Unit 4- Ch. 18-20, 25-26 Flashcards
Define mutation
an inherited change in DNA sequence of genetic information; the descendants that inherit the change may be cells or organism
Define base substitution
simplest type of gene mutation; the alteration of a single nucleotide in the DNA
What are the two types of base substitutions?
transitions and transversions
Differentiate between transitions and transversions
TRANSITIONS:
-a purine is replaced by a different purine (or pyrimidine by another pyrimidine)
TRANSVERSION:
-a purine is replaced by a pyrimidine (or pyrimidine replaced by purine)
Define insertions and deletions and state what type of mutation these cause
insertion: addition of one or more nucleotide pairs
deletion: removal of one or more nucleotide pairs
frameshift mutation: changes in the reading frame of the gene
Define in-frame insertions and deletions and describe how they arise
indels that do not affect the reading frame
result from insertion/deletion of three nucleotides leave the reading frame intact
Define expanding nucleotide repeats
mutations in which the number of copies of a set of nucleotides increases
Explain how strand slippage can cause expansion of nucleotide repeats
expansion of nucleotide repeats occurs in the course of DNA replication and appears to be related to the formation of hairpins and other secondary structures that form in single-stranded DNA consisting of nucleotide repeats
–> such structures may interfere with normal replication by causing strand slippage, misalignment of the sequences, or stalling of replication
Explain how expanding nucleotide repeats correspond to anticipation
the number of copies of the repeat often correlates with the severity or age of onset of the disease
number of copies of repeats correlates with its instability
anticipation: diseases caused by expanding nucleotide repeats become more severe in each generation
Define and describe 3 effects base substitutions can have on the amino acid sequence
- MISSENSE MUTATION: a base substitution that results in a different amino acid in the protein
- NONSENSE MUTATION: changes a sense codon (one that specifies an AA) into a nonsense codon (one that terminates translation)
- SILENT MUTATION: changes a codon to a synonymous codon that specifies the same amino acid, altering the DNA sequence without changing the amino acid sequence of the protein
Differentiate between forward mutation and reverse mutation
forward mutation: a mutation that alters the wild-type phenotype
reverse mutation: changes a mutant phenotype back to the wildtype
Define neutral mutation
a missense mutation that alters the amino acid sequence of a protein but does not significantly change its function
Define loss-of-function mutation
cause the complete or partial absence of normal protein function; alters the structure of the protein so that it no longer works correctly
Define gain-of-function mutation
causes the cell to produce a protein or gene product whose function is not normally present; result could be an entirely new gene product or one produced in an inappropriate tissue or at an inappropriate time in development
Define conditional mutation
expressed only under certain conditions
EX: elevated temperatures
Define lethal mutation
cause premature death
Define suppressor mutation
a genetic change that hides or suppresses the effect of another mutation
occurs at a site distinct from the site of the original mutation; thus an individual with a suppressor mutation is a double mutant (both the original mutation and the suppressor mutation but exhibiting the phenotype of the nonmutated wildtype)
Differentiate between intragenic and intergenic suppressor mutations
INTRAGENIC: intragenic suppressor mutation: takes place in the same gene that contains the mutation being suppressed
INTERGENIC: intergenic suppressor mutation: occurs in a gene other than the one bearing the original mutation that it suppresses
How does intragenic suppresor mutations occur?
how it works:
1. may change a second nucleotide in the same codon altered by the original mutation
- may work by suppressing a frameshift mutation
–> if the original mutation is a one-base deletion, then the addition of a single base elsewhere in the gene will restore the former reading frame - may work by making compensatory changes in the protein
How does intergenic suppresor mutations occur?
