Exam 1 (Ch. 1-6)

Avery, MacLeod, and McCarty Experiment

• Found that only DNA was able to transform the strains

  • DNA was transforming principle → suggested DNA may act as genetic material

Hershey and Chase “Blender Experiment”

Concluded DNA was genetic material

Schleiden & Schwann

• Described cells in plants & animals

  • proposed cell theory: all life is composed of cells; cells = basic building blocks of organisms

Rudolph Virchow

• Expanded on cell theory → “every cell stems from another cell”

  • gave cell theory an evolutionary basis

Germ plasm theory

• Posits reproductive organs carry full sets of genetic information and that the sperm & egg cells they produce carry the genetic information brought together in fertilization

• Proposed by August Weismann

The 4 Phases of Modern Genetics

1. Identification of cellular and chromosomal basis of heredity

2. Identification of DNA as hereditary material

3. Description of the informational and regulatory processes of heredity (the encoding of information in genes and processes of transcription and translation)

4. Genomic era: completion of first genome sequences → complete human genome produced

Eukaryote vs. Prokaryote

• Eukaryote

  • Multiple chromosomes organized by proteins

  • Membrane-bound nucleus, and intracellular membranes

  • Unicellular and multicellular

  • Larger genomes

• Prokaryote

  • lack nuclear membrane & typically no membrane bound organelles

Bacteria and archaea

• Single large chromosome (some also contain plasmids)

• No membrane-bound nucleus or intracellular membranes

• Unicellular

• Smaller genomes

What is the hereditary material of certain viruses?

RNA

Mitosis

Cell-division process where a complete set of nuclear chromosomes are transmitted to produce genetically identical daughter cells

Meiosis

Cell-division process that produces reproductive or sex cells (gametes)

• how sexual reproduction to produce offspring occurs

Haploid vs. Diploid

• Haploid: one copy of each gene in genome

• Diploid: twice the haploid number of chromosomes found in genome

How are zygotes produced?

Through the union of haploid gametes at fertilization producing a diploid fertilized egg that begins mitotic division to produce it

Genes

• Composed of defined DNA sequences that collectively control gene transcription + contain info to produce RNA (mRNA used to produce proteins through translation)

• Fundamental unit of heredity

  • come in multiple forms called alleles

  • give phenotypes

  • physical units of heredity (originally posited by Mendel)

Chromosomes

Long molecules of double-stranded DNA and protein, which contain genes

Sexually reproducing organisms usually have …

Homologous pairs (or homologs) of chromosomes, which carry genes for the same traits

Central dogma

• Describes the flow of hereditary information

• DNA is transcribed to RNA which is translated to PROTEIN

  • reverse transcription: turn RNA to DNA

1. Transcription: one strand of DNA (aka the template strand) is used by RNA polymerase to direct synthesis of a single strand of RNA (can produce various forms of RNA, like mRNA)

2. Translation: RNA is translated to sequences of amino acids (held together by peptide bonds) using the genetic code → resulting string of amino acids upon folding makes up protein at ribosomes

• rRNA: forms part of the ribosome (aka where protein assembly takes place)

• tRNA: carries amino acids (building blocks of proteins) to ribosomes

How to begin transcription?

• RNA polymerase must locate a gene and gain access to the template DNA strand by interacting w/ DNA sequences that control transcription

  • once coding sequence of gene has been transcribed, RNA polymerase must stop transcription and release the transcript

To transcribe

1. Identify the template strand

2. Read it in 3’ to 5’ direction and then pair complementary nucleotides

Promoters

The most common type of DNA sequences controlling transcription; are regulatory sequences- not transcribed

• are recognized by RNA polymerase and directs it to a nearby gene

Where transcription of a gene starts and ends

• Starts near the promoter at the start of transcription, the DNA location where transcription of a sequence begins

• Ends at the termination sequence, where another DNA sequence facilitates the stopping of transcription

Exons and Introns

Are what eukaryotic genes are subdivided into

• Exons: contain the coding information that will be used in translation

• Introns: intervene between exons and are removed from the transcript before translation (which occurs in nucleus)

  • are not in bacterial genes, some in archaeal

What’s the backbone of DNA?

Phosphate and sugar

Nucleic acid structure

a) Phosphate

b) Sugar (ribose or deoxyribose)

c) Nitrogenous base

• Purines

• Adenine and Guanine

• Pyrimidines

• Cytosine and Thymine/Uracil

How are nucleotides forming a strand linked together?

