Chapter 16 Notes - How Genes Work PDF

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Biological Science, 6th Edition Chapter 16 Summary/Notes on the topic of How Genes Work . ...

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Chapter 16 Notes - How Genes Work Review: Chromosome Theory of Inheritance→ genes are found on chromosomes Genes→ segments of DNA, carry instructions for making & maintaining an individual

How is the information in DNA actually put into action? This is the focus of chapter 16!

Section 16.1→ What do genes do? Up until 1941, no explicit hypothesis explaining what genes do George Beadle & Edward Tatum→ published experiments on bread mold (Neurospora crassa)  Central idea of their research: Wanted to discover what genes do by making them defective  Knock out a gene and infer what the gene does by observing the phenotype of the mutant Ex). Knock out a gene Observe that mutant organism develops no limbs The gene that was knocked out must code for limb development 

Null/ Loss-of-Function Alleles→ alleles that do not function at all

Experimental Setup: 1.) Expose a large number of N. crassa cells to radiation 2.) Look at cells and try to find mutants One mutant was unable to produce the compound pyridoxine 

Inability to synthesize pyridoxine was due to a defect in a single gene

This result led to the development of the One-Gene, One-Enzyme Hypothesis: One-Gene, One-Enzyme Hypothesis→ each gene contains the information needed to make 1 enzyme

Adrian Srb and Norman Horowitz→ wanted to test the 1 gene, 1 enzyme hypothesis   

Focused on ability of N. crassa to synthesize the amino acid arginine In the lab, normal cells of N. crassa grow on a medium without arginine o Why? → N. crassa can synthesize its own arginine through a metabolic pathway Specific enzymes are required to synthesize ornithine, convert ornithine to citrulline, and change citrulline to arginine

How did Srb & Horowitz find mutations that specifically knocked out a particular step in the metabolic pathway for arginine synthesis? Genetic Screen→ a technique for selecting for particular types of mutants from many randomly generated mutants

1.) Grow colonies of irradiated cells on a medium that contains arginine 2.) Transfer a sample of each colony to growth medium without arginine 

If a cell could grow with arginine but failed to grow without it, researcher concluded that the cell could not make its own arginine o These individuals have some defect in the metabolic pathway to produce arginine  At this point, it could be a mutation in enzyme 1,2 or 3

To test 1 Gene, 1 Enzyme Hypothesis: Grew each mutant that couldn’t synthesize arginine under 4 different conditions 1.) On a medium without added arginine 2.) On a medium with ornithine 3.) On a medium with citrulline 4.) On a medium with arginine

Mutants fell into 3 distinct classes: arg1, arg2, arg3

What can we conclude about arg 1, arg 2, and arg 3 based on experimental results?

Remember that in order to make arginine, we need to go through entire metabolic pathway.

Arg1, Arg2, and Arg3 correspond to defects in enzyme 1, enzyme 2, and enzyme 3 in the pathway for synthesizing arginine

Arg1- Since it has a defect in enzyme 1, it is unable to make Ornithine when given a growth medium with nothing in it. 

However, given mediums with Ornithine, Citrulline, and Arginine, it can proceed normally to produce Arginine

Arg2- Since it has a defect in enzyme 2, it is unable to make Citrulline when given a growth medium with nothing or a growth medium containing Ornithine. 

Given mediums containing Citrulline and Arginine, it can proceed normally to produce arginine

Arg3- Since it has a defect in enzyme 3, it is unable to make Arginine given a growth medium containing nothing, Ornithine, or Citrulline. 

It can only produce Arginine when placed in a growth medium containing Arginine

Srb & Horowitz concluded that:   

A specific genetic defect resulted in a specific enzymatic defect Therefore, genes encode for enzymes 1 gene,1 enzyme hypothesis is correct

Later research showed that genes contain the information for all the proteins produced by an organism-not just enzymes **Genes contain the information for making proteins!** Modified to One gene, One polypeptide hypothesis (1 gene encodes for each polypeptide)

Section 16.2→ The Central Dogma of Molecular Biology How does a gene specify the production of a protein? DNA is unlikely to catalyze reactions that produce proteins  Regularity of DNA double helix would not allow it to bind to variety of substrates needed for protein synthesis

Francis Crick: DNA= information storage molecule only, sequence of bases in DNA act as a code RNA→ acts as the intermediary between genes and proteins  RNA acts as a link between genes in the nucleus and the protein-manufacturing ribosomes that work in the cytoplasm Jacob & Monod’s Hypothesis: Messenger RNA (mRNA) carries information out of the nucleus from DNA and carries it protein-manufacturing centers (ribosomes)

RNA polymerase→ uses DNA template to polymerize ribonucleotides into strands of RNA  

Like DNA polymerase, it uses a DNA strand as a template Unlike DNA polymerase, RNA polymerase does not require a primer