how it works:
1. changing the way the mRNA is translated
2. can also work through gene interaction
Differentiate between spontaneous and induced mutations
spontaneous mutations: mutations that occur under normal conditions
induced mutations: mutations that result from changes caused by environmental chemicals or radiation
How does strand slippage causes insertions/deletions and nucleotide repeat expansion
strand slippage can occur when one nucleotide strand forms a small loop
if the looped-out nucleotides are on the newly synthesized strand, an insertion results
–> at the next round of replication, the insertion will be replicated and both strands will contain the insertions
if the looped-out nucleotides are on the template strand, then the newly replicated strand will have a deletion, and this deletions will be perpetuated in subsequent rounds of replication
How does unequal crossing over causes insertions/deletions
misaligned pairing can cause unequal crossing over which results in one DNA molecule with an insertion and the other with a deletion
How does depurination cause base substitutions
a spontaneous chemical change
depurination: the loss of a purine base from a nucleotide
–> An apurinic site (lack purine) cannot act as a template for a complementary base in replication
–>in the absence of base-pairing constraints, an incorrect nucleotide (usually A) is incorporated into the newly synthesized DNA strand opposite to the apurinic site (incorporated error)
How does base analogs cause mispairing during replication
base analogs is a chemical mutagen
base analogs: chemicals with structures similar to those of any of the four standard nitrogenous bases of DNA
–> DNA polymerase cannot distinguish these analogs from the standard bases, so if base analogs are present during replication, they may be incorporated into the newly synthesized DNA molecules
how do intercalating agents result in frameshift mutations and know that ethidium bromide is a type of intercalating agent
intercalating agents: produce mutations by sandwiching themselves (intercalating) between adjacent bases in DNA, distorting the 3D structure of the helix and causing single-nucleotide insertions and deletions in replication
these insertions/deletions frequently produce frameshift mutations
Name 2 types of radiation and briefly explain the types of mutations they cause
Ionizing radiation (X-rays, gamma rays, and cosmic rays) are all capable of penetrating tissues and damaging DNA
- ionizing radiation frequently results in double-stand breaks in DNA
- attempts to repair these breaks can produce chromosome mutations
Define transposable element (also called transposons)
DNA sequences that can jump about in the genome - are often a cause of mutations
Know that transposons can cause ——- mutations and ————- rearrangements
gene, chromosome
Know that there are several mechanisms that repair different types of errors and there is overlap between the mechanisms with respect to the types of mutations they repair
DNA is constantly under assault from radiation, chemical mutagens, and spontaneously arising changes.
In spite of these damaging agents, the rate of mutation remains remarkably low, thanks to the efficiency with which DNA is repaired
Describe how restriction enzymes can be used to create recombinant DNA
Describe how CRISPR-Cas9 is used for genome editin
-Scientists have engineered crRNA from bacteria with a sequence that is specific to the target sequence of interest
-The other part of the crRNA contains a sequence that pairs with CAS9 protein = crRNA/Cas9 complex
-This complex finds and binds to the target DNA sequence
-Cas9 makes double-stranded cuts within the target DNA sequence
-The cell’s DNA repair mechanisms kick in to try to repair the cut—2 things can happen
1. Nonhomologous end joining is a repair pathway that repairs chromosome breaks but often causes inserts/deletions within the process—this would inactivate the gene
2. Donor DNA can be inserted into the cell with ends complementary to the break sequence—homologous recombination would insert this sequence to repair the gene
How is gel electrophoresis used to separate DNA fragments by size
List the 5 components of a PCR reaction
Explain the steps in a PCR cycle
Define gene cloning and know the process for cloning a gene in bacteria
How can a foreign DNA fragment can be inserted into a plasmid
Define transformation
Explain how to use selectable markers to identify recombinant cells
Describe how next-generation sequencing works, specifically Illumina sequencing
Define DNA fingerprinting
What type of sequence that is analyzed in DNA fingerprinting
How does DNA fingerprinting works
Describe how RNAi could be used to turn off a gene
Differentiate between genetic maps and physical maps
List some problems associated with sequencing of an entire genome
Define Single Nucleotide Polymorphisms and haplotype
Explain how SNPs can be used for genome-wide association studies
Describe how bioinformatics can be used to identify a gene
Define annotation as it applies to bioinformatics
Define metagenomics and briefly explain why this field exists
Define homology search and explain how this can be used to understand the function of a gene
Differentiate between ortholog and paralog
List 2 techniques that can be used to study the expression of a gene
Describe how microarrays can be used to examine gene expression
Describe the process of RNA Seq
-Collect total RNA from cells
-Isolate mRNA
-Reverse transcribe into cDNA
-Fragment cDNA
-Sequence with next-gen sequencing
-Assemble sequences into RNA transcripts
Define evolution and explain the 2 steps involved
Explain how we observe genetic variation today
Describe the biological species concept
Define reproductive isolating mechanisms
Differentiate between prezygotic and postzygotic reproductive isolating mechanisms
List and describe the 5 types of prezygotic reproductive isolating mechanisms
List and describe the 3 types of postzygotic reproductive isolating mechanisms
Define speciation
List and define the two principle modes of speciation
Define phylogeny, phylogenetic tree, branches, nodes, rooted, and gene tree
Understand Figure 26.16
