BIOL 207 - Genetics & Heredity

everything for the midterm ig.

Genetics

• Uses manipulation of genes/genomes to study how genes function in fundamental biological processes.

• Alter gene sequence and/or gene function (i.e. mutations) and see how it affects a process.

Gene

• Has two main functions:

  • Operational.

  • Transmission.

• Transcribed region + all sequences necessary for correct expression.

Gene - Operational Function

• A gene is a (usually continuous) stretch of DNA (or in some organisms RNA) that contains information encoding a gene produced (usually an RNA and a protein).

• Codes a gene.

Gene - Transmission

• A gene carries information from one generation to the next.

• Or it carries information from parental to daughter cells.

Types of Genetic Material

• DNA or RNA as genetic material (RNA only in viruses).

• Linear (eukaryotes, many viruses) or circular (bacteria, mitochondria, some viruses).

• Double- or single-stranded.

• Segmented (some viruses) vs unsegmented (bacteria, eukaryotes, many viruses).

+ve vs. -ve Strands

• Positive strand → can go right in to be translated.

• Negative strand → must do reverse replication before translated.

DNA as Dynamic

• Not static.

• Can be heavily expressed, somewhat expressed, or not expressed at all.

Gene Activity

• Genes can produce different amounts of RNA.

• Gene A → many RNA transcripts → many protein molecules.

• Gene B → few RNA transcripts → few protein molecules.

• Level of transcription controls how much protein is made.

Gene Components

• Gene = transcribed region + all sequences necessary for correct expression.

• RNA corresponds to a region of DNA, called the transcribed region (transcription unit).

Regulatory Sequences

• Sequences in the gene tell the cell to turn “off” or “on.”

• Allows the gene to be appropriately expressed.

• Can be upstream, downstream, or within the gene.

Activator Protein

• Can recognize the regulatory region.

• Will recruit RNA polymerase which begins transcribing.

Repressor Protein

• Binds regulatory region.

• Blocks RNA polymerase.

• No transcription occurs.

• Gene inactive = not expressed.

Gene Expression (Active)

• RNA polymerase transcribes DNA.

• RNA is produced.

• Gene is expressed.

Gene Expression (Inactive)

• Transcription blocked.

• No RNA produced.

• Gene is not expressed.

“…omics”

• The characterization of the genome and what it means.

• High throughput sequencing.

  • i.e. to study the expression of all genes at once.

• Many types of these disciplines exist (metabolomics, lipidomics, glycomics, etc).

Genomics

• The study/cataloging of entire genomes.

Transcriptomics

• Studies genome-wide responses to different conditions.

• The quantification/cataloging of all RNAs in a sample.

• Powerful when comparing a controlled variable with a dependent variable.

Proteonomics

• The quantification/cataloging of all proteins in a sample.

Transcriptomics - Example

• Sample 1 (Control): Gene 5 = highly expressed. Gene 7 = not expressed.

• Sample 2 (Drug-treated): Gene 5 = repressed. Gene 7 = induced.

• Other genes → unaffected by drug.

• The drug treatment represses gene 5, while it induces gene 7 (all other genes remain unaffected).

Proteomics & Transcriptomics vs Genetics (Insect Example)

• Proteomics/Transcriptomics: find mRNAs or proteins that respond to a stimulus (e.g., light exposure changes expression).

• Genetics: find genes that are required for a process (e.g., mutants can’t fly to the light).

Transcriptomics or Proteonomics (Insect Example)

• Will identify mRNA/proteins that respond to a stimulus or upregulated during a biological process (light perception).

• Done by comparing tissues from flies receiving a light stimulus vs. flies who did not receive a light stimulus.

Genetics (Insect Example)

• Identifies genes that are required for the biological process.

• Mutanizes flies, breaks, checks results, analyzes, and finds the gene.

• Tests thousands of mutant fly lines and selecting those with a defect (flying to the light source).

Forward Genetics

• Genes first identified by their mutant phenotype.

• Mutations mapped to the corresponding gene.

• Gene characterized using molecular, cellular, or biochemical tools.

• Reveals genes with previously unknown functions in known processes.

Forward Genetics Advantage

• Unbiased and powerful.

• Identification of genes that nobody has ever linked to the biological process.

• Finds the unknown unknowns (the “surprises”).

Forward Genetics Disadvantage

• Slow.

• Identifying mutated gene can be tricky.

Reverse Genetics

• You mutate, remove, or modify a gene to test its function.

• Studies a known gene in a known or unknown process.

• Understanding the processes involved or understanding how modification affects the function of a gene product.

Reverse Genetics Advantage

• Extremely specific and versatile.

• Allows for the manipulation of genes with precision.

