AP Biology, Chapter 17
From Gene to Protein

Summary
Introduction
	1. Explain why dwarf peas have shorter stems than tall varieties
		a. Dwarfs lack the plant hormone gibberellin; applied gibberellin cures them
		b. Missing an enzyme required for gibberrellin synthesis		

THE CONNECTION BETWEEN GENES AND PROTEINS
	Introduction
	The study of metabolic defects provided evidence that genes specify proteins: science 
	as a process
		2. Explain the reasoning that led Archibald Garrod to first suggest that genes dictate 
		phenotypes through enzymes.
			a. Garrod was an MD
			b. Focused on rare and unusual birth defects; inborn errors of metabolism
			c. Example: alkaptonuria
				i. Urine turns black; contains alkapton
				ii. Hypothesized a missing enzyme for brealing down alkapton
		3. Describe Beadle and Tatum's experiments with Neurospora and explain the 
		contribution they made to our understanding of how genes control metabolism.
			a. Neurospora can grow on a minimal medium (MM): sucrose, salts, + biotin
				i. Can synthesize all other biomolecules: amino acids, nitrogen bases, 
				etc.
				ii. Biomolecules are made stepwise by a series of enzymes
			b. Beadle and Tatum collected mutants that required arginine in their MM
				i. Intermediates in the pathway were known
				ii. Intermediates: precursorornithinecitrullinearginine
				iii. Mutants can be grouped by which intermediate cures them
			c. Concluded that each group of mutants lack a different enzyme in the pathway
		4. Distinguish between the "one gene-one enzyme" hypothesis and the "one gene-one 
		polypeptide" hypothesis and explain why the original hypothesis was changed.
			a. One gene-one enzyme
				i. Each gene makes an enzyme
				ii. But some proteins are not enzymes 
				iii. Counter examples: insulin, keratin, hemoglobin
			b. One gene-one polypeptide
				i. More inclusive
				ii. Counter examples: RNA genes, regulatory sequences
	Transcription and translation are the two main processes linking gene to protein: an 
	Overview
		5. Explain how RNA differs from DNA.
			a. Uracil instead of thymine
			b. Usually single-stranded
			c. Used to express traits rather than store and transmit traits
		6. Briefly explain how information flows from gene to protein.
			a. In DNA, order of bases = information
			b. Copied by base-pairing rule into mRNA = transcription
			c. Ribosome clamps onto mRNA, moves along three bases at a time
			d. Each mRNA codon matches and anticodon on a specific tRNA
			e. tRNA carries a specific anticodon at one end, amino acid matching that 
			anticodon at the other end
			f. Ribosomes align proper tRNAs and form the peptide bonds
		7. Distinguish between transcription and translation.
			a. Transcription = DNA bases  RNA bases by complementarity
			b. Translation = RNA bases  amino acid sequence
		8. Compare where transcription and translation occur in prokaryotes and in eukaryotes.
			a. Prokaryotes
				i. No nucleus
				ii. Transcription and translation both in the cytoplasm
			b. Eukaryotes
				i. Transcription in the nucleus; pre-mRNA processed to mRNA
				ii. Translation in the cytoplasm (with possible exceptions)
	In the genetic code, nucleotide triplets specify amino acids
		9. Define "codon" and explain the relationship between the linear sequence of codons on 
		mRNA and the linear sequence of amino acids in a polypeptide.
			a. Codon = three base sequence signifying the position of an amino acid
			b. Order of codons gives the order of amino acids in protein
			c. In general, conserved; but with taxonomic variations, and mutant forms
		10. Explain the early techniques used to identify what amino acids are specified by the 
		triplets UUU, AAA, GGG, and CCC.
			a. Nirenberg, 1961
			b. Synthesized poly-uracil to serve as an artificial mRNA
			c. In vitro protein synthesis made only poly-phenylalanine
		11. Explain why polypeptides begin with methionine when they are synthesized.
			a. Don't always, see code variation link above
			b. Codon for met often signifies the starting place for the ribosome
			c. Often removed after translation
		12. Explain in what way the genetic code is redundant and unambiguous.
			a. Redundant: more than one codon for most amino acids
			b. Unambiguous: in an organism, each codon codes for a specific amino acid
		13. Explain the significance of the reading frame during translation.
			a. mRNAs are read first three, next three, next three, etc.
