Point mutation
A single-base change in the DNA sequence.
Frameshift mutation
Insertion or deletion of nucleotides, causing a shift in the reading frame.
Forward mutation
Changes a wild-type gene to a mutant phenotype.
Back mutation
Reverses an earlier mutation at the same site.
Suppressor mutation
Compensates for the effects of a previous mutation at a different site.
Silent mutation
A mutation that doesn't alter the encoded amino acid.
Know the difference between a transition and a transversion, including which is more common
Transition: Purine-to-purine or pyrimidine-to-pyrimidine substitution.
Transversion: Purine-to-pyrimidine or pyrimidine-to-purine substitution.
Transitions are more common than transversions.
Name two types of frameshift mutation
Insertion: Adds nucleotides, shifting the reading frame.
Deletion: Removes nucleotides, shifting the reading frame.
Compare and contrast back mutation and suppressor
Back mutation reverses the original mutation at the same site, while suppressor mutation compensates for the original mutation at a different site.
Understand why a neutral substitution is considered a silent mutation
A neutral substitution doesn't change the amino acid sequence due to redundancy in the genetic code, making it silent at the phenotypic level.
Genome
The complete set of genes present in an organism's DNA.
Transcriptome
The complete set of RNA molecules transcribed from the genes in a cell, tissue, or organism.
Proteome
The complete set of proteins encoded by the genome or produced by a cell, tissue, or organism.
Ortholog
Genes in different species that evolved from a common ancestral gene by speciation.
C-value
The total amount of DNA in a haploid genome.
Know the estimated number of genes encoded in the human genome
Approximately 20,000 genes
Describe the difference between repetitive and nonrepetitive genomic DNA
Nonrepetitive DNA consists of unique sequences that appear only once in the genome, typically encoding protein-coding genes.
Repetitive DNA consists of sequences that appear multiple times in the genome, classified as moderately repetitive (10-1,000 times) or highly repetitive (1,000s of times).
Discuss if (1) genome size and (2) organism complexity are correlated to the number of genes in eukaryotes
Genome size (in base pairs) does not always correlate with the number of genes.
There is a positive correlation between organism complexity and the number of genes.
Explain the C-value paradox
Lack of a clear relationship between genome size (C-value) and organism complexity. Despite variations in genome size, organisms of similar complexity may have vastly different amounts of DNA.
GWAS
Genome-wide association studies (GWAS) examine the entire genome to find genetic variations associated with traits or diseases.
Polymorphism
The presence of multiple alleles at a specific locus in a population.
SNP
Single nucleotide polymorphism (SNP) is a variation in a single nucleotide base in DNA.
Explain why SNPs are essential to perform GWAS
SNPs serve as genetic markers, helping researchers identify regions of the genome linked to traits or diseases
Know what data from GWAS can tell you (and what it can’t)
GWAS can identify associations between specific SNPs and traits or diseases, but it cannot directly pinpoint the specific genes involved
Understand the potential clinical impacts of GWAS
GWAS can lead to the discovery of new diagnostic markers and personalized treatment approaches based on individuals' genetic profiles.
Origin of Replication
The site on a chromosome where DNA replication begins.
Replication Fork
A Y-shaped structure formed during DNA replication where the double helix is unwound and new DNA strands are synthesized.
RNA Primer
A short chain of RNA that initiates DNA replication by providing a free 3’ -OH end for DNA polymerase to add nucleotides onto
DNA Polymerase
An enzyme responsible for synthesizing new DNA strands by adding nucleotides in a complementary fashion to the template strand
DNA Helicase
An enzyme that unwinds and separates the DNA double helix during replication
DNA Primase
An enzyme that synthesizes RNA primers needed to initiate DNA replication
DNA Ligase
An enzyme that joins Okazaki fragments on the lagging strand during DNA replication
Topoisomerase
An enzyme that relieves the tension caused by DNA unwinding during replication by making small cuts in the DNA strands
SSB Proteins
Single-strand DNA-binding proteins that stabilize single-stranded DNA during replication, preventing them from reannealing.
