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Chapter 14 DNA Synthesis and Repair

1. What are chromosomes composed of? DNA and protein.

2. What are the two major components of the primary structure of DNA? Backbone, nitrogen-

containing bases.

3. What is the backbone made of? Sugar and phosphate groups

4. The two DNA strands line up in the opposite direction, meaning they are __antiparallel.

5. Which of the bases pair with which other bases? Adeninethymine. Guaninecytosine.

6. How do the old and new DNA strands interact during replication? Semiconservative

replication, conservative replication, dispersive replication.

7. What is semiconservative replication? Parental DNA strands separate & each is used as a

template for the synthesis of a new strand. Daughter cells consist of one old & one new strand.

8. What is conservative replication? Parental molecule serves as a template for the synthesis of an

entirely new molecule.

9. What is dispersive replication? Parent molecule is cut into sections such that the daughter

molecules contain old DNA interspersed with newly synthesized DNA.

10. Which enzyme catalyzes DNA synthesis? DNA polymerase.

11. Which end of the molecule can it add deoxynucleotides to? Only to 3 end. DNA synthesis

always proceeds in the 5 --> 3 direction.

12. What is a replication bubble? Forms in chromosome that is actively being replicated.

13. What is an origin of replication? Single location where replication process begins.

14. Which domain uses one origin of replication? Bacterial chromosomes.

15. Which domain uses multiple replication bubbles? Eukaryotes.

16. What is a replication fork? Y-shaped region where the DNA split into two separate strands for

copying.

17. Which enzyme separates or unzips the DNA double helix?Helicase.

18. Which proteins attach to the separated strands to keep them from closing back? (cont.)

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Single-strand DNA-binding proteins (SSBPs).

19. What does DNA polymerase require in order to begin working? A primer.

20. Which enzyme synthesizes a short RNA sequence that allows DNA polymerase

to begin? Primase.

21. Which strand is synthesized continuously? Leading strand, or continuous strand.

22. Which strand is synthesized in pieces? Lagging strand.

23. What are these pieces called? Okazaki fragments.

24. Which enzyme removes all the primers from the pieces? DNA polymerase I.

25. Which enzyme glues the pieces together? DNA ligase.

26. What is the name for the combined enzymes around the replication fork? Replisome.

27. How does the cell defend against shortening of chromosomes? Telomeraseenzyme, adds

nucleotides to the lagging strand, carries its own primer.

28. Which enzyme is responsible for maintaining #17? Telomerase.

29. What is the error rate for DNA replication? Less than 1 mistake per billion bases.

30. What is the error rate for DNA polymerase? 1 every 100,000 bases.

31. Which portion of DNA polymerase III proofreads? DNA polymerase III can do this because

its (epsilon) subunit acts as an exonuclease that removes

32. What does this reduce the error rate to? 1 in 10 million.

33. What is mismatch repair? Occurs when mismatched bases are corrected after DNA synthesis

is complete.

34. What type of repair is involved in repairing DNA damaged by UV radiation?Nucleotide

excision repair.

Chapter 15 How Genes Work

1. What is gene expression? The process of translating the information in DNA into

functioning molecules within the cell.

2. What is a genotype? Genetic constitution of an individual organism.

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3. What is a phenotype? Set of observable characteristics of an individual resulting from the

interaction of its genotype with the environment.

4. What is the central dogma of biology? Summarizes the flow of information in cells. It

states that DNA codes for RNA, which codes for proteins: DNA -> RNA -> proteins

5. Which type of RNA carries information from DNA to the site of protein

synthesis? Messenger RNA (mRNA)

6. What enzyme synthesizes RNA from DNA? RNA polymerase.

7. What is transcription? The process by which the hereditary info in DNA is copied to RNA.

8. What is translation? The process wherein the language of nucleic acids, the order of the

nucleotide bases, is converted to the language of proteins, the order of amino acids.

9. Which RNAs are not translated into proteins? tRNA & mRNA

10. What enzyme synthesizes DNA from RNA? Reverse transcriptase.

11.

12. What is a codon? Group of three bases that specifies a particular amino acid.

13. What is a reading frame? Sequence of codons.

14. What is a start codon? (AUG)Signifies the start of the protein-encoding sequence in

mRNA. (methionine)

15. What is a stop codon? 3 stop codons (UGA, UAA, and UAG) that signal the end of the

protein-coding sequence.

16. What are the four important properties of the code? It is redundant, It is unambiguous, It

is nearly universal. It is conservative.

17. What is a point mutation? Result from a single base change.

a. What is a silent mutation? Does not change the amino acid sequence of the gene product.

b. What is a missense mutation? Changes in the amino acid sequence of the encoded protein.

c. What is a nonsense mutation? Results in an early stop codon (protein usually

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nonfunctional).

d. What is a frameshift mutation? Addition or deletion of a nucleotide (protein usually non

functional).

