DNA Synthesis, Gene Expression, and Mutation

Question 1

What is the central dogma of genetics?

Answer 1

genetic information flows in one direction:
1. from DNA
2. transcripted into RNA
3. translation to amino acids and then proteins

Question 2

What are the four characteristics of genetic material?

Answer 2

1. replication
2. storage of information
3. expression of information
4. variation by mutation

Question 3

What is recombinant DNA technology?

Answer 3

• splicing together DNA sequences from different organisms

Question 4

What are the components of nucleotides or nucleic acid molecules?

Answer 4

a nitrogenous base, pentose sugar, and phosphate group

Question 5

What differentiates purines from pyrimidines?

Name the 4 nucleic bases and classify them.

Answer 5

• purines have nine double rings (Adenine and Guanine)
• pyrimidines have six single rings (Cytosine, thymine, and uracil - RNA only)

Question 6

What is the difference in the chemical makeup of DNA vs RNA?

Answer 6

• DNA contains deoxyribose
• RNA contains ribose

Question 7

What is semiconservative replication?

Answer 7

DNA is produced by semiconservative replication, which means each new DNA molecule consists of one old and one new strand
* the unwound helix attracts its complementary nucleotide

Question 8

what is a replication fork?

Answer 8

• the point along the chromosome where replication is occurring
• strands are unwound
• appears at the point of origin of synthesis, then moves along the DNA duplex as replication proceeds

Question 9

What is a replicon?

Answer 9

the length of DNA that is replicated following one initiation event at a single origin

Question 10

Is replication unidirectional or bidirectional?

- one direction or in both directions away from the origin?

Answer 10

• DNA replication is bidirectional
• creates two replication forks that move in opposite directions away from the origin of synthesis

Question 11

What can be used to relax supercoiling during the unwinding process of DNA?

Define supercoiling

Answer 11

• supercoiling: added twists and turns of DNA, caused by coiling tension ahead of the replication fork during unwinding
• DNA gyrase is an exyme that makes single- or double-stranded cuts and catalyzes localized movments that undo the twists and knots that are created during supercoiling

Question 12

What is the role of DNA helicase?

Answer 12

recruits the holoenzyme to bind to the newly formed replication fork to intiate replication
- then it proceeds to move along the ssDNA (single-stranded), opening up the helix as it progresses

Question 13

What is the DNA Polymerase III Holoenzyme?

Answer 13

• made up of polypeptide subunits
• the subunits each have different jobs:
• DNA synthesis along template strands
• proofreading
• contains a sliding DNA clamp: encircles the duplex DNA, binds to the DNA polymerase and clamps them together

Question 14

What is primase?

Answer 14

• an RNA primer
• does not require a 3’-end to initaite synthesis
• builds a primer of RNA to the DNA template for polymerase III to add deoxyribonucleotides
• the RNA primer is later clipped out and replaced with DNA

Question 15

What is the difference between a lagging and leading strand in DNA synthesis?

Answer 15

• leading strand is the newly synthesized DNA, runs in the 3’ to 5’ direction
• lagging strand runs on the opposite strand, and needs multiple primers to continue running in the 3’ to 5’ direction

Question 16

What enzyme joins fragments of DNA once RNA primers are removed and Okazaki fragments are united?

Occurs on the lagging strand.

Answer 16

DNA ligase

Question 17

What are DNA polymerases?

Answer 17

DNA polymerases are enzymes (proteins) involved in DNA synthesis (elongation or polymerization).

Question 18

What do DNA polymerases I, II, and III require to elongate a DNA strand?

Answer 18

Apart from the appropriate temperature and environment, DNA polymerases require:
all four bases (in the form of deoxyribonucleoside triphosphates: dATP, dTTP, dGTP, and dCTP) and
a DNA template.

Question 19

What is the role of RNA in DNA synthesis?

Answer 19

None of the DNA polymerases I, II, or III can initiate synthesis although they can elongate an already existing strand, called a primer. The strand they use is, in fact, an RNA strand copied from the DNA template by the enzyme RNA primase, an RNA polymerase that does not require a free 3’ end to initiate synthesis, as do DNA polymerases.

Question 20

What is the template and coding strand in RNA transcription?

Answer 20

• the template strand is the DNA strand that serves as a template for RNA polymerase
• the coding strand is the complementary DNA strand.

Question 21

What are introns?

Answer 21

nucleotide sequences that intervene between sequences that code for amino acids
(do not code for anything)

Question 22

What are exons?

Answer 22

sequences that are expressed in RNA
some are coding, some are non-coding

Question 23

What is RNA splicing?

