Science Term 3: Biology

Vocabulary:

Monomers and polymers:

Phosphodiester bond: Nucleotides are connected to form polynucleotides through the sugar-phosphate backbone thanks to this covalent bond.

Directionality: Nucleotide strands run in a 5’ → 3’ direction

Purines: Double-ringed chemical compound found in nitrogenous bases. Adenine and Guanine

Pyrimidines: Single-ringed chemical compound found in nitrogenous bases. Cytosine, Thymine, and Uracil.

Complementary pairs: Nitrogenous bases connected via hydrogen bonds. Has to be exact. Cytosine - Guanine (3 H-bonds) and Adenine - Thymine/Uracil (2 H-bonds).

Messenger RNA (mRNA): transcript copy of a gene that reads the sequence in base triplets (codon) in the ribosome.

Ribosomal RNA (rRNA): responsible for the synthesis of protein in ribosomes.

Transfer RNA (tRNA): serves as the physical link between the mRNA and the amino acid sequence that will align opposite to a specific codon, transporting the latter to ribosomes.

Genes:

Gene: a specific sequence of DNA that encodes for a particular protein. Heritable

Locus (p: loci): specific position of a gene on a chromosome

Alleles: different possible variations of a gene

Gene mutation: change in the nucleotide sequence of a gene

Somatic: occurs in body cells and cannot be inherited

Germline: occur in sex cells (gametes) and is inherited

Genome: The complete set of DNA in an organism

Human genome: 46 chromosomes.

Gene splicing: The process used to add a gene into or remove genes from DNA.

Gene therapy: The process of replacing a defective gene with a normal gene.

Pluripotent embryonic stem cells: Cells that are able to self-renew by dividing and developing into the three primary groups of cells that make up a human body

Chromosome:

Chromosome: Single double-stranded DNA molecule

Plasmids: Autonomous genetic structure that can replicate independently of the chromosome, usually in prokaryotes.

Nuclear pores: a large complex of proteins that allows small molecules and ions to freely diffuse in and out of a nucleus

Cytosol: Aqueous component of the cell cytoplasm, in which various organelles and particles are suspended.

Diploid: two copies (complete set) of each chromosome (2n)

Haploid: one copy of each chromosome (n)

Homologous chromosomes: Paired maternal and paternal chromosomes found in diploid organisms.

Karyograms: Chromosome profile of an individual organism

Chorionic villi sampling: Cells are extracted from the placental tissue. Collected earlier (~11 weeks) - higher risk (1%).

Amniocentesis: Cells are extracted from the amniotic fluid. Collected later (~16 weeks) - lower risk (0.5%).

Autoradiography: A technique used to visualize uncondensed chromosomes by John Cairns.

Aneuploidy: The condition of having an abnormal number of chromosomes in a haploid set.

Polyploidy: The condition of having an abnormal number of chromosome sets due to malfunction of cytokinesis.

SIngle nucleotide polymorphism: Locations on chromosomes that differ by only one base from one human to another.

DNA → Protein:

Replication:

DNA replication: Duplicate DNA to create identical sister chromatids prior to cell division.

Transcription: Synthesise an RNA sequence from a DNA template.

Translation: The mRNA transcripts code for the production of polypeptides in ribosomes.

Semi-conservative: When new DNA molecules form they are composed of one strand from the original template and one newly synthesized.

Helicase: Enzyme that separates the DNA strands by breaking the hydrogen bonds between complementary base pairs.

Polymerase: Enzyme that covalently joins free nucleotides to their exposed complementary base pairs by using the energy from cleaving two of the phosphates.

Polymerase chain reaction:An artificial method of replication used to rapidly amplify DNA sequences.

Transcription:

RNA polymerase: Binds DNA and breaks the H-bonds and covalently joins RNA nucleotides

Antisense strand: RNA strand that is transcribed (the sequence is complementary to RNA script)

Sense: RNA strand that is not transcribed (the sequence is identical to script - except for T and U).

Translation:

Peptide: Two amino acids linked in a chain. Has a carboxyl and amino terminus.

Universality: All organisms use the same genetic code (few viral exceptions)

Degeneracy: More than one codon may code for the same amino acid, allowing silent mutations.

Cell division:

Cell cycle:

Interphase:

Interphase: An active period in the cell cycle where many key metabolic processes occur.

G1 phase: cell growth and metabolism.

S phase: DNA replication. The replicated chromosomes will consist of genetically identical sister chromatids.

G2 phase: cell growth and proof-reading

Chromatin: a mixture of DNA and proteins found in cells normally.

Chromosome: Chromatin strands that are condensed for mitosis.

Chromatid: one of the two identical halves of a chromosome

M phase:

Mitosis: Nuclear division, whereby each pair of sister chromatids are separated into two identical daughter nuclei.

Cytokinesis: Cytoplasmic division.

Prophase: DNA supercoils and chromosomes condense, the nuclear membrane breaks down, and centromeres go to opposite sides.

Metaphase: Mitotic spindle connects centromeres and centrosomes, aligning the chromosomes to the center.

