CHAPTER 16 The MOLECULAR BASIS of INHERITANCE Pages 305-323 1. Scientists knew that chromosomes carried genes as early as 1905.

Why did it take until 1953 for the structure of DNA to be understood?

1953, Watson and Crick presented the world with a double-helix structural representation of DNA. Previous to this, lots of scientists discovered other clues that would lead to this conclusion. It took that long for the structure to be understood because Watson and Crick needed the help and discoveries of others and need to look at DNA with X-ray crystallography to figure out the structure.

2. Explain what each of the following scientists contributed to the "story of DNA": (a) Griffith, (b) Avery et al, (c) Hershey & Chase, (d) Chargaff, (e) Watson & Crick

Griffith: attempting to develop a vaccine against pneumoniastudying two different strains of the disease. When he killed pathogenic bacteria with heat and then mixed the cell remains with the nonpathogenic strain, he discovered that these living cells became pathogenic. This new trait was inherited by all of the descendents of the transformed bacteria. Avery: American bacteriologist searching for the identity of the transforming substance. He focused on DNA, RNA and protein. He broke open the bacteria and examined the cell contentsonly when DNA was allowed to remain reactive did transformation occur. Hershey and Chase: performed experiments showing that DNA is the genetic material of a phage of T2. Wanted to see which molecules entered and reprogrammed the cell. Powerful evidence that nucleic acids, not proteins, were the hereditary material for viruses. Chargaff: analyzed base composition of DNA and established the rules that adenosine always binds with thymine and cytosine always binds with guanine. Watson and Crick: first to come up with the correct structure of DNA. They studied protein structure with X-ray crystallography. Studied Franklins X-ray diffraction photo of DNA to correctly determine the structure.

3. Know the basic structure and nomenclature for nucleotides, including: which bases are purines, which bases are pyrimidines, difference between ribose and deoxyribose, variety of mono-, di-, and tri-phosphate forms. What is a nucleotide? How many phosphates are

present in the nucleotides from which DNA is synthesized? How many phosphate molecules are present per nucleotide in a DNA chain? Nucleotide: The building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group. 4. Identify the role of each of the following proteins in DNA replication: DNA polymerase, helicase, DNA primase, DNA ligase, Okazaki fragments. (see Fig. 16.17). DNA polymerase: Catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain. Require a a primery and a DNA template strand. Helicase: Enzymes that untwist the double helix at the replication folds, separating the two parental strands and making them available as template strands. DNA primase: Synthesizes an RNA primer at 5 end of leading strand and of each okazaki fragment lagging strand. DNA ligase: Joins 3 end (the sugar-phosphate backbones) of all the Okazaki fragments into a continuous DNA strand. Okazaki fragments: The segments of the lagging strands (strand in direction away from replication fork) each segment must be primed separately. 5. What is meant by "antiparallel strands" in DNA? What restriction does this place on replication? The two strands of DNA in a double helix are oriented in opposite directions to each other. 6. Note that, because the energy for adding new nucleotides to DNA comes from hydrolysis of phosphate bonds, it is only possible to add new nucleotides to a DNA (or RNA) strand at its 3terminus. Thus all growth of nucleic acids occurs at the 3-end; another way of saying this is that new DNA (and RNA) chains are synthesized in the 5 to 3 direction. Using this fact, explain what is meant by a "lagging strand" in DNA replication. What is meant by "leading strand". lagging: discontinuously DNA strand that elongates by Okazaki fragments. 5'-3' direction away from replication fork leading strand: new complementary DNA, toward replication fork 7. DNA polymerase also carries out proofreading and repair functions, including the excision or incorrectly paired bases and reinsertion of new DNA. CHAPTER 17

FROM GENE To PROTEIN Pages 325-344 1. How much DNA is there in a bacterial cell? a human cell? How many proteins could be encoded if all this DNA coded for protein sequences? Approximately what % of this DNA actually codes for proteins sequences? 2. What is meant by "transcription"? What molecules are needed for this to occur?

Transcription is the synthesis of RNA under the direction of DNAinformation is transcribed or copied and provides a template for the synthesis of a new complementary strand. For it to occur, DNA and RNA needed.

3. What is a promoter?

The DNA sequence where RNA polymerase attaches and initiates transcription.

