Chapter 17 Outline - Lecture notes Test 4 PDF

Preview

Summary

Danielle Maxwell...

Description

Chapter 17 Outline READING:     

17.1 Gene Expression 17.2 Transcription 17.3 RNA modifications 17.4 Translation 17.5 Mutations

335-342 342-344 345-347 347-355 357-360

TERMS: gene expression

5’ cap

stop codon

transcription

poly-A tail

gene mutation

translation

exons

germ-line mutation

messenger RNA (mRNA)

introns

somatic mutations

primary transcript

RNA splicing

spontaneous mutations

genetic code

alternative RNA splicing (a.k.a. exon shuffling)

induced mutations

codon template strand RNA polymerase promoter terminator transcription unit

transfer RNA (tRNA) anticodon ribosome

mutagens carcinogens point mutations frameshift mutations

ribosomal RNA (rRNA) start codon

Questions to Consider: 1. What is the function of a gene? Explain why modern geneticists have modified Beadle and Tatum’s “one gene-one enzyme” hypothesis. 2. How does prokaryotic and eukaryotic transcription differ? Where does transcription take place in a eukaryotic cell? Where does translation take place in a eukaryotic cell? Can translation and transcription take place concurrently in prokaryotic cells? Why or why not? 3. What does the genetic code consist of? Describe the components of the genetic language; what are the “letters”, what are the “words”, what is the equivalent of a “sentence”? What

are the properties of the genetic code? Who was responsible for “cracking” the genetic code? 4. Briefly describe the 3 steps of the transcription of RNA off a DNA template. What is the function of RNA polymerase? What is a promoter? Is it located at the upstream or downstream end of a transcription unit? 5. There are about 20,000 human protein-coding genes. How can human cells make 75,000100,000 different proteins? 6. How is mRNA processed before leaving the nucleus? How does exon shuffling (alternative RNA splicing) contribute to a diversity of possible polypeptides from one DNA sequence? 7. If I give you a sequence of DNA bases (i.e. TAGC), you should be able to give me the sequence of transcribed mRNA bases (i.e AUCG). If I give you a table of amino acids that correspond with mRNA codons, you should be able to use that table to tell me the amino acid sequence for a given sequence of mRNA. How many tRNA molecules would be needed to make up that amino acid sequence (not including stop and start codons)? 8. Know the basic steps of the translation of an mRNA molecule into a polypeptide. What are the roles of tRNA and ribosomes? During what steps of translation does the cell expend energy? 9. What are some causes of mutations (i.e. induced vs spontaneous mutations)? What is the difference between mutagens and carcinogens? What types of mutations are induced mutations? 10. What is the difference between point mutations and frameshift mutations and how do they affect protein synthesis? Mutations in what types of cells can cause cancer? What types of mutations are heritable?

Lecture Outline CONCEPT 17.1 Genes specify proteins via transcription and translation

Genotype to Phenotype »

An organism’s genotype is its genetic makeup, the sequence of nucleotide bases in DNA.

»

The phenotype is the organism’s physical traits, which arise from the actions of a wide variety of proteins.

»

Gene expression, the process by which DNA directs protein synthesis includes two stages: 1. transcription, the transfer of genetic information from DNA into an RNA molecule and 2. translation, the transfer of information from RNA into a protein (polypeptide).

Beadle & Tatum 1930s »

George Beadle and Edward Tatum exposed bread mold, Neurospora crassa, to X-rays, creating mutants that were unable to survive on minimal media

»

Using crosses, they and their coworkers identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for synthesizing arginine

»

They developed a one gene–one enzyme hypothesis, which states that each gene dictates production of a specific enzyme

»

See Figure 17.2

The Function of a Gene »

The one gene–one enzyme hypothesis has since been modified.

»

The function of a gene is to dictate the production of a polypeptide. ˃

Some proteins aren’t enzymes

˃

A protein may consist of two or more different polypeptides.

