Cell and Molec Lecture Exam 3

Question 1

How could a gene get duplicated?

Answer 1

replication of DNA

Question 2

Why does gene duplication not solve the problem of the origin of the first version of the gene?

Answer 2

There had to be an original DNA to be duplicated

Question 3

In an organism, what cell lineages will enable mutations to be carried to the offspring?

Answer 3

Germ line cells must be altered to affect the offspring

Question 4

The textbook argues the the globin gene family arose through duplication, what is an alternative explanation from a design perspective?

Answer 4

Common design over common descent. God found a good way that something works and chose to use it over again in multiple species

Question 5

What is exon shuffling and why is it used to try to explain the formation of new genes?

Answer 5

-Exon Shuffling: mechanism for the evolution of new genes; in the process, coding sequences from different genes are brought together to generate a protein with a new combination of domains
-Domains exist that are found in multiple genes and these domains can be shuffles around in the genome

Question 6

What is common ancestry? What do evolutionists look at to determine how closely related two genes or organisms might be?

Answer 6

-Common Ancestry: a method to determining lineage that is based on similarity?
-Evolutionists look at the percentage of the genome that is shared between two species

Question 7

What are mobile genetic elements? Why do some scientists believe these came from viruses?

Answer 7

-Mobile Genetic Elements: short segment of DNA that can move, sometimes through an RNA intermediate, from one location in a genome to another; an important source of genetic variation in most genomes
-Scientists believe that these came from viruses as they are able to move from one cell to another?

Question 8

What are some roles of mobile genetic elements?

Answer 8

-Encode the components they need for movement
-Using cut-and-paste transposition and replicative transposition
-Contain two major families of transposable sequences
-Viruses can move between cells and organisms
-Retroviruses reverse the normal flow of genetic information

Question 9

How much of the human genome is unique vs. repetitive sequences?

Answer 9

-Approximately 50% of the genome is in a high copy repetitive sequences
-50% of the human genome is unique sequences

Question 10

How much of the human genome encodes proteins?

Answer 10

-approximently 19,000 genes

Question 11

How much do humans typically differ from one another genetically?

Answer 11

-approximately 0.1%

Question 12

What is the difference between exogenous and endogenous DNA damage factors? Give an example.

Answer 12

-Exogenous Factors: factors that originate externally
-Example: environmental factors
-Endogenenous Factors: factors that originate internally
-Example: oxygen radicals, replication errors

Question 13

What happens to a cell if the DNA damage can be repaired? What happens if the damage cannot be repaired?

Question 14

What is a transition mutation?

Answer 14

a point mutation when a pyrimidine substitutes for another pyrimidine OR a purine substitutes for another purine

Question 15

What is a transversion mutation?

Answer 15

a point mutation when a pyrimidine substitutes for a purine or vice versa

Question 16

What does it mean for something to alkylate DNA?

Answer 16

it refers to the addition of an alkyl group

Question 17

What is a DNA intercalator?

Answer 17

binds DNA and inserts itself into the DNA structure

Question 18

What types of mutation can result from UV damage?

Answer 18

Pyrimidine (thymine) dimers

Question 19

What is a translocation?

Answer 19

-swapping of chromosome segments after a double strand break
-In this case, the repair process incorrectly fuses chromosome break
-Some translocations lead to cancer

Question 20

In genetics, what is the difference between a polymorphism and a mutation?

Answer 20

-Polymorphism: is a variation in the DNA sequence that is present at an allele frequency of 1% or greater in a population
-2 Major Types:
-Single Nucleotide Polymorphism (SNPs)
-Insertions/Deletions (Indels)

Question 21

What does the term indel mean?

Answer 21

-Insertion/Deletion
-Insertion: addition of an additional base pair or multiple base pairs
-Deletion: one or more base pairs are lost from DNA

Question 22

What does SNP mean?

Answer 22

-Single Nucleotide Polymorphisms
-The most common genetic variation
-There are an estimated 10-11 million common SNPs in human populations
-1 SNP for every 300 BP

Question 23

What is the difference between nonsynonymous, synonymous, and nonsense SNPs in coding regions?

Answer 23

-Nonsynonymous (missense)
-Amino acid substitiution
-Synonymous
-NO amino acid substition
-Nonsense
-STOP codon is created

Question 24

What are some locations were noncoding SNPs could occur?

