Marshall's Genetics Final Exam

Q: What is the Central Dogma?

A: The Central Dogma of molecular biology describes the flow of genetic information: DNA → RNA → Protein.

Q: What are the types of RNA molecules?

-Messenger RNAs (mRNAs)

-Transfer RNAs (tRNAs)

-Ribosomal RNAs (rRNAs)

-Small nuclear RNAs (snRNAs)

-Micro RNAs (miRNAs)

mRNA

Intermediates that carry genetic information from DNA to the ribosomes

tRNA

Adaptors between amino acids and the codons in mRNA

rRNA

Structural and catalytic components of ribosomes

snRNA

Structural components of spliceosomes

miRNA

Short single stranded RNAs that block expression of complementary mRNAs

Q: What are general features of RNA synthesis?

Similar to DNA Synthesis except

-The precursors are ribonucleoside triphosphates.

-Only one strand of DNA is used as a template.

-RNA chains can be initiated de novo (no primer required)

-The RNA molecule will be complementary to the DNA template strand and identical (except that uridine replaces thymidine) to the DNA nontemplate strand.

-RNA synthesis is catalyzed by RNA polymerases and proceeds in the 5'➔3' direction.

Q: What is a transcription bubble?

A: A region of unwound DNA where RNA synthesis occurs, involving RNA polymerase and other transcription factors.

Q: What are the three stages of transcription in prokaryotes?

A: Initiation (RNA polymerase binds to the promoter), Elongation (RNA is synthesized), and Termination (transcription stops at the terminator sequence).

Q: What are the details of transcription and RNA processing in eukaryotes?

A: Transcription occurs in the nucleus and involves additional RNA processing, including capping, splicing, and polyadenylation.

Q: What are introns and exons?

A: Introns are non-coding regions of RNA that are removed during RNA splicing, while exons are coding regions that remain in the mature mRNA.

Q: What is splicing?

A: Splicing is the process of removing introns and joining exons together to form the mature mRNA.

Q: What are the differences in transcription between prokaryotes and eukaryotes?

A: In prokaryotes, transcription occurs in the cytoplasm and is coupled with translation, while in eukaryotes, transcription occurs in the nucleus and involves RNA processing before translation.

Three major differences between prokaryotic and eukaryotic transcription?

Transport mRNA

Prokayotes multigenic transcription units

Introns and exons in eukaryotes

Q: What is protein structure?

A: Proteins have four levels of structure: primary (amino acid sequence), secondary (alpha-helices and beta-pleated sheets), tertiary (3D shape), and quaternary (multiple polypeptide chains).

More on protein structure from slides

Proteins are complex macromolecules composed of 20 different amino acids.

Q: What are the macromolecules involved in translation?

◼ Polypeptides (> 50) and RNA molecules (3-5) of the ribosome

◼ Amino-acid Activating Enzymes (20)

◼ tRNA Molecules (40-60)

◼ Soluble proteins involved in polypeptide chain initiation, elongation, and termination

Q: How does the genetic code work?

A: The genetic code consists of codons (three-nucleotide sequences) that specify amino acids during protein synthesis.

Q: What are the general steps of translation?

A: 1) Initiation: Ribosome assembles at the start codon. 2) Elongation: tRNAs bring amino acids, and the polypeptide chain is extended. 3) Termination: Translation stops at the stop codon.

Translation

◼ Activating Enzymes prepare tRNA- tRNA attaches to specific amino acid - Met tRNA binds to small ribosomal subunit = initiation complex

◼ mRNA molecule binds to IC. Large ribosomal subunit binds to mRNA + IC.- Ribosome moves along mRNA three nucleotides (codon) at a time. • Start signal codon = AUG • Stop codons = UAA - UAG - UGA.

◼ tRNA - complimentary anticodon binds to exposed codon on mRNA. • Peptide bond formed between amino acids

◼ Genetic code is universal- Prokaryotes, eukaryotes, mitochondria, chloroplast

Q: What are the types of mutations?