4. What are the 3 types of RNA, and what role does each play? 1) rRNA: (ribosomal) The most abundant type of RNA which together with proteins make up ribosomes 2) tRNA(transfer): Functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA 3) mRNA (messenger): synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein

5. What is meant by "translation"? Where does this occur in the cell? What molecules are needed for this to occur? The synthesis of a polypeptide, which occurs under the direction of mRNA. Cell translates base sequence of mRNA molecules into the amino acid sequesnce of a polypeptide. Occurs in a ribosome in the cytoplasm. tRNA reads codons off mRNA to create amino acids, which create the polypeptide. A molecule of mRNA has the following structure: ...... A A A U G G G G G U C U U U G U G C U A G G G U G A U U G ....... Write the sequence of the translated protein (use the genetic code at the end of this handout) Note: where is the "start" codon? Does this protein have a "stop" codon?

Lys-Gly-Gly-Phe-Cys-Ala-Arg-Val-Ile (Start)-This protein does not have a stop codon 6. What is the role of a ribosome? Where are they found? Are there different ribosomes to make different proteins? Sites of translation found in the cytoplasm. Complex particles that facilitate the orderly linking of amino acids into polypeptide chains. All ribosomes are the same. The mRNA determines the protein, not the ribosome. 7. What do activating enzymes (technically, "aminoacyl tRNA synthetases) accomplish? Approximately how many of them are there? The correct matching up to tRNA and amino acid is carried out by a family of related enzymes called aminoacyl-tRNA synthetase. There are 20 of them (1 for each amino acid). The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP. The resulting aminoacyl tRNA, aka charged tRNA is released from the enzyme and is then available to deliver its amino acid ti a growing polypeptide chain on a ribosome. 8. "Codons" represent a series of 3 bases in DNA or RNA that specify a single amino acid. "Anticodons" are found on transfer RNA molecules. Theoretically, if there are 64 different codons, how many anticodons must there be? 64 9. Note that the "start" codon AUG is also the first amino acid of a protein, methionine (abbreviated met). Does this mean that every protein should start with met? Yup 10. Note that the "stop" codons do not specify any amino acid but instead cause termination of protein growth. What are the 3 stop codons? UAA, UGA and UAG 11. The process of protein synthesis is pretty complicated see Figs. 17.16-19. mRNA attaches to a ribosome; tRNA molecules bring amino acids into the ribosome, match up their anticodons with appropriate codons on the mRNA, and locate amino acids at the appropriate positions. Note that there are only two sites on the ribosome at which tRNA can bind. Why are these called A and P? What binds to each of these two sites? P site (peptidyl-tRNA site): holds the carrying and growing polypeptide chain

A site (aminoacyl-tRNA site): holds the tRNA carrying the next amino acid to be added to the chain. 12. Besides ribosomes, m-RNAs and AA-tRNAs, what other factors are required for protein synthesis? What is a termination factor? When is it required? -Energy provided by the hydrolysis of GTP -A small ribosomal subunit that binds to mRNA and a specific initiator tRNA, which carries the AA met -Proteins called initiation factors are required to bring together mRNA, initiator tRNA and a small ribosomal subunit followed by a large ribosomal subunit. -A protein called a release factor binds directly to the stop codon in the A site, The release factor causes the addition of a water molecule instead of an AA to the polypeptide chain 13. What is a polyribosome? Found in both bacterial and eukaryotic cells, they enable a cell to make many copies of a polypeptide very quickly. 14. How is protein synthesis different between prokaryotes and eukaryotes? 15. What is an exon? an intron? a spliceosome? Be sure you understand Fig. 17.10. Exon: A sequence that remains in the RNA after RNA processing. The region of DNA from which the RNA sequence was transcribed. Intron: A noncoding intervening sequence that is removed from the transcript during RNA processing. The region of DNA from which the sequence was transcribed. Spliceosome: A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons. 16. What is a ribozyme? Give two examples. A RNA molecule that functions as a cite of protein synthesis in the cytoplasm. 17. What is a mutation? Give an example of a point mutation, an insertion, and a deletion mutation. A change in the nucleotide sequence of an organisms DNA.

