Chapter 5 Fundamental Genetic Mechanisms

Question 1

What are Watson-Crick base pairs? Why are they important?

Answer 1

• interactions between a larger purine and a smaller pyrimidine base in DNA.
• interactions result in primarily G-C and A-T base pairing in DNA and A-U base pairs in double-stranded regions of RNA.
• important because they allow one strand to function as the template for synthesis of a complementary, anti-parallel strand of DNA or RNA.

Question 2

What are the 3 DNA excision-repair systems in eukaryotes?

Answer 2

• Base excision repair
• Mismatch excision repair
• Nucleotide excision-repair

Question 3

What is base excision repair?

Answer 3

repairs guanine-thymine mismatches caused by the chemical conversion of cytosine to uracil or by deamination of 5-methyl cytosine to thymine

Question 4

What is mismatch excision repair?

Answer 4

eliminates base pair mismatches and small insertions or deletions of nucleotides generated accidentally during DNA replication

Question 5

What is nucleotide excision-repair?

Answer 5

fixes DNA strands that contain chemically modified bases

Question 6

What characteristic of DNA results in the requirement
that some DNA synthesis be discontinuous? How are
Okazaki fragments and DNA ligase used by the cell?

Answer 6

DNA double helix consists of two anti-parallel strands and DNA polymerase can synthesize DNA only in the 5’ to 3’ direction. Thus, one strand is synthesized continuously at the growing fork, but the other strand is synthesized utilizing Okazaki fragments that are joined by DNA ligase.

Question 7

What is homologous recombination?

Answer 7

• A process that can repair DNA damage & generate genetic diversity during meiosis
• For both, repair is to double-strand breaks
• RecA/Rad51-like proteins play key roles in the recombination process
• Holliday structures form, followed by cleavage and ligation to form two recombinant chromosomes
• the damaged sequence is copied from an undamaged copy of the homologous DNA sequence on the homologous chromosome or sister chromatid

Question 8

anticodon

Answer 8

Sequence of three nucleotides in a tRNA that is complementary to a codon in an mRNA. During protein synthesis, base pairing between a codon and anticodon aligns the tRNA carrying the corresponding amino acid for addition to the growing polypeptide chain. (Fig 5-20)

Question 9

codon

Answer 9

Sequence of three nucleotides in DNA or mRNA that specifies a particular amino acid during protein synthesis; also called triplet. Of the 64 possible codons, three are stop codons, which do not specify amino acids and cause termination of synthesis. (Table 5-1)

Question 10

complementary

Answer 10

(1) Referring to two nucleic acid sequences or strands that can form perfect base pairs with each other.
(2) Describing regions on two interacting molecules (e.g., an enzyme and its substrate) that fit together in a lock-and-key fashion.

Question 11

DNA polymerase

Answer 11

An enzyme that copies one strand of DNA
(the template strand) to make the complementary strand, forming a new double-stranded DNA molecule. All DNA polymerases add deoxyribonucleotides one at a time in the 5’ - 3’ direction to the 3’ end of a short preexisting primer strand of DNA or RNA.

Question 12

Holliday structure

Answer 12

An intermediate in DNA recombination with

four DNA strands. (Figure 5-42)

Question 13

leading strand

Answer 13

One of the two daughter DNA strands formed at
a replication fork by continuous synthesis in the 5’ - 3’ direction. The direction of leading-strand synthesis is the same as movement of the replication fork. (Figure 5-29)

Question 14

lagging strand

Answer 14

One of the two daughter DNA strands formed at
a replication fork as short, discontinuous segments (Okazaki fragments), which are synthesized in the 5’ - 3’ direction and later joined. (Figure 5-29)

Question 15

Okazaki fragments

Answer 15

Short (<1000 bases), single-stranded DNA
fragments that are formed during synthesis of the lagging strand in DNA replication and are rapidly joined by DNA ligase to form a continuous DNA strand. (Figure 5-29)

Question 16

phosphodiester bond

Answer 16

Chemical linkage between adjacent nucleotides in DNA and RNA; consists of two phosphoester bonds, one on the 5’ side of the phosphate and another on the 3’ side.
(Figure 5-2)

Question 17

reading frame

Answer 17

The sequence of nucleotide triplets (codons) that
runs from a specific translation start codon in an mRNA to a stop codon. Some mRNAs can be translated into different polypeptides by reading in two different reading frames. (Figure 4-18)

Question 18

primer

Answer 18

A short nucleic acid sequence containing a free 39-hydroxyl group that forms base pairs with a complementary template strand and functions as the starting point for addition of nucleotides to copy the template strand.