A: Mutations can be point mutations (substitution), frameshift mutations (insertions or deletions), or chromosomal mutations (duplications, deletions, inversions, translocations).

Q: What are DNA repair mechanisms?

A: Repair mechanisms include proofreading by DNA polymerase, base excision repair, nucleotide excision repair, and mismatch repair.

Amino Acids

◼ Proteins are made of polypeptides.

◼ A polypeptide is a long chain of amino acids.

◼ Amino acids have a free amino group, a free carboxyl group, and a side group (R).

Peptide Bonds

◼ Amino acids are joined by peptide bonds.

◼ The carboxyl group of one amino acid is covalently attached to the amino group of the next amino acid.

Transfer RNAs (tRNAs)

◼ tRNAs are adapters between amino acids and the codons in mRNA molecules.

◼ The anticodon of the tRNA base pairs with the codon of mRNA.

◼ The amino acid is covalently attached to the 3' end of the tRNA.

◼ tRNAs often contain modified nucleosides.

Specificity of tRNAs

◼ tRNA molecules must have the correct anticodon sequence.

◼ tRNA molecules must be recognized by the correct aminoacyl-tRNA synthetase.

◼ tRNA molecules must bind to the appropriate sites on the ribosomes.

Germinal mutations

occur in germ-line cells and will be transmitted through the gametes to the progeny.

Somatic mutations

occur in somatic cells; the mutant phenotype will occur only in the descendants of that cell and will not be transmitted to the progeny.

Spontaneous mutations

occur without a known cause due to inherent metabolic errors or unknown agents in the environment.

Induced mutations

result from exposure of organisms to mutagens

mutagens

physical and chemical agents that cause changes in DNA, such as ionizing irradiation, ultraviolet light, or certain chemicals

synonymous mutation

A mutation that does not result in a different amino acid

non-synonymous mutation

a nucleotide mutation that alters the amino acid sequence of a protein

Transition mutation

purine to purine or pyrimidine to pyrimidine

Transversion mutation

A point mutation in which a pyrimidine is substitued for a purine, or vice versa.

DNA Repair Mechanisms in E. coli

Light-dependent repair (photoreactivation)

Excision repair

Mismatch repair

Postreplication repair

Error-prone repair system (SOS response)

Light-Dependent Repair

Photolyase Cleaves Thymine Dimers (thymine dimer is were they are glued together....?)

DNA repair endonuclease

recognizes, binds to, and excised the damaged base or bases.

DNA Polymerase

fills in the gap, using the undamaged complementary strand of DNA as a template.

DNA ligase

seals the break left by DNA polymerase

Q: How are genes amplified in vitro and in vivo?

A: In vitro amplification is done via PCR (Polymerase Chain Reaction), while in vivo amplification occurs through methods like cloning in bacteria.

Q: How do restriction enzymes work and what are they used for?

A: Restriction enzymes cut DNA at specific sequences, which are used in cloning, recombinant DNA technology, and creating genetic maps.

Q: What is gene cloning and recombinant DNA technology?

A: Gene cloning involves copying a gene in a host organism, and recombinant DNA technology combines DNA from different sources to create new genetic material.

Q: What are the steps of PCR (Polymerase Chain Reaction)?

A: Denaturation (DNA strands separate), Annealing (primers bind to the DNA), and Extension (DNA polymerase synthesizes the new strand).

Q: How is PCR used to sequence DNA?

A: PCR amplifies a target DNA region, which is then sequenced using methods like the Sanger method.

Q: What are the steps in automated DNA sequencing?

A: DNA is amplified, then sequenced using fluorescently labeled dNTPs, and the sequence is read via capillary electrophoresis.

Q: What are the differences between automated sequencing and traditional Sanger method?

A: Automated sequencing uses fluorescent labels and capillary electrophoresis for faster and more high-throughput sequencing than traditional Sanger sequencing.

Q: What is next/second-generation sequencing?