Reverse Genetics Disadvantage

• Biased (tests the known unknowns).

• The gene that you modified may not have a obvious phenotype.

• One gene at a time.

Cell Biology

• Study cells directly (i.e microscopy) to learn about fundamental cellular processes.

Biochemistry

• Study biological phenomena on a molecular level to understand the mechanistic aspects of a process.

  • i.e. protein-protein interactions.

Genome

• A complete set of genetic material found in the somatic cell.

• Includes the coding and non-coding strands.

Preformationism

• Sperm were homunculi.

• Preformed humans.

Inheriting Traits

• Genetic traits are inherited by both parents.

• A child can only inherit 50% of genetic information from their parents.

Information

• First level of DNA structure.

• Encodes the characteristics of an organism.

Replication

• Second level of DNA structure.

• Can be copied.

Transmission

• Third level of DNA structure.

• Is passed from parents to offspring during reproduction.

Variation

• Fourth level of DNA structure.

• Subject to occasional modifications that result in differences between individuals.

Forms of Genetic Information

• Different forms of the same kind of information exist: alleles and polymorphisms.

Genotype

• Entire genetic information inherited by an organism: refers to all of the specific information stored in the genome.

• The genetic information with respect to a single gene or group of genes.

  • More used definition.

Phenotype

• Can be genetic or environmental.

• Detectable manifestation of a specific genotype.

• Includes morphological, behavioral, physiological, or molecular traits.

Reaction Norm

• Two genetically identical individuals can look very different.

• This is usually due to environmental differences.

• Limited nutrients or stress may restrict growth.

• This reflects the “flexibility” of certain traits in response to different environments within an individual.

“Extended Phenotype”

• Argues that phenotypes should not be limited to organismal traits.

• Proposed by Richard Dawkins.

• Would apply to gene-dependent, visible impact on habitats, driven by behaviours.

Central Dogma

• Central dogma of molecular biology.

  • DNA → RNA → Protein.

Gene Expression

• Information stored in DNA is accessed through the process of transcription (“copying”) into (messenger) RNA molecules.

• Many RNAs are translated into proteins, leading to observable traits.

Genetic Variation

• Describes differences among individuals within a population.

Morphs

• Contrasting, but recurring forms or types within a single population of a species.

  • i.e. melanistic forms of cats.

• A race/subspecies is different because they form a geographically isolated and distinct population.

Mutation

• A process that introduces a lasting change into the genetic material (DNA & sometimes RNA).

• If the change occurs in the germline, the mutation can be passed from parent to offspring.

• In somatic cells, mutations are transferred to daughter cells.

Point Mutation

• A type of mutation that affects only a single nucleotide.

• This may cause changes in gene expression and/or affect the function of the corresponding gene product.

Chromosomal Alterations

• Multiple genes are affected by the loss, rearrangement, reattachment of a chromosome (also considered mutations).

Continuous Variation

• Refers to traits for which the phenotypes change gradually.

  • i.e adult height in humans.

Discontinuous Variation

• Traits that fall into distinct groups (i.e. blood type).

• Morphs and mutants would also fall into this group, such as albinos.

Polymorphisms

• Generally considered relatively frequent discontinuous variants in a population.

• Individual forms are called morphs.

• It is frequency-based, and one has to make an arbitrary cutoff (often stated as 1%).

Mutants

• Rare discontinuous variants in a population.

Polymorphisms and Mutants

• Both result from occasional changes in the genetic material (mutations in DNA or RNA).

• For some reason, changes in the morph are relatively common. However, mutations remain rare.

• ∴ No conceptual difference.

Alleles

• Gene variants are different versions of the same gene within a population or cell.

• They include sequence differences in coding, intron, or regulatory regions.

• Many differences are inconsequential; from a geneticist’s view, such variants are functionally equivalent.

• The term applies only to variation of a gene within a species.

Homologs

• Gene inherited in two species from a common ancestor.

• Pair of chromosomes, one from each parent.

• Identical in size, banding pattern, and gene locations.

• Human cells have 23 pairs of homologous chromosomes (not alleles).

BRCA1 Gene

• Located on chromosome 17.

• Involved in repairing damaged DNA.

• Chromosome 17 contains ~1100–1200 genes.

• A single mutant copy greatly increases the risk of breast cancer.

• The mutant copy is an allele of the wild-type gene (the normal version).

Chromosome

• DNA + associated proteins.

• Linear in eukaryotes, usually circular in prokaryotes.

• For viruses, the term “viral genome” is used.

• For mitochondria, the term “mitochondrial DNA” (mtDNA) is used.

Historical Milestones for Chromosomes

• 1880s - Dyes reveal the thread-like chromosomes; number is constant in a species.

• Cell division - Chromosomes condense and segregate equally to daughter cells.