RNA polymerase synthesizes RNA according to the rules of complementary base pairing Central Dogma: DNA→RNA→Proteins 1.) Transcription→ process of using a DNA template to make an mRNA using RNA polymerase 2.) Translation→ mRNA is translated into proteins by ribosomes  

Transcription-make a copy of the information Translation-convert information in 1 language into another o Conversion from language of mRNA to amino acid-based language of proteins

Extension of Crick’s Dogma: DNA→ RNA→ Proteins→ Phenotype  

Physical traits (phenotype) are a product of the proteins that are produced The Central Dogma explains the relationship between genotype and phenotype

**Result of these different DNA sequences is the production of proteins that differ in their amino acid sequence→ Different genotype leads to a different phenotype**

Exceptions to the Central Dogma: 1.) Many genes code for RNA molecules that are transcribed but never translated into proteins →Some RNA molecules form part of the ribosome, some regulate genes expression 2.) Information sometimes flows from RNA back to DNA. →Reverse Transcriptase: Synthesizes a DNA version of RNA

Section 16.3- The Genetic Code 

Genetic code→ specifies how a sequence of nucleotides code for a sequence of amino

How many bases of mRNA are needed to specify a single amino acid? 

Crick & Gamow→ three bases code for one amino acid

How did they come up with this? There are four bases in DNA Thus, a 1 base code would only allow for the creation of 4 amino acids A 2 base code would allow for the creation of 16 amino acids (4x4)

A 3 base code would allow for the creation of 64 amino acids- more than enough to cover the 20 amino acids that our cells produce

Codon= a group of 3 bases that specify a particular amino acid

 

Work by Crick and Brenner further confirmed that codons are 3 base pairs long They used chemicals to cause a deletion or addition of 1 base pair

An addition or deletion for 1 base pair led to the loss of function for the gene being studied Reading Frame Shift!

Ex.) THE FAT CAT ATE THE RAT THE ATC ATA TET HER AT

 

(Frameshift caused by 1 deletion)

Crick and Brenner figured out that the reading frame was not destroyed by adding or subtracting a multiple of 3 Verified the hypothesis that codons were made out of 3 base pairs

THE CAT ATE THE RAT



Nirenberg and Heinrich Matthaei→determined which codon coded for each amino acid

1.) Start codon: Met (AUG)

2.) Stop Codons(3): UAA,UAG, UGA

Important distinction→ The start codon also codes for the amino acid methionine. However, the stop codons don’t code for any particular amino acids. They simply signal the end of translation (protein is complete).

Properties of the Genetic Code: 1.) Redundant→ all but 2 amino acids (methionine and tryptophan) are encoded by more than 1 codon Degeneracy of the code: the code is degenerate because there are many instances in which different codons specify the same amino acid. Ex. UAU and UAC both encode the amino acid tyrosine 2.) Unambiguous→ A codon never codes for more than 1 amino acid 3.) Non-overlapping→ each codon is read one at a time. Once the ribosome locks onto the first codon, the reading frame is established and every codon is read one at a time 4.) Universal→ in almost every organism, all codons specify the same amino acids 5.) Conservative→ In codons that specify the same amino acid, the first two bases are usually identical

Question: If a change in DNA sequence causes a change in the ___________ position, then it is less likely to alter the amino acid sequence of the protein

Answer: Third position, most codons that have the same first two letters will code for the same amino acid

What can we predict based on the genetic code and the central dogma? 1.) We can predict codons and amino acid sequence based on a particular DNA sequence 2.) We can guess mRNA and DNA sequence that codes for a particular amino acid (more of a guess though because of the redundancy of the genetic code)

Section 16.4- What are the types and consequences of mutation? Mutation→ any permanent changes in an organism’s DNA Point Mutation→ mutation that alters the sequence one or a small number of bases pairs Types: 1.) Missense: change the identity of an amino acid in the protein 2.) Silent: does not change amino acid sequence due to redundancy in the genetic code 3.)Frameshift: shift the reading frame through the addition or deletion of base pairs 4.) Nonsense: a codon that should have produced an amino acid is changed into a stop codon

Mutation consequences? 1.) Beneficial- mutation increases the fitness of the organism 2.) Neutral- mutation has no effect on fitness (silent mutations are normally neutral) 3. Deleterious- mutations that lower the fitness of the organism



Most point mutations are neutral or slightly deleterious

Chromosome Mutations→ larger-scale mutations that change either the structure or number of chromosomes 

A change in chromosome number can lead to polyploidy or aneuploidy o Polyploidy= state of having more than two types of each chromosome o Aneuploidy= state that results from addition/deletion of individual chromosomes

Types: 1.)Inversion-segment of a chromosome is flipped and reattached 2.) Translocation- segment of a chromosome is attached to another chromosome 3.) Deletion-segment of a chromosome is lost 4.) Duplication-presence of one or more additional copies of a segment 

Like point mutations, chromosomal mutations can be beneficial, neutral, or deleterious...