By a covalent phosphodiester bond between the 5’ phosphate group of one nucleotide and the 3’ hydroxyl (OH) group of the adjacent nucleotide

• it leads to alternation of deoxyribose sugars & phosphate groups along the strand + gives molecule a sugar-phosphate backbone

Molecular Structure of DNA

• Discovered by Watson, Crick, Franklin

• A double helix composed of two strands of DNA, with an invariant sugar-phosphate backbone on the outside and nucleotide bases (ATCG) forming complementary base pairs within the center of the molecule

  • hydrogen bonds hold complementary base pairs in DNA together

    • 2 between A-T

    • 3 between G-C

Chargaff’s Rule

• Percentages of adenine and thymine are equal

  • A = T

• Percentages of guanine and cytosine are equal

  • G = C

• Note:

  • A + T doesn’t equal to G + C

  • suggested that nucleotides are arranged in complementary base pairs to Watson and Crick

Direction of transcription

From 5’ to 3’ (Coding strand; non-template strand)

Template strand

The DNA strand from which the mRNA transcript is synthesized from

Coding strand

The complementary partner of the DNA template strand

• aka is complementary and antiparallel to it (so has same 5’→ 3’ polarity as RNA transcript made from template strand)

Complementary strand

• Is antiparallel (one strand is 5’ to 3’, the other is 3’ to 5’)

• A pairs w/ T, C pairs w/ G

mRNA transcript

Is antiparallel to the DNA template strand

DNA Coding strand vs mRNA transcript

Both have same polarity and sequence, substituting U in mRNA for T in DNA

• aka same direction (i.e. both 5’ to 3’) and same sequence except in mRNA, T is replaced w/ U

DNA replicates by …

Semiconservative replication

• Both parental DNA are templates for new DNA

• Each double stranded DNA has one parental (old) and one “new” daughter strand

RNA Structure

• Mostly similar to DNA except:

  • Uracil replaces thymine

  • 2’ hydroxyl on all bases

  • Usually single stranded

Protein Structure

• Composed of amino acids linked together in a chain

• Each of the 20 amino acids have a unique R-group

• Have N-terminus and C-terminus

Mendelian/Transmission genetics

The study of transmission of traits and characteristics in successive generations

Evolutionary genetics

The study of the origins of and genetic relationships between organisms and examines the evolution of genes and genomes

Molecular genetics

The study of inheritance and variation in nucleic acids (DNA and RNA), proteins, and genomes and tries to connect them to inherited variation and evolution in organisms

Evolutionary principles developed by Darwin

• Variation exists in populations

• Hereditary transmission allows that variation to be passed along to subsequent generations

• Variants survive differentially due to environmental pressures

• Variants that lead to increased survivorship increase in frequency in the population

Class definition of evolution

• Change over time

  • doesn’t have to take a long long long time

  • i..e antibiotic resistance

Phylogenetics

The study of evolutionary relationships

• uses multiple markers, but DNA is one of the most robust

• General principle: the most closely related species will have the smallest number of differences between shared genes

  • the same principle as determining relatedness within human populations, just extended to other species

Mendel’s Experiment

• Goal: to determine the pattern by which inheritable characteristics were transmitted to the offspring

• Conclusions

  • characteristics were governed by distinct units of inheritance (genes)

    • each organism has/inherits two copies of each gene, one from each parent

    • the two genes may be identical to one another or non-identical (alleles)

  • Gametes (reproductive cells) must therefore carry only one copy of the gene for each trait

• Monohybrid cross → parents differ by a single trait

Principle of Independent Segregation

An organism’s alleles separate from one another during gamete formation and are independently transmitted to offspring

Principle of Independent Assortment

Each pair of alleles segregates independently from other pairs during gamete formation

Concepts for Mendelian Inheritance

• Aka looking at 2+ traits simultaneously

• Alleles for each trait segregate independently and don’t influence the inheritance (independent assortment) of the second trait

• Results in definite ratios for progeny phenotypes based on initial frequencies

Monohybrid cross

Follows 1 homo: 2 hetero: 2 homo ratio

Equation for total number of gametes each parent produces

2ⁿ where n = # of heterozygous alleles in parent

True breeding

Homozygous (TT or tt)

Test cross

Homozygous recessive (known) x heterozygous dominant

• Getting 4 phenotypes of equal frequencies

Forked line method

1. Consider only one allele at a time and cross them; do this for each trait

2. Then cross all of the results making sure to multiply the fractions

In a dihybrid test cross, the phenotypic ratio is always …

1:1:1:1

In monohybrid test crosses, the phenotypic ratio is always …

1:1

Product rule (or multiplication rule)

• Use if two or more events are independent of one another → their joint probability is the product of the individual probabilities

• Chances of g AND g happening (multiply both the probability of both by each other)

  • P_(g) = 1/2 , P_(g) = ½

  • P_(gg) = ½ x ½ = ¼

Sum rule (or addition rule)

• Use if finding joint probability of two or more mutually exclusive events (not independent)

• Events is the sum of probabilities of each event

• Probability of obtaining any heterozygote is equal to the sum of the probabilities of each possible heterozygote

• The chances of Gg OR other Gg happening: add probabilities of each event together