Anaphase: Spindle fiber contracts, separating the sister chromatids.

Telophase: Chromosomes de-condense as the nucleus reforms. Cytokinesis occurs concurrently.

Cytokinesis (in animals): Microtube filaments form a cleavage furrow that contracts. it is centripetal.

Cytokinesis (in plants): vesicles form at the center of the cell to form a cell wall. It is centrifugal.

Cyclins: A family of regulatory proteins that control cell cycle progression.

Necrosis: Uncontrolled cell death

Apoptosis: Controlled cell death

Binary fission: Asexual reproduction by a separation of the body into two new bodies.

Cancer:

Cancer: caused by uncontrolled cell division.

Tumors: abnormal cellular growths formed as a result of cancer

Metastasis: The spread of cancerous tissue

Mutagen: an agent that causes a change in the genetic material of an organism. Can be physical, chemical, or biological

Carcinogens: Mutagens that cause cancer.

Oncogene: A gene that has the potential to cause cancer.

Meiosis:

Meiosis: Cell division for gametes.

Gametes: Haploid sex cells produced by sexually reproducing organisms. Female: ovum. Male: sperm.

Gametogenesis: the production and differentiation of gametes from haploid cells.

Bivalents: Homologous chromosomes associated in pairs.

Chiasma: The contact point between the two chromatids of a chromosome during meiosis.

Chiasmata: a point at which paired chromosomes remain in contact during the first metaphase of meiosis

Crossing over: Homologous chromosomes connect via chiasmata to form bivalents (tetrads) and exchange small portions of genetic information.

Random assortment: Homologous chromosomes line up in random orientation during metaphase I, giving humans 2^23 gamete combinations.

Gamete fusion: The diploid zygote will contain genetic formation from both parents’ gametes.

Non-disjunction: Chromosomes fail to separate during anaphase I or II, causing aneuploidy.

Inheritance:

Law of Segregation: Alleles are separated when haploid gametes form.

Law of Independent Assortment: The separation of alleles for a particular gene is independent of any other gene.

• Genes on the same chromosome do not independently assort.

Principle of Dominance: Recessive alleles will be masked by dominant alleles.

Alleles: Variations of a specific gene.

Three types of allele combinations:

• Homozygous: Alleles are the same.
• Heterozygous: Alleles are different.
• Hemizygous: There is only one allele.

Genotype: Allele combination for any given characteristic.

Phenotype: Physical expression of a characteristic influenced by genotype and environment.

Complete dominance: One allele is expressed over another in the phenotype. Capital for dominant and normal for recessive.

Co-dominance: both alleles are expressed equally in the phenotype. Uses superscripts

Sex-linked: Alleles are located on sex chromosomes.

Pedigree: a genetic history of a family over several generations.

Pure breeding: Where all individuals have the same genetic information through generations.

Mutations:

Mutagen: An agent that changes the genetic material of an organism. Physical, chemical, or biological in origin.

Point mutation: Modification of a single nucleotide within a sequence. Substitution, transition, and transversion.

Substitution mutations can cause:

• Silent mutation - No change to the polypeptide sequence.
• Missense mutation - A single amino acid is changed in the polynucleotide.
• Nonsense mutation - A stop codon (three consecutive nucleotides) is created, truncating (shortening) the polypeptide.

Transition: substitution of one purine for another purine or one pyrimidine by another pyrimidine.

Transversion: substitution of a purine by pyrimidine and vice versa.

Frameshift mutation: The result of the addition or deletion of nucleotides in the sequence of DNA, causing a shift of the reading frame of mRNA.

Insertion mutation: Addition to the nucleotide sequence that causes frameshift mutations (changes the reading frame)

Deletion mutation: Removal of parts of the nucleotide sequence that causes frameshift mutations (changes the reading frame).

Evolution:

Evolution: Cumulative change in the heritable characteristics of a population. It is the change in frequency of a gene pool across generations.

Gene pool: Sum total of all alleles present in a population.

Gene flow: The movement of genes between disparate populations via immigration or emigration.

Genetic drift: Change in gene pool composition due to chance events.

Population bottlenecks: An event reduces population size by an order of magnitude (>50%)

Founder effect: When a new population is established as a small subset of a larger population.

Artificial selection: Humans determine the trait by DNA manipulation.

Natural selection: Change in the composition of a gene pool as a result of selective environmental pressures.

Adaptations: Features that make an individual suited to their environment.

Analogous: Structures that appear similar or have the same function but are unrelated.

Australopithecus: A genus in the family Hominidae that is probably ancestral to the genus Homo.

Cross-breeding: Selective breeding combines a desirable feature with an individual desirable feature from another.

Generation: Time between birth and their own offspring.

Hominidae: The family to which humans belong

Homo: The genus to which humans belong.

Hybrid: Offspring of parents with different genotypes.

Inbreeding: Selective breeding between two closely related individuals

Linnaean classification: A hierarchical system of classifying organisms aimed at reflecting their evolutionary relationships.

Morphology: The physical form or structure of an organism.

Selection pressure: The effects of the selective agents on a population.