A: Next-generation sequencing allows massively parallel sequencing, enabling the sequencing of entire genomes quickly and cost-effectively.

Gene cloning

the isolation and amplification of a given gene

recombinant DNA molecule

a DNA molecule made by joining two or more different DNA molecules.

Restriction endonucleases

make site specific cuts in DNA.

restriction sites

The nucleotide sequences are called

methylation

how bacteria protect endogenous restriction sites

Restriction enzymes

prepare homogenous samples of specific segments of chromosomes

Gel electrophoresis

procedures able to resolve DNA fragments differing in length by a single nucleotide

Gene-cloning techniques

allowing preparation of large quantities of a DNA molecule

Q: What is epigenetics?

A: Epigenetics refers to changes in gene expression that do not involve changes to the DNA sequence, such as DNA methylation and histone modification.

Q: What is imprinting?

A: Imprinting is a process where the expression of a gene depends on whether it is inherited from the mother or father.

Q: What are methylation and acetylation?

A: Methylation involves adding a methyl group to DNA, silencing gene expression. Acetylation involves adding an acetyl group to histones, which generally promotes gene expression.

Q: What are microarrays and how do they work?

A: Microarrays are used to measure the expression levels of many genes simultaneously by hybridizing labeled cDNA to a grid of probes.

Q: What is the history of Pitcairn Island?

A: Pitcairn Island was settled by descendants of the HMS Bounty mutineers, and its population genetics provides insights into founder effects and genetic drift.

Q: What is the Hardy-Weinberg model/principle?

A: The Hardy-Weinberg equilibrium states that allele frequencies in a population will remain constant if certain conditions are met (no mutation, migration, natural selection, or genetic drift).

Q: What are the Hardy-Weinberg assumptions?

A: Large population size, random mating, no mutation, no migration, and no natural selection.

Q: How do you calculate Hardy-Weinberg Equilibrium (HWE)?

A: Using the equation p² + 2pq + q² = 1, where p and q are the frequencies of the dominant and recessive alleles, respectively.

Q: How do you estimate allele frequencies for X-linked genes?

A: For X-linked genes, females are XX and males are XY. The allele frequencies differ between males and females due to the hemizygous nature of males for X-linked genes.

Q: How do you estimate allele frequencies for recessive alleles?

A: The frequency of the recessive allele can be found by taking the square root of the recessive phenotype frequency (q = √q²).

Q: How do you predict allele frequencies from genotype frequencies?

A: Allele frequencies can be calculated by using the genotype frequencies in the population and applying the Hardy-Weinberg equation.

Q: What happens when mating is not random?

A: Non-random mating (such as assortative mating) can alter allele frequencies by favoring certain genotypes over others.

Q: What happens when the population is subdivided?

A: Population subdivision can lead to genetic differentiation and can influence allele frequencies in different subpopulations.

Q: What happens when there is migration?

A: Migration introduces new alleles into a population, which can change allele frequencies and impact genetic diversity.

Allelic variation

among individuals

Transmission of allelic variants

from parents to offspring generation after generation

Temporal changes

the genetic makeup of a population due to systematic and random evolutionary forces

polymorphic

When the second most frequent allele of a gene has a frequency greater than 0.01

Exceptions to the Hardy Weinberg Principle

Nonrandom mating

Unequal survival

Population subdivision

Migration

Nonrandom mating

Consanguineous mating and Assortative mating

Consanguineous mating

mating between genetically related individuals

Assortative mating

mating between individuals with similar phenotypes

panmictic

population is a single interbreeding unit

Panmixis

any member of the population is able to mate with any other member

Migration

Movement of genes from one population to another

Northern blotting technique

A technique that enables specific nucleotide sequences to be detected in samples of mRNA. It involves gel electrophoresis of RNA molecules and their transfer to a membrane (blotting), followed by nucleic acid hybridization with a labeled probe.

Southern Blot Analysis

technique in which labeled probes are used to detect specific DNA fragments that have been separated by gel electrophoresis