  • P_{(one Gg)} = ¼ , P_{(other Gg)} = ¼

  • P_{(any Gg)} = ¼ + ¼ = ½

Conditional Probability (prior probability)

• The probability of an event (A), given that another (B) has already occurred

• Is asked after the cross has been made, is applied when information about the outcome modifies the probability calculation

  • Note: the product and sum rules are used before a cross is made, in order to predict the likelihood of certain outcomes

Binomial Expansion and Probability

• The probability that a binomial experiment results in EXACTLY X successes

  • predicting the likelihood of a series of events

• Two variables, each representing the frequency of one of two alternative outcomes

• P_{(outcome 1)} = p ; P_{(outcome 2)} = q

• If p and q are the only possible outcomes → p+q = 1

• In examining probable outcomes (i.e. coin flips), we expand the expression by n events → (p+q)ⁿ = 1

Method to solve problems w/ binomial expansion: Pascal’s Triangle

• Binomial coefficient

  • (p+q)ⁿ where …

    • n = # of events

• Each line is total # of outcomes

  • i.e. (p+q)² , n=2, so can expand to: 1p² + 2 (p¹q¹) + 1q² = 1

Normal distribution

• A binomial distribution depicting all of the experimental outcomes

• μ = the average outcome

• σ = one standard deviation

• A result is considered statistically significant if it falls more than ~2σ away from μ

• It has a probability (p-value) of < 0.05

• The p-value is the probability of a result deviating by at least that much by chance

Chi-square (X²) analysis

• A method to statistically evaluate the relationship between observed and expected values; are the results statistically significant?

• Dependent on sample size, # of outcome classes, # of observations in each class

• Larger # of outcome classes or more observations = larger X² values

  • So can’t compare experiments that have diff #s of outcome classes or observations

Steps to calculate X² value for Chi-square analysi

1. Calculate the difference between the observed (O) and expected (E), then square it and divide by E

2. Sum for each outcome class

• Then, find where X² falls on a normal distribution to determine p-value

• Need to also know degrees of freedom (df = n-1)

• If fail to reject = they assort independently

Pedigree symbol meanings

Pedigree line meanings

Autosomal inheritance

The transmission of genes that are carried on autosomes (non-sex chromosomes)

• found in pairs

• Split up during gamete formation (segregation)

• Individual chromosomes are distributed in gametes w/out regard to other chromosomes (independent assortment)

Autosomal dominant

The trait isn’t controlled by sex chromosomes; allele can be shown/transmit in either male or female

• Males and females are impacted equally

• If offspring are affected, at least one parent should be affected

• In crosses where one parent is affected but the other isn’t, ~half of offspring should be affected

  • Gg x gg → ½ Gg & ½ gg

• Two affected parent may produce unaffected offspring

  • Gg x Gg → ¼ GG + ½ Gg + ¼ gg

Autosomal recessive

The trait is controlled by recessive gene and the affected can often be born to parents that are both unaffected

• If one parent is affected, risk to the child is dependent on the other parent

• If both parents are affected, all offspring will be affected

• The trait may not show up in every generation

• If allele is rare, unaffected parents of affected children are likely to be closely related

Chromatin

The material of which eukaryotic chromosomes are composed; protein, RNA, and DNA

Euchromatin

Chromosomal material that isn’t densely compacted during normal cell operation; comprises many functional (genes) parts of the genome

Heterochromatin

Chromosomal material more densely packed and containing few expressed genes

Chromosome

A DNA-containing structure that has a centromere

• at end of S-phase, consists of two replicated structures, joined at the centromere

Homologous

Having the same structural features and patterns of genes

Chromatid

One of the replicated structures

Sister chromatids

The two replicated chromosomes as a unit

Diploid

2n chromosomes present in pairs

Haploid

1n

• only 1 chromosome pair

Somatic cells

Non-reproductive cells, usually diploid “body cells”

• produced through mitosis

Gametes

Reproductive cells, germ-line cells (sex cells)

• contain haploid (n) chromosome number

• produced through meiosis

Meiosis

Produces gametes that have half the number of chromosomes as the original cell (reduction type division)

• the gametes aren’t genetically identical to one another

2 Major Cell Cycle Phases

• M phase

  • includes mitosis (duplicated chromosomes are separated into 2 nuclei (karyokinesis) AND cytokinesis (entire cell & its cytoplasm divide into 2 daughter cells

• Interphase

  • divided into G1 (first gap), S (synthesis), & G2 (second gap)

Interphase → occupies bulk of cycle

• Days, weeks, or longer, depending on cell type

• Most DNA is unpacked and distributed throughout the nucleus; i.e. euchromatin

• Cells prepare for mitosis, replicate DNA, perform normal metabolic functions (glucose oxidation, replication, transcription, translation)