Answer 24

-Intronic Regions: exon/intron boundaries (could affect splicing)
-Promoter Regions: could alter cis/trans acting elements that regulate gene transcription or regulate gene expression
-Intergenic Regions: could affect DNA tertiary structure, interaction with chromatin and topoisomerases, or DNA replication

Question 25

How could indels have little impact on a protein structure even if they are within the coding region?

Answer 25

-If there is a multiple of 3 then it will avoid a frameshift mutation which will minimize the impact on the protein structure

Question 26

What is the general process or steps of DNA repair?

Answer 26

1. Recognition of damage and removal/excision of damage
2. Replacement of DNA by polymerase
3. Ligation of nick by DNA ligase
   -Each process requires a series of enzymes

Question 27

What type of damage does base excision repair fix?

Answer 27

deamination of cytosine

Question 28

What type of damage does nucleotide exclusion repair fix?

Answer 28

thymine dimers, pyrimidine dimers (caused by UV light)

Question 29

What type of damage does nonhomologous end-joining fix and homologous recombination fix?

Answer 29

crosslinks or double strand breaks (chemicals, radiation, heat, oxidative reactions)

Question 30

What type of damage does mismatch repair fix?

Answer 30

mismatched base (misincorporation during synthesis)

Question 31

What mutation leads to cystic fibrosis? What does that change about the functioning of the protein?

Answer 31

-Delta F508
-is characterized by the deletion of the three base pairs in the CFTR nucleotide sequence, causing the loss of the amino acid phenylalanine located at the position 508
-CFTR protein opens channels in cell wall which release chloride ions out of cells. This causes osmosis to draw water out of the cell.
-This mutation can prevent CFTR from moving into its proper position in the cell

Question 32

What mutation leads to resistance to HIV?

Answer 32

CCR5 delta 32

Question 33

What is meant by CYP polymorphisims? How can these genetic differences affect drug metabolism?

Question 34

What are the implications of CYP polymorphisims on drug therapies given to different ethnic populations?

Question 35

What is precision medicine?

Answer 35

-Precision medicine: using all available information (from genome, blood and saliva, gut microbiome, and lifestyle) to improve the precision with which patients are catagorized for selection of the appropriate therapy or medical interventions

Question 36

How can genetic profiling help select the correct cancer drug therapy?

Answer 36

a targeted theraphy is a drug which is designed to work directly on a single protein or enzyme with the fewest possible side effects

Question 37

How are genetic profiling studies influencing drug development?

Answer 37

genetic studies are propelling the development of targeted therapies

Question 38

What are some factors that can contribute to variable drug response?

Answer 38

comedication, gender, body mass, age, environmental agents, disease, genetic factors, and diet

Question 39

Define pharmacogenetics and pharmacogene

Answer 39

-Pharmacogenetics: study of genetic influences on an individual’s response to drugs
-analysis of specific gene, or group of genes, may be used to predict responses to a specific drug or drug class
-Pharmacogene: any gene involved in the response to a drug
-Pharmacogenomics is the study of ALL genes involved in a response to a new drug

Question 40

How does CYP2D6 impact codeine metabolism? What effect does CYP2D6 polymorphisms have on drug metabolism?

Answer 40

-Codeine is a commonly used opiod that must be metabolized/bioactivated into morphine for activity
-CYP2D6 is the protein that performs this metabolism in the liver
-Patient who are deficient in 2D6 activity are bochemically unable to convert codeine into the active analog morphine
-They are likely to experience treatment failure
-pateints with the UM phenotype will convert codeine to morphine much more quicly than normal, resulting in higher exposure to morphine occurring more quickly
-has resulted in patient deaths

Question 41

What does it mean for something to be a poor, intermediate, extensive, or ultrarapid metabolizer?

Answer 41

-A person with two nonfunctional alleles at CYP2D6 is considered to have poor drug metabolism (PM)
-A person with one or two functional alleles is considered to have extensive metabolism (EM)
-One who has duplicated or amplified active CYP2D6 genes is considered to have ultrarapid metabolism (UM)

Question 42

What are some effects of genetic polymorphisms on expression of CYP genes?

Question 43

What are some lessons from pharmacogenetics?

Answer 43

-All drug effects vary from person to person and all drug effects are influenced by genes
-Most drug responses are multifactoral
-Genetic polymorphisms of single genes, including mutations in coding sequences, gene duplications, gene deletions and regulatory mutations affect numerous drug-metabolizing enzymes