Point mutation: chemical changes in a single base pair of a gene. Ex. Hereditary disease like sickle cell. Insertions and deletions: Additions or losses of nucleotide pairs in a gene. Alters the reading frame of the genetic message. 18. What are some common causes of mutations? Errors in DNA replication, physical and chemical agents (mutagens) 19. In the following list, identify which components are required for DNA replication (label "1"), transcription (label "2"), and translation (label "3"). (a) DNA polymerase (b) tRNA (c) elongation factors (d) mRNA (e) ribosomes (f) primase (g) helicase (h) "AUG" codon (i) RNA polymerase (j) ATP (k) amino acids (l) initiation factor (m) release factor (n) promoter

CHAPTER 18, REGULATION of GENE EXPRESSION

(Part 1, pages 351-356) 1. Recognize and be able to answer questions involving the following terms: operatoroperon-repressor-regulatory gene-inducer-cyclicAMP and cAMP receptor protein (CRP) Operator: The switch in a segment of DNA. Positioned within the promoter or, in some cases, between the promoter and the enzyme-coding genes, the operator controls the access of RNA polymerase to the genes. Operon: the operator, the promoter, and the enzyme-coding genes, the operator, and the genes they control constitute an operon. Repressor: Has the ability to switch the operon off. The repressor binds to the operator and blocks attachment of RNA polymerase to the prooter, preventing transcription of the genes. A repressor protein is a specific for the operator of a particular operon. Regulatory gene: The repressor is the product of a regulatory gene. It is located some distance away from the operon it controls and has its own promoter. Are expressed continuously, although at a low rate. Inducer: a molecule that inactivates the repressor. Cyclic AMP: Accumlates when glucose is scarce. Senses glucose concentration and relays information to the genome. cAMP receptor protein (CRP): When the amount of glucose in the cell increases, the cAMP concentration falls, without cAMP, CAP detaches from the operon. 2. What is a repressible enzyme? Inducible enzyme? Inducible Enzymes: Synthesis is induced by a chemical signal. Function in catabolic pathways, which break down a nutrient to simpler molecules. By appropriate enzymes only when the nutrient is available, the cell avoids wasting energy and precursers making proteins that are not needed. Repressible Enzymes: generally function in anabolic pathways, which synthesize essential end products from raw materials (precursors). By suspending production of an end product when it is already present in sufficient quantity, the cell can allocate its organic precursors and energy for other uses. 3. How are the enzymes in question 2 examples of the negative control of genes? The operons are switched off by the active form of the repressor proton. Gene regulation is said to be only positive when a regulatory protein interacts directly with the genome to switch transportation on.

CHAPTER 18 (Part 2, pages 356-364) 1. Distinguish between DNA and Chromatin A eukaryotic cell is packed with protein in an elaborate complex known as chromatin, the basic unit of the nucleosome. The structural organization of chromatin not only packs a cells DNA into compact form that fits inside the nucleus but also helps regulate gene expression in several ways. 2. What is the relationship between histones and the nucleosome? Chemical modifications to histones, the proteins around which the DNA is wrapped in nucleosomes, helps regulate gene transcription. 3. How does the genome of a prokaryotic cell differ from a eukaryotic cell? How are they similar? The genomes of eukaryotes may contain tens of thousands of genes, but for quite a few species, only a small amount of the DNA codes for protein. 4. What is a telomere? The tandemly repetitive DNA at the end of a eukaryotic chromosomes DNA molecule that protects the organisms genes from being eroded during successive rounds of replication. 5. What is the significance of gene amplification in cells?

6. What is a genome? A genetic material of an organism or virus and its noncoding nucleic acid sequence. 7. Transposons vs Retrotransposons. Why are these significant? Transposons- an element that moves within a genome by means of a DNA intermediate. Retrotransposons: a transposon that moves within a genome by means of a RNA intermediate. 8. Review and understand the basics ( what is known about gene expression in eukaryotes.) Be able to recognize and answer questions relevant to the following terms: cellular differentiation, DNA methylation, genomic imprinting, Histone acetylation.

-In the nucleus where a signal stimulates chromatin modification where the DNA is unpacked then the gene is available for transcription. Where the spicesome takes out the intron, then the RNA process starts. -The mRNA transports into the cytoplasm where the process of translation starts. -Degradation of the mRNA where a polypeptide -Transcript to cellular destination. 9. DNA Transcription in eukaryotes. Be familiar with the following: Control elements, enhancers, DNA-binding domain. 10. What is meant by the following expression: The expression of a protein-coding gene is ultimately measured in terms of the amount of functional protein a cell makes? 11. What is DNA amplification? Would introns be an example? 12. Why/how does RNA processing give eukaryotes an advantage over prokaryotes? 13. Oncogenes, what are they? 14. What is an inherited cancer allele?