the gene-enzyme relationship is - deer valley unified ...the gene-enzyme relationship is one-gene,...

12From DNA to Protein:

Genotype to Phenotype

12.1 What Is the Evidence that Genes Code for Proteins?

The gene-enzyme relationship is one-gene,

one-polypeptide relationship.

Example: In hemoglobin, each polypeptide

chain is specified by a separate gene.

12.2 How Does Information Flow from Genes to Proteins?

Expression of a gene to form a

polypeptide takes 3 main processes:

• Transcription—copies information from

gene to a sequence of pre-mRNA.

• RNA Processing-converts pre-mRNA to

mRNA

• Translation—converts mRNA sequence

to amino acid sequence.


RNA, ribonucleic acid differs from DNA:

• Single strand-so what’s that mean?

• The sugar is ribose

• Contains uracil (U) instead of thymine (T)


RNA can pair with a single strand of

DNA, except that adenine pairs with

uracil instead of thymine.

Single-strand RNA can fold into much

more unique and differing shapes by

internal base pairing. (This flexibility is

not seen in DNA)

Figure 12.2 The Central Dogma

The central dogma of molecular biology for

eukaryotes: information flows in one direction

when genes are expressed (Francis Crick).


ONE Exception to the central dogma:

Viruses: acellular particles that reproduce

inside cells; many have RNA instead of DNA

so reverse the process. Synthesis of DNA

from RNA is called reverse transcription.

Viruses that do this are called retroviruses


Messenger RNA (mRNA) forms as a

complementary copy of DNA and

carries information to the cytoplasm.

(WHY use a copy of DNA?)

This process is called transcription and

occurs in the nucleus.

RNA polymerase is the enzyme that runs

the same direction as it’s “cousin”. Will

we have a leading or lagging strand

now? Why or why not?

Figure 12.3 From Gene to Protein

12.3 How Is the Information Content in DNA Transcribed to

Produce RNA?

Transcription occurs in three phases:

• Initiation

• Elongation

• Termination


Produce RNA?

Initiation requires a promoter—a special

sequence of DNA.

RNA polymerase binds to the promoter.

Promoter tells RNA polymerase where to

start, which direction to go in, and which

strand of DNA to transcribe. In

eukaryotes it is the “TATA” region called

the initiation site.

Figure 12.5 DNA Is Transcribed to Form RNA (A)


Produce RNA?

Elongation: RNA polymerase copies

base pairs of DNA into pre-mRNA.

RNA polymerase also runs in a 5-3

direction. (So what DNA template will

we use? Why? What about the other

one?)

Figure 12.5 DNA Is Transcribed to Form RNA (B)


Produce RNA?

Termination: specified by a specific DNA

base sequence.

Mechanisms of termination are complex

and varied.

Figure 12.5 DNA Is Transcribed to Form RNA (C)

Eukaryotes—first product is a pre-

mRNA that is longer than the final

mRNA and must undergo processing.

The Pre mRNA must be readied for

travel so 5’ caps and poly A tails (3’)

are added to the strand. Non coding

regions called introns are also

removed leaving only exons. Once

RNA processing is complete, we

have mRNA

• Please get a book and turn to page

262

Before we begin today, we need to understand that RNA is extremely flexible!

• There are 4 types of RNA, each encoded by its own type of gene:

• mRNA - Messenger RNA: Encodes amino acid sequence of a

polypeptide. Linear and made as the first product of transcription (pre-

MRNA)

• tRNA - Transfer RNA: Brings amino acids to ribosomes during

translation. (Folded mRNA bonded together into a “t” shape using H

bonds)

• rRNA - Ribosomal RNA: With ribosomal proteins, makes up the

ribosomes, the organelles that translate the mRNA. (Quaternary

protein structure, many more complex H bonds holding many linear

mRNA’s together)

• snRNA - Small nuclear RNA: Work with regulatory enzymes

(spliceosomes) to form complexes that are used in RNA processing in

eukaryotes. (Not found in prokaryotes.) (This is what splices out

introns!)

12.4 How Is RNA Translated into Proteins?

Let’s look at each type of RNA now….

Functions of tRNA:

• Carries an inactive amino acid

• Carries an active amino acid

• Interacts with ribosomes by providing

the anticodon

Figure 12.8 Transfer RNA


The conformation (three-dimensional shape) of tRNA results from base pairing (H bonds) within the molecule.

Anticodon: site of base pairing with mRNA. Unique for each species of tRNA.

Formula for building a protein is

Codon + anticodon + inactive aa= specific aa in polypeptide chain


Example:

DNA codon for alanine: GCC

Complementary mRNA: CGG

Anticodon on the tRNA: GCC

Active amino acid would be: alanine


Wobble: specificity for the base on tRNA

so one tRNA can decode up to 3

different codons.