• 1900s - Mendel’s work rediscovered.

• 1902 - Sutton & Boveri: chromosome movements mirror Mendel’s factors → genes are on chromosomes.

Chromosome Location in E&P

Gene Location

• Found at specific locations.

• The location does not change!

Gene - Locus (Loci)

• Gene are usually represented with some sort of symbol (letter, number, symbols, etc).

• Specific physical location of a gene or other DNA sequence on a chromosome, like a genetic street address.

Fred Griffith (1928)

• Studied Streptococcus pneumonia, which causes pneumonia in mice.

• Forms a diplococcus, where a pair of cells remain attached due to incomplete cell division.

• He cultured the infectious bacteria on plates and later saw a “rough-looking” strain.

• Found that the new strain lacks the glycocalyx.

S. pneumonia “S” Strain

• “S” forms smooth colonies, is virulent (causes pneumonia).

• → inject → mice dead.

• “S” form is virulent because the glycocalyx protects bacteria from mouse immune system.

• Colonies look smooth because they have the glycocalyx.

S. pneumonia “R” Strain

• “R” forms rough colonies— not virulent (no pneumonia).

• → inject → mice live.

• Not virulent because they lack the glycocalyx.

• Colonies look rough because they lack the glycocalyx.

Inactivating S. pneumonia “S” Strain

• Heat treatment inactivates the S strain.

• Heat-killed “S” is not virulent.

• → inject → mice live.

• No S strain can be obtained from the mice after injection.

S. pneumonia Co-Injected S&R Strain

• Heat-killed “S” nor “R” are virulent on their own.

• Injected together → mice dead.

• Both “S” and “R” strains can be obtained from the mice after injection.

Fred Griffith’s Transformation Experiment

• Live S. pneumonia cells could be recovered from these dead mice.

• Streptococcus cells contained “S” strain (formed smooth colonies).

• The “S” strain bacterial were virulent upon subsequent injections.

Transforming Principle

• Living cells "(“R”) could be “transformed” by dead (“S”) cells.

• Something in the S-cell debris could convert R cells into S cells.

• Called transformation.

Competent

• State in which bacteria can take up DNA from the environment.

• Requires specific proteins called competence factors.

• Enables incorporation of foreign DNA into the genome.

• Used in molecular biology to introduce and amplify DNA.

Competence Factors

• Proteins that bind single-stranded DNA.

• Induce or maintain bacterial competence.

• Help incorporate ingested DNA into the genome.

• Support laboratory transformation techniques.

Homologous Recombination

• Type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA.

• Similar to meiosis.

Homologous Bacterial Transformation

• Donor DNA from another strain aligns with a homologous site on the host chromosome.

• Requires breaks in the host DNA.

• Donor DNA acts as a “repair template,” replacing the host sequence at that locus.

• Produces a transformed cell carrying the donor gene (e.g., S DNA for the glycocalyx locus).

Avery, MacLeod & McCarty Experiment (1944)

• S-strain extracts treated with destroying agents.

• Removing polysaccharide, lipids, RNA, or proteins → activity intact.

• Removing DNA (with DNase) → activity lost.

• ∴, DNA is the transforming substance.

Avery’s + Co. Experiment Aftermath

• The data from the experiment was conclusive, but there was reluctance to accept DNA as the genetic material.

• DNA didn’t seem complex enough to be the base for genetic material.

• Additional experiments added more evidence.

• ∴ acceptance that DNA is the carrier of all genetic material.

Hershey and Chase Experiment (1952)

• Grew T2 phages in media containing either ³²P (to label DNA) or ³⁵S (to label protein).

• Allowed labeled phages to infect E. coli.

• Blended and centrifuged to separate bacterial cells from phage “ghosts.”

• Found ³²P inside bacteria, while ³⁵S stayed with ghosts → DNA, not protein, entered cells.

Hershey & Chase - T2 Phage

• Bacteriophage T2 is made of protein and DNA (no RNA or saccharides).

• Genetic material had to be either protein or DNA.

• Composition of the two components was unclear at the time.

• Showing which part entered the cell would reveal the genetic material.

Hershey & Chase - Radioactive Isotopes

• ³²P (radioactive phosphorus) labels DNA; P not found in protein.

• ³⁵S (radioactive sulfur) labels protein; S not found in DNA.

• Two cultures prepared: one with ³²P-labeled DNA, the other with ³⁵S-labeled protein.

• Used to follow each component during phage infection of E. coli.

Hershey & Chase - Insertion

• Phages infected E. coli, then cells were blended and centrifuged.

• ³⁵S (protein) radioactivity stayed with phage “ghosts,” not in bacteria.

• ³²P (DNA) radioactivity was found inside the bacteria.

