequence of DNA that is not involved in coding for a protein

• Exons: expressed sequence of DNA; codes for a protein

• Introns OUT• Exons IN

DNA

DNA

RNA

Pro-tein

DNA

DNA

RNA

Pro-tein

Replication

DNA

DNA

RNA

Pro-tein

Replication

Transcription

DNA

DNA

RNA

Pro-tein

Replication

Transcription

Translation

DNA

DNA

RNA

Pro-tein

Replication; DNA Polymerase

Transcription;RNA Polymerase

Translation

13.2 Ribosomes and Protein Synthesis

• The Genetic Code– How to read codons– Start and Stop codons

• Translation– Steps in Translation– Roles of tRNA and rRNA in Translation

• Molecular Basis of Heredity

Genetic Code

• 20 different amino acids• Specific amino acids and order determine

the properties of proteins• Sequence of a.a. influences shape of pro-

tein, which determines function• Codon: group of 3 nucleotide bases that

specifies a particular amino acid• 4 “letters” (AUGC) ;

3 “letters at a time” (codon) ie. AUG, UAC

How to Read Codons• In total, 64 possible three-base

codons– 4 x 4 x 4 = 64

• Several combinations of codons spec-ify one amino acid– Ex. Leucine: UUA, UUG, CUU, CUC, CUA,

CUG

• But, only one codon UGG specifies Tryptophan– UGG can ONLY be Tryptophan

Start and Stop Codons

START CODONS:

• AUG STOP CODONS:

• UAA• UAG• UGA

Start and Stop Codons

START CODONS:

• AUG(Methionine)

STOP CODONS:

• U Are Annoy-ing• U Are Gongjubyung• U Go Away

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)2. Count three codons

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)2. Count three codons

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)2. Count three codons

3. Look for Stop Codons (UAA, UAG, UGA)

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)2. Count three codons

3. Look for Stop Codons (UAA, UAG, UGA)

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)2. Count three codons

3. Look for Stop Codons (UAA, UAG, UGA)

4. Look for corresponding amino acid

Example

ACCAAUGAUAGCCGAUGGGUGAG-GAG

1. Look for Start Codon (AUG)2. Count three codons

3. Look for Stop Codons (UAA, UAG, UGA)

4. Look for corresponding amino acid

Met – Ile – Ala – Asp - Gly

Translation

April 7, 2014

Translation

• Sequence of nucleotide bases gives the order in which amino acids join to produce a polypeptide

• Ribosomes use the sequence of codons in mRNA to assemble amino acids into polypeptide chains

• Translation = decoding of mRNA into protein

Eukaryote• Transcription in

NUCLEUS• Translation in

CYTOPLASM

Prokaryote• Transcription in

NUCLEUS• Translation in

NUCLEUS

(Step A) Transfer RNA

1. Begins at AUG (start codon)2. As each codon passes through ribo-

some, tRNAs bring proper amino acids into ribosome– Each tRNA has anticodon whose bases are

complementary to bases of codon– Anticodon for AUG is UAC

3. One at a time, ribosome attaches amino acids to growing chain

(Step B) Polypeptide Assembly Line

1. Ribosome forms peptide bond between first and second amino acids

2. The bond between the amino acid and its tRNA breaks apart

3. The tRNA floats away from ribosome, and the next tRNA binds to the ribo-some

4. Ribosome moves from right to left, binding new tRNA molecules and amino acids

(C) Completing the Polypep-tide

1. The process continues until ribosome reaches a stop codon.

2. The mRNA + polypeptide are then re-leased from the ribosome.

Central Dogma

• DNA RNA Protein

• Exception: Viruses (RNA DNA)

Gene Expression

• DNA carries information for specify-ing traits

• The codons of mRNA specify the se-quence of amino acids in a protein

• Proteins play a key role in producing the traits

13.3 Mutations

April 9, 2014

Mutations

• Mutation: (“to change”); heritable changes in genetic information

• Two categories of mutations:– Gene mutations (changes in single gene)– Chromosomal mutations (changes in

whole chromosomes)