Answer 23

the process of remvoing introns form a pre-mRNA and joining together exons

Question 24

What do the abbreviations STR and VNTR stand for?

Answer 24

STR: Simple tandem repeat.

VNTR: Variable number tandem repeat.

Question 25

Name three disorders found in humans and due to an abnormal increase in the number of trinucleotide repeats.

Answer 25

Fragile X syndrome, Huntington disease, Myotonic dystrophy, and Kennedy disease.

Question 26

What is a point mutation?

Answer 26

a change of one base pair to another
a.k.a base substitution

Question 27

What is a missense mutation?

Answer 27

a change of one mucleotide of a tripelt within a protein-coding portion of a gene that results in the creation of a new triplet that codes for a different amino acid in the protein product

Question 28

What is a nonsense mutation?

Answer 28

When a nucleotide changes in a triplet that codes for a stop codon, resulting in the termination of translation of the portein

Question 29

What is a silent mutation?

Answer 29

a point mutation that alters a codon but does not change the amino acid at that position in the protein

Question 30

What is a transition? What is a transversion?

Answer 30

transition: when a pyrimidien replaces a pyrimidine or a purine replaces a purine
transversion: when a purine replaces a pyrimidine or vice versa.

Question 31

What is a frameshift mutation?

Answer 31

the insertion or deletion of one or more nucleotides at any point within the gene
- causes the frame of triplet reading during translation to be alteted

Question 32

What is a null mutation?

Answer 32

a mutation that results in a complete loss of function

Question 33

What is a recessive mutation?

Answer 33

• results in a wild-type phenotype when present in a diploid organism and the other allele is wild type
• most loss-of-function mutations are recessive

Question 34

What is a dominant mutation?

Answer 34

• results in a mutant phenotype in a diploid organism, even when the wild-type allele is present

Question 35

What is a dominant negative mutation?

Answer 35

• can interfere with the function of the product of the wild-type allele
• can reuslt from haploinsufficiency: occurs when one allele is inactivated by mutant, leading the individual with only one functional copy of a gene

Question 36

What is a suppressor mutation?

Can be intragenic or intergenic - describe both

Answer 36

• a second mutation that either reverts or relieves the effects of a previous mutation
• intragenic mutations are suppressor mutations that occur within the same gene that suffered the first mutation
• intergenic mutations are suppressor mutations that occur elsewhere in the genome

Question 37

What is the difference between spontaneous and induced mutations?

Answer 37

• spontaneous mutations occur naturally. There are no specific agents associated with their occurance
• induced mutations may be the result of natural or artificial agents (radiation, mineral sources etc.)

Question 38

What are mutation hot spots?

Answer 38

DNA sequences that appear to be highly susceptible to mutation

Question 39

What is a polygenic disease?

Answer 39

Variations caused by several genes

Question 40

What is a monogenic disease

Answer 40

caused by single-gene mutations

Question 41

Give an example of disorders for the following types of mutations:
- missense
- nonsense
- insertion
- deletion
- trinucleotide repeat expansions

Answer 41

• achondroplastia
• Marfan syndrome
• Familial hypercholesterolemia
• Cystic fibrosis
• Huntington disease

Question 42

What is a trinucleotide repeat?

Answer 42

• 3 nucleotides consecutively repeated
• they are fragile sites
• recognized in many disorders

Question 43

What are endonuclease and exonuclease enzymes?

Answer 43

they are repair enzymes that removed incorrect nucleotides and insert the correct one.
endonuclease: creaks a nick in the backbone of the newly synthesized DNA strand
exonuclease: unwinds and degrades the nicked strand until the regio of the mismatch is reaches

Question 44

What are transposable elements?

Answer 44

• known as “jumping genes”
• DNA sequences that can move or transpose within and between chromosomes
• range from 50 to 10,000 base pairs in length

Question 45

What are DNA transposons?

Answer 45

they move from one location to another without going through an RNA intermediate stage
* abundant in many organisms including humans and bacteria

Question 46

What is Crick’s wobble hypothesis?

Answer 46

the prediction that the intitial two ribonucleotides of triplet codes are more critical than the third in attracting the correct tRNA during translation
- makes for a flexible set of base-pairing rules at the third position of the codon
- e.g. GCU, GCA, GCC, GCG all code for Ala

Question 47

What is the “new dogma”?

Answer 47

sequence implies structure, and structure implies function

Question 48

What is the protein structure?

Answer 48

B-pleated sheet
* single polypeptide chain folds back on itself, or several chains run in either parallel or antiparallel fashion next to one another
* each structure is stablized by H bonds