Question 19

retroviruses

Answer 19

Type of eukaryotic virus containing an RNA genome
that replicates in cells by first making a DNA copy of the RNA. This viral DNA is inserted into cellular chromosomal DNA, forming a provirus, and gives rise to further genomic RNA as well as the mRNAs for viral proteins. (Figure 5-48)

Question 20

double helix

Answer 20

The most common three-dimensional structure for cellular DNA in which the two polynucleotide strands are antiparallel and wound around each other with complementary bases hydrogen-bonded. (Figure 5-3)

Question 21

gene conversion

Answer 21

A type of DNA recombination in which one DNA sequence is converted to the sequence of a second homologous DNA sequence in the same cell.

Question 22

genetic code

Answer 22

The set of rules whereby nucleotide triplets (codons)

in DNA or RNA specify amino acids in proteins. (Table 5-1)

Question 23

isoform

Answer 23

One of several forms of the same protein whose amino
acid sequences differ slightly and whose general activities are similar. Isoforms may be encoded by different genes or by a single gene whose primary transcript undergoes alternative splicing.

Question 24

mRNA (messenger RNA)

Answer 24

Any RNA that specifies the order of amino acids in a protein (i.e., the primary structure). It is produced
by transcription of DNA by RNA polymerase. In eukaryotes, the initial RNA product (primary transcript) undergoes processing to yield functional mRNA. (Figure 5-15)

Question 25

mutation

Answer 25

In genetics, a permanent, heritable change in the nucleotide sequence of a chromosome, usually in a single gene; commonly
causes an alteration in the function of the gene product.

Question 26

polyribosome

Answer 26

A complex containing several ribosomes, all translating a single messenger RNA; also called polysome. (Figure
5-27)

Question 27

promoter

Answer 27

DNA sequence that determines the site of transcription

initiation for an RNA polymerase. (Figure 5-11)

Question 28

recombination

Answer 28

Any process in which chromosomes or DNA molecules are cleaved and the fragments are rejoined to give new combinations. Homologous recombination occurs during meiosis, giving rise to crossing over of homologous chromosomes. Homologous recombination and nonhomologous recombination (i.e., between chromosomes of different morphologic type) also occur during several DNA-repair mechanisms and can be carried out in vitro with purified DNA and enzymes.
(Figure 6-10)

Question 29

replication fork

Answer 29

Y-shaped region in double-stranded DNA at which the two strands are separated and replicated during DNA
synthesis; also called growing fork. (Figure 5-29)

Question 30

reverse transcriptase

Answer 30

Enzyme found in retroviruses that catalyzes a complex reaction in which a double-stranded DNA is synthesized
from a single-stranded RNA template. (Figure 8-14)

Question 31

rRNA (ribosomal RNA)

Answer 31

Any one of several large RNA molecules that are structural and functional components of ribosomes. Often designated by their sedimentation coefficient: 28S, 18S,
5.8S, and 5S rRNA in higher eukaryotes. (Figure 5-22)

Question 32

ribosome

Answer 32

A large complex comprising several different rRNA
molecules and as many as 83 proteins, organized into a large subunit and small subunit; the engine of translation (protein synthesis). (Figures 5-22 and 5-23)

Question 33

RNA polymerase

Answer 33

An enzyme that copies one strand of DNA (the template strand) to make the complementary RNA strand using as substrates ribonucleoside triphosphates. (Figure 5-11)

Question 34

transcription

Answer 34

Process in which one strand of a DNA molecule is used as a template for synthesis of a complementary RNA by
RNA polymerase. (Figures 5-10 and 5-11)