M phase

• Activities necessary for cell division; usually lasts ~ 1 hour

• Only a small percentage of cells in a tissue are in mitosis at any given time

• DNA is tightly packed (heterochromatic) and inaccessible

• Usual processes of protein synthesis are largely shut down

Mitosis

• Process of nuclear division (karyokinesis) / cell division that produces two genetically identical daughter cells from one original parental cell

• Is precisely controlled to prevent either an excess of an insufficient # of cells

• Replicated DNA molecules of each chromosome are faithfully partitioned into 2 nuclei

• Usually accompanied by cytokinesis → dividing cell splits into 2

• Maintains chromosome number & is necessary to generate new cells for organism growth, maintenance, and repair

• Happens in diploid OR haploid cells

• Usually divided into 5 distinct stages

• Sex chromosomes do go through this

Mitosis Start and End

• Start: one cell w/ a diploid number of chromosomes

  • diploid: 2 copies of each chromosome

• End with: two cells w/ diploid complements of each chromosome

5 Phases of Mitosis? (in order)

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

What happens in the Prophase?

• Mitotic chromosomes condense to appear as distinct, rodlike structures

• Two mirror-image sister chromatids formed during replication

  • 1. Held together along its length with a multi-protein complex called cohesion

  • Holds the 2 sister chromatids together through G2 and into mitosis

• Microtubules appear in sunburst arrangement (aster) around each centrosome during early prophase

What happens in Prometaphase?

• Starts w/ dissolution of nuclear envelope

  • A) Mitotic spindle assembly is completed

  • B) Chromosomes are moved into position at center of cell

• When it starts, compacted chromosomes are scattered throughout space that was nuclear region

  • microtubules penetrate central cell region

  • free ends grow & shrink as if searching for chromosome

  • those that contact a kinetochore are captured & stabilized

What happens in Metaphase?

• Starts with chromosomes aligned at spindle equator in a plane (metaphase plate)

• One chromatid attached by its kinetochore to spindle fiber from one pole, other from opposite pole

What happens in Anaphase?

• All metaphase plate chromosomes split synchronously

• The chromosomes (formerly sister chromatids) begin to migrate poleward

  • accompanied by shortening of microtubules attached to kinetochore

• Chromosomes move at ~1 μm/min

• 2 types of movement: movement of chromosomes toward poles and the 2 spindle poles move farther apart

What happens in Telophase?

• Chromosomes collecting as they near their respective poles

• Daughter cells return to their interphase condition

  • A) Nuclear envelope reforms

  • B) Chromosomes disperse until they disappear from view under microscope

What happens in Cytokinesis?

• Is a process which the cell is divided into 2 daughter cells, usually coordinated with mitosis

• First evidence of cytokinesis occurs in late anaphase w/ cell surface indentation in narrow band around cell

  • as time progresses, indentation deepens & forms furrow completely encircling cell

Meiosis

• Produced haploid gametes for sexual reproduction

• Union of haploid gametes produces diploid progeny

• Distinguished from mitosis by different products and different meiotic M phase

• Meiotic interphase is followed by two divisions with no DNA replication between them:

  • 1) meiosis I

  • 2) meiosis II

• Characterized by recombination or crossing over aka exchange of material between homologous pairs of chromosomes

Where is Meiosis happening?

Where is Mitosis happening?

What happens in Meiosis I?

• Separation of homologous pairs of chromosomes

• 3 hallmarks:

  • Homologous chromosomes pair (synapsis)

    • synapsis: pairing of homologous chromosomes

  • Crossing over (recombination) occurs at chiasmata

  • Segregation of homologous chromosomes occur to make haploid complements

• Subdivided into prophase I, metaphase I …. with similar (but different) events to mitosis happening in each

Chromosome theory of heredity & experimental evidence: Mendel

Pea plants

Chromosome theory of heredity & experimental evidence: Thomas Morgan

Fruit flies

Chromosome theory of heredity & experimental evidence: Sutton and Boveri

Sea urchin eggs

Chromosome theory of heredity & experimental evidence: Nettie Stevens

Beetles

Model organism

• A non-human species that is extensively studied to understand particular biological phenomena, w/ expectation that discoveries made in organism model will provide insight into workings of other organisms

• For chromosomes, the earliest productive model was Drosophilia melanogaster

• Thomas Hunt Morgan tested the chromosome theory of inheritance in D. melanogaster

  • only four chromosome pairs, easy to identify phenotypes

Nettie Stevens

• Most work to that time was focused on autosomes

• Nettie Stevens noticed that there were differences between male and female chromosomes in many (but not all) species

  • heterogametic

• In Tenebrio molitor (a beetle)

• Stevens concluded that sex-dependent hereditary differences are due to the presence of two X chromosomes in females and an X and a smaller Y chromosome in males

• Not always true and are variations but works as a general rule