Example: codons for alanine—GCA,

GCC, and GCU—are recognized by the

same tRNA.

Allows cells to produce fewer tRNA.


Ribosome: the workbench—holds

mRNA and tRNA in the correct positions

to allow assembly of polypeptide chain.

Ribosomes are not specific, they can

make any type of protein.


rRNA:

AKA the Ribosomes have two subunits,

large and small.

The subunits are made of rRNA or

ribosomal RNA.

Figure 12.10 Ribosome Structure


Large subunit has three tRNA binding sites:

• A site binds with anticodon of charged tRNA. Activation

• P site is where tRNA adds its amino acid to the growing chain. Polypeptide chain is held and built

• E site is where tRNA sits before being released. Exit


Translation also occurs in three steps:

• *Initiation-start codon (AUG) first amino

acid is always methionine

• Elongation of the polypeptide chain

• Termination- stop codon enters the A

site.

Methionine (AUG) hits the P site of the small

ribosomal sub-unit

that action initiates the process.

One of the first things that happens is the large

ribosomal sub-unit

joins with the small unit and makes an rRNA

Figure 12.11 The Initiation of Translation (Part 1)

Figure 12.11 The Initiation of Translation (Part 2)

Figure 12.12 The Elongation of Translation (Part 1)

Figure 12.12 The Elongation of Translation (Part 2)

Figure 12.13 The Termination of Translation (Part 1)

Table 12.1

Figure 12.14 A Polysome (Part 1)

Figure 12.14 A Polysome (Part 2)

• http://highered.mheducation.com/sites/

0072507470/student_view0/chapter3/a

nimation__how_translation_works.html

• http://www.stolaf.edu/people/giannini/fla

shanimat/molgenetics/translation.swf

• http://www.phschool.com/science/biolog

y_place/biocoach/transcription/difgns.ht

ml

http://highered.mheducation.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html

http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf

Figure 12.15 Destinations for Newly Translated Polypeptides in a Eukaryotic Cell

12.6 What Are Mutations?

Somatic mutations occur in somatic

(body) cells. Mutation is passed to

daughter cells, but not to sexually

produced offspring.

Germ line mutations occur in cells that

produce gametes. Can be passed to

next generation. This is the key to

evolution and are available to occur in

transcription.


All mutations are alterations of the

nucleotide sequence. 2 levels of

mutation….

Point mutations: change in a single

base pair—loss, gain, or substitution

of a base.

Chromosomal mutations: change in

segments of DNA—loss, duplication, or

rearrangement.


Point mutations can result from replication and proofreading errors, or from environmental mutagens.

Silent mutations have no effect on the protein because of the redundancy of the genetic code.

Silent mutations result in genetic diversity not expressed as phenotype differences.


KEY! These CAN be beneficial!

Missense mutations: base substitution

results in amino acid substitution.


Sickle allele for human β-globin is a

missense mutation.

Sickle allele differs from normal by only

one base—the polypeptide differs by

only one amino acid.

Individuals that are homozygous have

sickle-cell disease.

Figure 12.18 Sickled and Normal Red Blood Cells


Nonsense mutations: base substitution

results in a stop codon.


Frame-shift mutations: single bases

inserted or deleted—usually leads to

nonfunctional proteins.


Chromosomal mutations:

Deletions—severe consequences unless

it affects unnecessary genes or is

masked by normal alleles.

Duplications—if homologous

chromosomes break in different places

and recombine with the wrong partners.

Figure 12.19 Chromosomal Mutations (A, B)


Chromosomal mutations:

Inversions—breaking and rejoining, but segment is “flipped.”

Translocations—segment of DNA breaks off and is inserted into another chromosome. Can cause duplications and deletions. Meiosis can be prevented if chromosome pairing is impossible.

Figure 12.19 Chromosomal Mutations (C, D)


• Replication errors—some escape

detection and repair.

• Nondisjunction in meiosis.


Mutation provides the raw material for

evolution in the form of genetic diversity.

Mutations can harm the organism, or be

neutral.

Occasionally, a mutation can improve an

organism’s adaptation to its

environment, or become favorable as

conditions change.

Eukaryotic gene regulation-

TATA REGION=3'-TATAAT-5’

RNA PROCESSING


Induced mutation—due to an outside

agent, a mutagen.

Chemicals can alter bases

Prokaryotic gene regulation much simpler!

Operons are repeating regions that make up the prokaryote’s genome

They include; regulatory genes, promoter, structural genes

2 main regulatory options for ALL genes, inducible (lac)

or repressible (trp)

the gene-enzyme relationship is - deer valley unified ...the gene-enzyme relationship is one-gene,...

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