˃

Therefore more than one gene may be responsible for the production of a single protein

»

Genetic information in DNA is ˃

transcribed into RNA, then

˃

translated into polypeptides,

˃

which then fold into proteins

Basic Principles of Transcription and Translation »

RNA is the bridge between genes and the proteins for which they code

»

Transcription is the synthesis of RNA using information in DNA ˃

»

Transcription produces messenger RNA (mRNA)

Translation is the synthesis of a polypeptide, using information in the mRNA ˃

Ribosomes are the sites of translation

CONCEPT 16.1 DNA is the genetic material

Prokaryotic vs Eukaryotic Cells »

In prokaryotes, translation of mRNA can begin before transcription has finished ˃

Both transcription and translation take place in the cytoplasm of the cell

»

In a eukaryotic cell, the nuclear envelope separates transcription from translation

»

Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA

»

A primary transcript is the initial RNA transcript from any gene prior to processing

»

See Figure 17.3

The Central Dogma of Biology »

The central dogma is the concept that cells are governed by a cellular chain of command: DNA → RNA → protein

»

This concept was dubbed the central dogma by Francis Crick in 1956

The Genetic Code »

The unit of the genetic code consists of codons, each of which is a unique arrangement of symbols

»

Each of the 20 amino acids found in proteins is uniquely specified by one or more codons ˃

The symbols used by the genetic code are the mRNA bases +

˃

Codons in the genetic code are all three bases (symbols) long +

˃

Function as “letters” of the genetic alphabet (U, A, C, G)

Function as “words” of genetic information

Permutations:

+

There are 64 possible arrangements of four symbols taken three at a time

+

Often referred to as triplets

˃

Genetic language only has 64 “words”

˃

See Figure 17.4

Gene Expression: An overview »

During transcription, one of the two DNA strands, called the template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript ˃

»

The template strand is always the same strand for a given gene

During translation, the mRNA base triplets, called codons, are read in the 5′ → 3′ direction

»

Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide

Cracking the Genetic Code »

Nirenberg and Matthei (1961) ˃

Used enzymes to construct synthetic RNA

˃

Synthetic RNA was added to a test tube of cytoplasmic material

˃

Synthetic RNA was translated into amino acids

˃

Started with UUU to construct phenylalanine and was later able to translate 3 nucleotides at a time and assign an amino acid to each of the mRNA codons

˃

See Figure 17.5

Properties of the Genetic Code »

Universal ˃

The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals

˃

Genes can be transcribed and translated after being transplanted from one species to another

»

»

Redundant ˃

There are 64 codons available for 20 amino acids

˃

Most amino acids encoded by two or more codons

˃

Helps protect against harmful mutations

Unambiguous (codons are exclusive)

»

˃

None of the codons code for two or more amino acids

˃

Each codon specifies only one of the 20 amino acids

Contains start and stop signals ˃

Punctuation codons

˃

Like the capital letter we use to signify the beginning of a sentence, and the period to signify the end

˃

Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced

CONCEPT 17.2 Transcription is the DNA-directed synthesis of RNA: A closer look

Transcription »

RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and joins together the RNA nucleotides

»

Transcription ˃

The RNA is complementary to the DNA template strand

˃

RNA polymerase does not need any primer

˃

RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine

»

See Figure 17.7

Synthesis of an RNA Transcript »

»

The three stages of transcription: ˃

Initiation

˃

Elongation

˃

Termination

The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator ˃

Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point

»

The stretch of DNA that is transcribed is called a transcription unit

Elongation of the RNA strand »

As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time

»

Transcription progresses at a rate of 40 nucleotides per second in eukaryotes ˃

»

A gene can be transcribed simultaneously by several RNA polymerases

Nucleotides are added to the 3′ end of the growing RNA molecule

»

See Figure 17.9

Termination of Transcription »

The mechanisms of termination are different in bacteria and eukaryotes

»

In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification

»

In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence(AAUAAA); the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence

CONCEPT 17.3 Eukaryotic cells modify RNA after transcription

RNA processing »

In prokaryotes, the completed mRNA transcript can be translated after transcription without additional modifications

»

Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm

»

During RNA processing, both ends of the primary transcript are usually altered

»

Also, usually certain interior sections of the molecule are cut out, and the remaining parts spliced together

Alteration of mRNA Ends »

Each end of a pre-mRNA molecule is modified in a particular way ˃

The 5′ end receives a modified nucleotide 5′ cap +

˃

The 3′ end gets a poly-A tail +

»

A modified guanine molecule is added to the 5’ end

50-250 adenine nucleotides are added to the 3’end

These modifications share several functions ˃

They seem to facilitate the export of mRNA to the cytoplasm

˃

They protect mRNA from hydrolytic enzymes

˃ »