Gene Mutations• Point mutation: gene mutation in which

a single base pair in DNA has been changed – Generally occur during replication– If a gene in one cell is altered, it can be

passed on to every cell that develops from the original one

• Three types of point mutations:– Substitutions: one base changed to differ-

ent base– Insertions: one base is inserted–Deletions: one base is removed

Frameshift mutation

Chromosomal Mutations• Changes in the number or structure of

chromosomes• These mutations can change the location

of genes and even change the number of copies of genes

• Four types of Chromosomal Mutations:–Deletion: all/part of a chromosome removed–Duplication: extra copy of all/part produced– Inversion: direction of parts reversed– Translocation: one part breaks off and at-

taches to another

Effects of Mutations

• Mutations may/may not affect organism• Errors in genetic processes cause many

mutations (ie. DNA replication)• Incorrect base insertion 1/10,000,000

bases, but small changes can accumu-late over time

• Causes: natural events, artificial means, errors in replication, stressful environmental conditions, mutagens

Mutagens• Mutagens: chemical or physical agents

in the environment• Chemical mutagens: certain pesticides,

plant alkaloids, tobacco smoke, envi-ronmental pollutants

• Physical mutagens: electromagneitc ra-diation (X-rays, ultraviolet light)

• Increases error rate of DNA replication; Weakens DNA strand causing breaks/in-versions

Harmful Effects

• Cancer: some arise from mutations that cause uncontrolled growth of cells

• Sickle cell disease: disorder associate with changes in shape of red blood cells– Point mutation in polypeptides in hemo-

globin (oxygen-carrying protein)– Symptoms: anemia, severe pain, frequent

infections, stunted growth

Beneficial Effects• Some mutations highly beneficial• Resistance to chemical pesticides (insects)– African mosquitoes resistant to chemical pesti-

cides– Bad for humans, but very beneficial to mosquito

• Adaptation to new chemicals in environment• Increased bone strength and density (less

likely for fractures)• Increased resistance to HIV (AIDS)• Polyploid plants are larger and stronger than

diploid plants

13.4 Gene Regulation and Expression

April 15, 2014

Prokaryotic Gene Regulation

• By regulating gene expression, bacteria can respond to changes in their environ-ment

• DNA-binding proteins in prokaryotes regu-late genes by controlling transcription

• Regulatory proteins turn genes on or off• Operon: group of genes that are regulated

together– Ex. Cluster of 3 genes (lac operon) must be

turned on together in E. coli before it can use lactose sugar as food

Lac Operon

• Lactose is made up of 2 sugars: galac-tose + glucose

• E. coli bacteria must transport lactose across its cell membrane and break the bond b/w glucose and galactose to use lactose for food

• If lactose is ONLY food source, lac operon must be produced

• If lactose not present, lac genes turned off and blocks transcription

Promoters and Operators• Operon has two regulatory regions:– Promoter (P): where RNA polymerase can bind

to begin transcription– Operator (O): where lac repressor binds to DNA

• Lac repressor blocks transcription1. Lac repressor binds to O region2. RNA polymerase cannot begin transcription3. Operon turned “off”

• Lactose turns operon “on”1. Lactose attaches to lac repressor2. Repressor changes shape and falls off operator3. RNA polymerase binds to promoter transcrip-

tion

Eukaryotic Gene Regulation

• TATA box: short region of 25-30 base pairs of TATATA or TATAAA– Binding site for RNA polymerase

• Transcription factors: control gene expression by binding DNA se-quences in the regulatory regions – Open up chromatin– Attract RNA polymerase– Block repressor proteins

Eukaryotic Gene Regulation• Cell Specialization: Gene regulation

more complex than prokaryotes– All cells in multicellular organism carry same

genetic code in nucleus, complex gene regu-lation allows genetic specialization

• RNA Interference (RNAi): small RNA molecules that interfere with mRNA– Fold into double-stranded hairpin loops– “Dicer” enzyme cuts (“dices”) double-

stranded loops into microRNA–MicroRNA + protein cluster silencing com-

plex

Question

• To make the mouse gene work inside the cells of a fly, researchers at-tached a new promoter sequence to the gene. Why do you think they did that?

Answer

• Researchers added new promoter sequence to mouse eye gene so that RNA polymerase would have a point to start transcription of the gene.

Genetic Control of Development

• Different specialized cell types origi-nates from same fertilized egg cell

• Different sets of genes are regulated by transcription factors and repressors

• Environmental Influences: tempera-ture, salinity, nutrient availability (lac operon); metamorphosis (series of transformations from one life stage to another)

• Differentiation: allows cells to become specialized in structure and function

• Homeotic Genes: regulates organs that develop in specific parts of the body–Mutation results in fly with a leg on its head

• Homeobox Genes: code for transcrip-tion factors that activate other genes in cell impt in development and differentia-tion

• Hox Genes: determine the identities of each segment of a fly’s body; arranged in exact order in which they’re expressed; mutation can completely change organs