			b. Shifting the start one base changes the triplets downstream
	The genetic code must have evolved very early in the history of life
		14. Explain the evolutionary significance of a nearly universal genetic code.
			a. Lateral transfer (species-to-species) of genetic material is fruitful
			b. Homologous structures signify a common ancestor with the structure
			c. Universal code indicates a single common ancestor for all living systems

THE SYNTHESIS AND PROCESSING OF RNA
	Transcription is the DNA-directed synthesis of RNA: a closer look
		15. Explain how RNA polymerase recognizes where transcription should begin. Describe 
		the promoter, the terminator, and the transcription unit.
			a. RNA polymerase binds at the promoter
				i. Promoter includes transcription start point
				ii. Extends upstream
				iii. Determines template strand
			b. Eukaryotes
				i. Protein transcription factors bind to the promoter first
				ii. + RNA polymerase = transcription initiation complex
				iii. In prokaryotes, proteins bound to RNA polymerase specify binding 
			c. Transcription unit extends from within the promoter past the terminator
			d. Palindromic terminator sequence may form a hairpin loop
		16. Explain the general process of transcription, including the three major steps of 
		initiation, elongation, and termination.
			a. Initiation
				i. Eukayotes: half of promoters have TATAAAA; binds transcription factor
				ii. Prokaryotes: TATAAAT is a common RNA polymerase binding site
			b. Elongation
				i. RNA polymerase adds nucleotides to 3' end
				ii. No proofreading function
			c. Termination
				i. Terminator sequence is transcribed
				ii. Transcribed sequence forms hairpin in prokaryotes
				iii. AAUAAA termination sequence in eukaryotes reveals 3' processing site
	Eukaryotic cells modify RNA after transcription
		17. Explain how RNA is modified after transcription in eukaryotic cells.
			a. 5' cap
				i. Methyl-G and PPP added
				ii. Protects from degradation and allows ribosome binding
			b. 3' poly(A) tail
				i. Pre-mRNA cut downstream from AAUAAA; poly(A) added
				ii. Same functions as 5' cap
			c. Introns removed
				i. Exon = expressed sequence; intron = interspersed sequence
				ii. Precise, complex excision involving spliceosomes
		18. Define and explain the role of ribozymes.
			a. RNA-only enzymes involved in RNA processing
			b. Introns may also catalyze their own excision
		19. Describe the functional and evolutionary significance of introns.
			a. Functional
				i. Introns may control gene activity
				ii. Alternate splicing can give >1 protein from the same gene
			b. Evolutionary
				i. Exons code for functional domains of proteins
				ii. Widely spaced functional components allows recombination  new 
				proteins

THE SYNTHESIS OF PROTEIN
	Introduction
	Translation is the RNA-directed synthesis of a polypeptide: a closer look
		20. Describe the structure and functions of tRNA.
			a. Structure
				i. Short, about 80 nucleotides
				ii. Folded with four base-paired regions
				iii. Amino acid attachment site at 3' end
				iv. Anticodon at the other end of folded molecule
				v. Modified after transcription
			b. Functions
				i. Transfer amino acids to ribosome
				ii. Anticodon matches amino acid
				iii. Anticodon hydrogen bonds to mRNA codon
				iv. Wobble allows fewer than 61 tRNAs
			c. Charging
				i. Amino acids added by aminoacyl-tRNA synthetases
				ii. Only 20, not one to recognize each anticodon
				iii. Recognize the end with the amino acid attachment site
		21. Describe the structure and functions of ribosomes.
			a. Structure
				i. Large with 60% rRNA and 40% protein
				ii. Two subunits found separately unless actively translating
				iii. Groove for mRNA
				iv. P-, A-, and E- sites for tRNA binding
			b. Function
				i. Clamp onto mRNA at start codon
				ii. Align tRNAs
				iii. Form peptide bonds
				iv. Move codon-by-codon along mRNA 
		22. Describe the process of translation (including initiation, elongation, and termination) 
		and explain which enzymes, protein factors, and energy sources are needed for each 
		stage.