They help ribosomes attach to the 5′ end

See Figure 17.10

RNA Splicing »

Pre-mRNA, is composed of exons and introns. ˃

The exons are coding regions that will be expressed and translated to an amino acid sequence

˃ »

The introns, occur in between the exons and are non-coding regions of DNA

RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence ˃

In some cases, RNA splicing is carried out by spliceosomes

˃

Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

˃ »

The RNAs of the spliceosome also catalyze the splicing reaction

See Figure 17.11 and 17.12

Alternative RNA Splicing »

It was once believed that introns were “junk DNA” but we now know their function and evolutionary importance

»

Some introns contain sequences that may regulate gene expression

»

Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing ˃

This is called alternative RNA splicing or exon shuffling

˃

Consequently, the number of different proteins an organism can produce is much greater than its number of genes

»

See Figure 17.13

CONCEPT 17.4 Translation is the RNA-directed synthesis of a polypeptide: A closer look

Molecular Components of Translation »

A cell translates an mRNA message into protein with the help of transfer RNA (tRNA) ˃

»

tRNAs transfer amino acids to the growing polypeptide in a ribosome

Molecules of tRNA are not identical ˃

Each carries a specific amino acid on one end

˃

Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA

»

A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long

˃

Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf

»

See Figure 17.15

Ribosomes »

Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis

»

The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)

»

A ribosome has three binding sites for tRNA

»

˃

The P site holds the tRNA that carries the growing polypeptide chain

˃

The A site holds the tRNA that carries the next amino acid to be added to the chain

˃

The E site is the exit site, where discharged tRNAs leave the ribosome

See Figure 17.17

Building a Polypeptide »

The three stages of translation ˃

Initiation

˃

Elongation

˃

Termination

»

All three stages require protein “factors” that aid in the translation process

»

Energy is required for some steps

Translation: 3 Steps »

Initiation ˃

˃

˃

The step that brings all the translation components together (initiation factors): +

Ribosome (small and large subunits)

+

mRNA transcript

+

Initiator tRNA

+

Initiation factors (special proteins that bring the above together)

Initiator tRNA: +

Always has the UAC anticodon (start codon)

+

Carries the amino acid methionine

+

Binds to the P site on the ribosome

The cell expends energy by hydrolyzing a GTP molecule to form the initiation complex

˃ »

See Figure 17.18

During elongation, amino acids are added one by one to the C-terminus of the growing chain

˃

Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation

˃

Energy expenditure occurs in the first and third steps

˃

Translation proceeds along the mRNA in a

˃

See Figure 17.19

5′ → 3′ direction

Termination »

Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome

»

The A site accepts a protein called a release factor

»

The release factor causes the addition of a water molecule instead of an amino acid

»

This reaction releases the polypeptide, and the translation assembly comes apart

»

See Figure 17.20

Protein Folding and Post-Translation Modifications »

During its synthesis, a polypeptide chain begins to coil and fold spontaneously to form a protein with a specific shape—a three-dimensional molecule with secondary and tertiary structure ˃

»

A gene determines primary structure, and primary structure in turn determines shape

Post-translational modifications may be required before the protein can begin doing its particular job in the cell

CONCEPT 17.5 Mutations of one or a few nucleotides can affect protein structure and function Gene Mutations »

A gene mutation is a permanent change in the sequence of bases in DNA.

»

The effects of a gene mutation can range from

»

˃

No effect on protein activity to

˃

Complete inactivation of the protein

Germ-line mutations occur in sex cells ˃

»

Germ-line mutations can be passed on to future generations

Somatic mutations occur in body cells ˃

Somatic mutations are not passed on to future generations but can lead to the development of cancer

»

Spontaneous mutations ˃

Chemical changes in DNA that lead to mispairing during replication

˃

Replication Errors »

DNA polymerase

» »

»

Proofreads new strands

»

Generally corrects errors

Overall mutation rate is 1 in 1,000,000,000 nucleotide pairs replicated

Induced mutations ˃

˃

Caused by mutagens such as radiation and organic chemicals »

Mutagens alter base composition of DNA

»

Cancer causing mutagens are carcinogens

Environmental Mutagens »

Ultraviolet Radiation »

UV radiation is absorbed by thymine molecules causing them to bond together creating thymine dimers

»

Tobacco Smoke »

»

»

»

A known carcinogen

Poin...