Semi-conservative Replication
The mechanism of DNA replication where each parental strand serves as a template for the synthesis of a new complementary strand
What allows DNA replication to happen quickly in our cells?
Replication can be fast because it is semi-conservative, initiated at multiple origins, and proceeds bidirectionally from each origin
What are the molecular events during the initiation, elongation, and termination phases of replication?
Initiation involves DNA helicase unwinding DNA, single-strand DNA-binding protein keeping strands separate, and topoisomerase relieving tension. Elongation includes DNA polymerase synthesizing DNA, exonuclease activity proofreading, and DNA ligase sealing fragments. Termination involves completion of replication
How and why does DNA replication differ on the leading and lagging strands?
The leading strand is made continuously in the 5’ to 3’ direction, while the lagging strand is made discontinuously in short fragments (Okazaki fragments) in the 3’ to 5’ direction
What is the Telomere Problem and its biological solution?
The Telomere Problem refers to the shortening of telomeres during replication, leading to cell aging. Telomerase is the enzyme that replicates telomeres, preventing their shortening and enabling cells to continue dividing.
List the (5) components of a PCR and what they do in the reaction
DNA Template: Target DNA sequence for amplification.
Primers: Bind to flanking sequences for DNA synthesis initiation.
dNTPs: Building blocks for DNA synthesis.
DNA polymerase: Catalyzes DNA strand synthesis.
Buffer (+ Mg2+): Provides optimal reaction conditions.
Explain what happens during the denaturation, annealing, and extension steps of a PCR cycle
Denaturation: 95°C for 15-30 seconds
Annealing: 50-65°C for 30-60 seconds
Extension: 72°C for 1 minute/kb
Compare and contrast PCR and DNA replication
PCR: Amplifies specific DNA sequence, uses synthetic primers, occurs in vitro
DNA replication: Copies entire genome, uses RNA primers, occurs in vivo
recombinant DNA
artificial DNA molecules made by combining 2+ pieces of DNA from different sources
vector
plasmid used to replicate a cloned DNA segment
insert
fragment of DNA that is to be cloned
restriction enzyme
endonuclease that ‘cuts’ a specific DNA sequence
blunt end
a DNA cutting result where both strands of the DNA molecule are cleaved at the same point, producing ends with no overhanging nucleotides, resulting in a flat or blunt terminus.
sticky end
DNA cut, leaves overhang, can bind with complementary sequence.
multiple cloning site (MCS)
Region with many unique restriction sites (cut sites)
•Allows ‘easy’ insertion of gene of interest
Know the function of the ori
Allows plasmid to replicate in the host
Know the function of Selection markers
Gene that allows cell to survive under specific selection conditions
•Ex. antibiotic resistance gene
Allows you to pick out bacteria that carry your vector
Know the function of MCS in a cloning vector
Region with many unique restriction sites (cut sites)
Allows ‘easy’ insertion of gene of interest
Explain how you can verify your gene of interest was successfully incorporated into a vector
Transform cells, plate on antibiotic media.
White colonies indicate successful ligation (recombinant plasmid), blue colonies indicate unsuccessful ligation (non-recombinant plasmid).
Understand what you can study ask using (1) an expression vector and (2) a reporter gene
Produces proteins for commercial use
Studies promoter activity in vivo.
Discuss several ways vectors can be introduced into different target cells
Heat shock, electroporation, chemical transformation.
DNA profiling
Analysis of specific DNA regions to create unique genetic fingerprints.
minisatellite
DNA sequences with repeats of 10bp – 1000bp
Microsatellite
DNA sequences with repeats of 2-10bp
Explain why microsatellites/minisatellites are useful in DNA profiling
Variation in repeat number creates unique genetic profiles.
Enables accurate identification and differentiation between individuals.