• DNA, not protein, entered the cells.

Hershey & Chase - Conclusion

• DNA entered E. coli and could be recovered from new phage progeny.

• Protein (³⁵S) remained outside in phage ghosts.

• Therefore, for bacteriophage T2, genetic information is in DNA, not protein.

• DNA is the hereditary material, at least for T2 phage.

Proteins Contain Sulfur

• Some proteins are phosphorylated after translation by protein kinases.

• Phosphorylation targets the non-carboxyl –OH groups in serine, threonine, and tyrosine.

• Cysteine and methionine instead contain sulfur.

DNA Contains Phosphorus

• Rich in P but lacks sulfur.

If DNA is the Hereditary Material…

1. Cells must be able to replicate DNA.

2. Carries hereditary information.

3. Transfer information to control a cell’s activity.

4. Must be able to change (mutate).

Nucleotides

• Composed of a phosphate group, pentose sugar, and a nitrogenous base.

• Base + sugar + phosphate = nucleotide.

• Named after the base used.

• Numbering system of atoms in sugars and nitrogenous bases.

Pyrimidines & Purines

• Pyrimidines: thymine, cytosine, uracil (RNA).

• Purine: adenine, guanine.

Nucleotide Rotation & Flipping

• Nitrogenous base is linked to the sugar by a single (glycosidic) bond.

• This bond allows the base to rotate freely relative to the sugar.

• Sugar-phosphate backbone bonds (3′ and 5′ carbons) also rotate, giving flexibility.

• Bases can “flip out” of the helix for repair or binding events.

Phosphodiester Bond

• Phosphate group at 5’ position on the sugar of one nucleotide is covalently bonded to the 3’ position of the sugar on the next nucleotide.

• Condensation reaction (H₂O is produced).

Rosalind Franklin

• Produced a X-ray diffraction image of DNA. 

• Data is interpreted by Watson and Crick (1953). 

• Built a structural model that accounted for Franklin’s data.

Nucleotides linked to Polymer Strands

• Strand directionality is based on orientation of the sugar molecules.

• Phosphate backbone is negatively charged.

Chargaff (1940s)

• Determines the nucleotide distribution across species.

• Finds that chemical composition is the same.

• Finds that each species has a specific quantity of DNA.

• Determines that DNA found in different species shows the same ratio of bases.

  • i.e. the amount of A = T.

Rosalind Franklin

• Produces a X-ray diffraction image of DNA.

• Data is interpreted by Watson & Crick (1953).

• Built a structural model that accounted for Franklin’s data.

DNA-Binding Proteins

• Important for proteins to bind to the major groove.

• Most DNA binding proteins recognize the major groove.

Structure of DNA

• Helical molecule (2nm wide).

• Made of two antiparallel nucleotide polymer strands.

• Covalent bonds between phosphates and sugars connect nucleotides.

• Sugar and phosphate groups face “out.”

• Nitrogenous bases of two strands face the “inside” of the helix.

DNA is Antiparallel

• Covalent bonds between phosphates and sugars connect nucleotides.

• Sugar and phosphate groups face “out.”

• Nitrogenous bases of two strands face the “inside” of the helix.

• ~10 base pairs per helical turn.

Complementary Base Pairing

• Spacing led to conclusion that a purine pairs with a pyrimidine.

• Chargraff’s data suggested that.

  • A pairs w T.

  • C pairs w G.

• H-bonds connect the base pairs.

DNA Replication

• Structure of DNA predicts a mechanism for how it is copied (relies on complementary base pairing).

• Two parental strands separate and act as templates for the synthesis of new daughter strands.

Conservative Replication Model

• In each, parental strands separate and act as templates that are copied.

• Parental strands reanneal and new daughter strands anneal.

• If true, one expects all newly formed DNA duplexes to harbour exactly 100% new DNA.

Semi-Conservative Replication Model

• New DNA molecules are composed of a parental (old) and daughter (new) strand.

• If true, each DNA molecule has exactly 50% from the original (parental) DNA molecule.

Dispersive Replication Model

• Proposes strand breaks at every node (~5 bases) where new DNA joins parental DNA.

• Results in alternating segments of ~5 bases parental DNA and ~5 bases of new daughter DNA, where new DNA base pairs with parental DNA.

• If true, each DNA strand harbours slightly varying amounts of old and new DNA, but each contribution would be close to 50%.

The Pulse-Chase Experiment

• In living organisms, metabolism results in constant turnover of biomolecules.

• By adding a isotope-labelled nutrient (i.e. sugar or aa) for a limited time (the “pulse”) one can follow the fate of the isotope over time (the “chase”).

• Before and after the pulse (= unlabelled) nutrients are provided.