			a. Initiation
				i. Small subunit binds to mRNA leader or 5' cap and tRNAmet in P-site
				ii. Large subunit then binds
				iii. Protein initiation factors and energy from GTP are required
			b. Elongation
				i. Next tRNA binds codon under A-site; uses elongation factors and GTP
				ii. Peptide bond formed
				iii. Growing polypeptide chain bound to tRNA in A-site
			c. Translocation
				i. Ribosome, mRNA, and tRNAs shift over one codon
				ii. tRNA in E-site is released
				iii. Uses GTP
			d. Termination
				i. Release factor binds stop codon (UAA, UAG, or UGA) under A-site
				ii. Water molecule added (hydrolysis)
				iii. New polypeptide released from last tRNA
		23. Describe the significance of polyribosomes.
			a. Ribosomes can sequentially attach to mRNAs
			b. Allows many copies of a protein to be made using the same message
	Signal peptides target some eukaryotic polypeptides to specific destinations in the 
	cell
		24. Explain what determines the primary structure of a protein and describe how a 
		polypeptide must be modified before it becomes fully functional.
			a. Primary structure = amino acid order dictated by mRNA
			b. Chaperone proteins enable folding
			c. Sugars, lipids, or phosphates may be added
			d. Pieces may be removed
			e. More than one chain may be bound together
		25. Describe what determines whether a ribosome will be free in the cytosol or attached 
		to the rough endoplasmic reticulum.
			a. Membrane-bound ribosomes make endomembrane and secreted proteins
			b. Amino-terminal signal peptide is bound by signal-peptide recognition particle
			c. Complex binds to rough ER
			d. Signal peptide is removed from finished protein
	RNA plays multiple roles in a cell: a review
		26. Describe two properties of RNA that allow it to perform so many different functions.
			a. Can hydrogen bond to other nucleic acids
			b. Can fold by forming complementary base pairs with itself
	Comparing protein synthesis in prokaryotes and eukaryotes: a review
		27. Compare protein synthesis in prokaryotes and eukaryotes.
			a. RNA polymerases
				i. Eukaryotes have 3, prokaryotes have 1
				ii. Initiation factors bind to promoter first in eukaryotes
			b. Different termination signals and ribosome sizes
			c. Prokaryotes can have simultaneous transcription and translation
	Point mutations can affect protein structure and function
		28. Define "point mutations." Distinguish between base-pair substitutions and base-pair 
		insertions. Give examples of each and note the significance of such changes.
			a. Point mutations change one or a few base pairs
			b. Substitutions
				i. Change a single base, maybe a single amino acid (missense)
				ii. Don't affect codons downstream
				iii. Usually have less drastic effects
				iv. Example: sickle-cell; one amino acid changed, altered protein shape
			c. Base insertions/deletions
				i. Change the reading frame = frameshift mutations
				ii. Change all codons downstream often to a stop codon (nonsense)
				iii. May change all amino acids downstream and can truncate
		29. Describe several examples of mutagens and explain how they cause mutations.
			a. Mutagens
				i. Radiation: gamma, X, UV, cosmic rays
				ii. Chemical: nitrous acid, sodium azide, bromine, arsenic, base analogs
			b. Mechanisms
				i. Radiation can break bonds holding DNA together
				ii. Base analogs are incorporated but base-pair incorrectly
				iii. Reactive chemical mutagens react with bases in DNA 
	What is a gene: revisiting the question
		30. Describe the historical evolution of the concept of a gene.
			a. Mendel: discrete unit of inheritance that affects phenotype
			b. Morgan: place on a chromosome, locus
			c. Region of a specific nucleotide sequence
			d. DNA sequence coding for a protein
			e. Any sequence that change be changed to alter phenotype