Question 35

transfer RNA (tRNA)

Answer 35

A group of small RNA molecules that function as amino acid donors during protein synthesis. Each tRNA becomes covalently linked to a particular amino acid,
forming an aminoacyl-tRNA. (Figures 5-19 and 5-20)

Question 36

translation

Answer 36

The ribosome-mediated assembly of a polypeptide whose amino acid sequence is specified by the nucleotide sequence in an mRNA. (Figure 5-17)

Question 37

excision-repair system

Answer 37

One of several mechanisms for repairing DNA damage due to spontaneous depurination or deamination
or exposure to carcinogens. These repair systems normally operate with a high degree of fidelity and their loss is associated
with increased risk for certain cancers.

Question 38

Double-stranded break

Answer 38

Form of DNA damage where both phosphate-sugar backbones of the DNA are severed.

Question 39

What difference between RNA and DNA helps to explain the greater stability of DNA? What implications does this
have for the function of DNA?

Answer 39

RNA is less stable chemically than DNA because of the presence of a hydroxyl group on C-2 in the ribose moieties in the backbone.
Additionally, cytosine (found in both RNA and DNA) may be deaminated to give uracil. If this occurs in DNA, which does not normally contain uracil, the incorrect base is recognized and repaired by cellular enzymes.
In contrast, if this deamination occurs in RNA, which normally contains uracil, the base substitution is not corrected.
Thus, the presence of deoxyribose and
thymine make DNA more stable and less subject to spontaneous changes in nucleotide sequence than RNA. These properties might explain the use of DNA as a long-term information-storage molecule.

Question 40

What are the major differences in the synthesis and structure of prokaryotic and eukaryotic mRNAs?

Answer 40

In prokaryotes, many protein-coding genes are clustered in operons where transcription proceeds from a single promoter that gives rise to one mRNA encoding
multiple proteins with related functions. In contrast, eukaryotes do not have operons but do transcribe intron sequences that must be spliced out of mature
mRNAs. Eukaryotic mRNAs also differ from their prokaryote counterparts in that they contain a 5’ cap and 3’ poly(A) tail. Also, ribosomes have immediate
access to nascent mRNAs in bacteria so that translation begins as the mRNA is being synthesized. In contrast, in eukaryotes, mRNA synthesis occurs in the nucleus, whereas translation by ribosomes occurs in the cytoplasm. Consequently, only fully synthesized and processed mRNAs are translated in eukaryotes.

Question 41

What is an operon? What advantages are there to having genes arranged in an operon, compared with the arrangement in eukaryotes?

Answer 41

An operon is an arrangement of genes in a functional group that are devoted to a single metabolic purpose. In the case of tryptophan synthesis, the DNA for five
genes is arranged in a contiguous array that gets transcribed from a single promoter into a continuous strand of mRNA encoding fi ve proteins. In this manner,
the cell simply has to induce one promoter, which transcribes all the necessary genes encoding the proteins (enzymes) to make the amino acid tryptophan.
Splicing out intronic sequences or transcribing multiple mRNAs from genes on different chromosomes, as seen in eukaryotic systems, is unnecessary; thus, operons
are a logical way to economize on the amount of DNA needed by genes to encode a number of proteins. In addition, this arrangement allows all the genes
in an operon to be coordinately regulated by controlling transcription initiation from a single promoter.

Question 42

How would a mutation in the poly(A)-binding protein
gene affect translation? How would an electron micrograph of polyribosomes from such a mutant differ from the normal pattern?

Answer 42

Since poly(A)-binding protein is involved in increasing the effi ciency of translation, a mutation in poly(A)-binding protein would cause less effi cient translation. Polyribosomes in a cell with such a mutation would not contain circular structures of mRNAs during translation because lack of the poly(A)-binding protein would eliminate the 3’ binding site for eIF4G.

Question 43

What excision-repair system corrects thymine-thymine dimers that form as a result of UV light damage to DNA?

Answer 43

Nucleotide excision repair