18. What is a chromosome-level mutation? Changes in chromosome number. (polyploidy,

aneuploidy).

a. What is polyploidy? Having more than 2 sets of each chromosome. (3n, 4n etc)

b. What is aneuploidy? The addition or deletion of a chromosome.

c. What are inversions? Occur when sections of a chromosome break and rotate before

rejoining the chromosome.

d. What are translocations? Occurs when a broken section of one chromosome becomes

attached to another chromosome.

Chapter 16 Transcription and Translation

1. Which enzyme synthesizes RNA from a DNA template? RNA polymerase.

2. What is the name of the strand that gets copied? Template strand.

3. What is the name of the other strand?Non-template, or coding strand.

4. What is the first phase of transcription? Inititation.

5. Where does this phase occur in eukaryotes?Nucleus. (Prokaryotesno nucleus)

6. What is the signal found within DNA for the beginning of gene transcription? Transcription

termination signal.

7. Where is this found in relation to the gene? DNA template.

8. What are the locations and sequences of bacterial promoters? -10 box is found 10 bases

TATAAT. The -35 box, consisting of the sequence TTGACA.

9. What are the locations and sequences of eukaryotic promoters? TATA box -30.

10. Which protein binds the promoter in bacteria? Sigma factor

11. Which protein binds the promoter in eukaryotes? Basal transcription factors.

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12. What is the elongation phase of transcription? RNA polymerase moves along the DNA

template and synthesizes RNA in the 5 -> 3 direction.

13. What is the termination phase of transcription? (Transcription ends)RNA polymerase

encounters a transcription termination signal in the DNA template.

14. Name five differences between bacterial and eukaryotic RNA transcription. Transcription in

eukaryotes: Occurs in the nucleus, different promoters, basal transcription factors vs Sigma,

Multiple types of RNA polymerases, RNA processing.

15. What are the three steps in RNA processing in eukaryotes? 5 cap, 3 poly A tail, Splicing.

16. What are introns and exons? Introns are noncoding sequences that need to be removed. Exons

are the coding regions of mRNA.

17. What is the function of a spliceosome? Spliceosome catalyzes the splicing reaction.

18. What type of proteins form it? Small nuclear ribonucleoproteins. (snRNPs)

19. What is the purpose of the 5 cap?Serves as recognition signal for the translation machinery.

20. What is the purpose of the poly-A tail? Extends life of an mRNA by protecting it from

degradation.

21. How do bacterial and eukaryotic transcription/translation differ in terms of time

and space? Bacteriacoupled (time and space). Eukaryotesserparated (time and space).

22. What is the term for multiple ribosomes attached to an mRNA? Polyribosome.

23. What is the function of a tRNA? Bring amino acids to the ribosome.

24. What is the anticodon? Triplet on the loop at the opposite end. Base pairs with mRNA codon.

25. Which sequence attaches to amino acids? CCA sequence.

26. Which enzymes catalyze the addition of amino acids to tRNAs? Aminoacyl tRNA

synthetases.

27. Which two types of biomolecule make up ribosomes? Protein and ribosomal RNA (rRNA).

28. What is the function of the small unit and the large subunit in ribosomes? small subunit holds

the mRNA in place during translation. Large subunit, peptide bonds form.

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29. What happens at the:

a. A site of a ribosome? Acceptor site for an aminoacyl tRNA.

b. P site of a ribosome? Peptide bond forms that adds an amino acid to the growing polypeptide

chain.

c. E site of a ribosome? tRNAs no longer bound to an amino acid exit the ribosome.

30. What allows binding between the small subunit and mRNA? Initiation factors.

31. What are the three steps of translation initiation? 1. mRNA binds to a small ribosomal subunit

via initiation factors, 2. The initiator aminoacyl tRNA binds to the start codon (AUG), 3. The

large ribosomal subunit binds, completing the complex.

32. What happens in elongation? 1. Initiator tRNA is in the P site and the E and A sites are

empty. 2. An aminoacyl tRNA binds to the codon in the A site via complementary base pairing

between anticodon and codon. 3. Peptide bonds form between amino acids on the tRNAs in the P

and A sites.

33. What is a ribozyme? RNA molecule that is capable of performing specific biochemical

reactions, similar to the action of protein enzymes.

34. Why are ribosomes considered to be ribozymes? Ribosomal RNA catalyzes peptide bond

formation and the ribosome is a ribozyme, not an enzyme.

35. What is translocation? Occurs when elongation factors move the mRNA down the ribosome

three nucleotides at a time, and the tRNA attached to the growing protein moves into the P site.

36. What causes termination of translation? When the A site encounters a s top codon.

37. What type of protein binds at a stop codon? Release factor.

38. What type of molecules help proteins fold? Molecular chaperones.

39. What type of group is added to many proteins in order to either activate or

deactivate them? Phosphate group.