Selective agent: An environmental factor that acts on a population during natural selection

Sexual selection: Natural selection where the environmental factor is the selection of a mate.

Classification:

Artifical classification: Classifies species based on non-predictive features. Easy to develop and stable, but are not commonly used because they don’t consider species relatedness.

Natural classification: Classifies species based on evolutionary relationships. Highly predictive and mutable.

Phylogenetic: Classifies species based on genetic features.

All living organisms are categorized into 3 domains:

• Eukarya: eukaryotic organisms.
• Archaea: extremophilic prokaryotic organisms.
• Bacteria: common prokaryotic organism.

Taxon (pl. taxa): Standard classification unit of organisms derived from a single common ancestor.

Dichotomous keys: A method of identification where a group of organisms is repeatedly divided into two categories until each organism has been identified.

Plant phyla list: Bryophyte, filicinophyte, coniferophyte, angiosperms.

Animal phyla list: porifera, cnidaria, Platyhelminthes, annelids, molluscs, arthropods, chordates

Vertebrata classes list: Fish, amphibians, Reptiles, Birds, and mammals.

Speciation:

Stabilizing: An intermediate phenotype is featured over the extremes.

Directional: One phenotypic extreme is selected at the expense of another.

Disruptive: Both extremes are selected over an intermediate phenotype.

Speciation: An evolutionary process that results in the formation of a new species

Species: Organisms that can interbreed to produce fertile, viable offspring.

Phyletic Gradualism: Speciation resulting from a continuous change at a constant pace as a result of the gradual accumulation of genetic mutation over time. Supported by intermediate phenotypes in fossil records.

Punctuated Equilibrium: Speciation resulting from abrupt bursts that intersperse periods of stability, usually by rapid environmental changes. Supported by many gaps in fossil records.

Two main mechanisms by which speciation can occur:

• Allopatric speciation: Divergence due to geographical isolation.
• Sympatric speciation: Divergence within the same geographical location.

Pre-zygotic: Barrier that occurs before fertilization can occur (no offspring are produced)

Post-zygotic: Barrier that occurs after fertilization (offsprings are not viable or infertile)

Evidence for evolution:

Paleontology:

Fossils: Preserved remains or traces of organisms from the remote past.

Fossil record: Totality of fossils discovered and undiscovered.

Law of fossil succession: Over time changes occur in ancestral organisms with different species appearing in the fossil records in a systematic order.

Transitional fossil: An intermediary form of an evolutionary pathway that connects species to its ancestor or predicted descendant.

Comparative anatomy (homologous structure):

Homologous structures: Characteristics that share a common basic structure but used in different ways.

Adaptive radiation: A rapid increase in the number of species with a common ancestor when members occupy niches with different conditions.

Niche: The role an organism plays in a community

Vestigial organs: Reduced remnants of functional organs present in ancestors

Selective breeding:

Biogeography:

Biogeography: Distribution of life forms over different geological areas.

Notes:

Nucleic acid

DNA and RNA are made out of nucleotide monomers which contain: pentose (5C) sugar, a phosphate group, and a nitrogenous base.

Contributed to the foundation of the double-helix model: Watson, Crick, Pauling, Levene, Chargaff, Franklin.

DNA → Chromatin → Chromosome

Chromosomes

Prokaryotes:

• No nucleus
• DNA contained in ^^nucleoid^^
• Single chromosome (genophore)
• Circular and naked
• Genome more compact (usually no intron)
• may contain extra DNA molecules in addition to the genophore, known as plasmids.

Eukaryotes:

• Stored in a membrane-bound nucleus
• Nuclear pores allow the transport of RNA to the cytosol
• Multiple linear chromosomes
• DNA bound to histone proteins to form chromatin
• Genome less compact (has many introns)
• Exist as uncondensed chromatin except during cell division

Gene loci can be identified according to @@chromosome number@@, arm, and %%banding region%%

Homologous chromosomes:

• Identical structure features (size, band pattern, etc.)
• The same genes at the loci positions.
• Because paired chromosomes were of different origins (paternal and maternal), the alleles may be different.
• The 23rd pair of chromosomes is a heterosome because sex determination requires distinct chromosomes. Male (XY) and Female (XX).

Karyograms:

• Homologous pairs are arranged by length.
• Chromosomes there were arrested during mitosis.
• Used to identify sex or find abnormalities (aneuploidy).

DNA → Protein:

DNA replication:

Semi-conservatism:

• Each nitrogenous base needs its complementary pair so the base sequence is conserved.

• ^^Meselson-Stahl^^’s experiment supported the semi-conservative replication theory.

  

Polymerisation:

• New nucleotides align opposite their complementary base pairs as dNTPs (deoxyribonucleoside triphosphate)
• Synthesis occurs in a 5’ → 3’ direction.

Polymerase chain reaction:

There are three steps:

• Denaturation: Heat separates strands (no helicase)
• Annealing: Primers designate copying sequence.
• Elongation: Taq polymerase copies the sequence.

Transcription:

• The enzyme ^^RNA polymerase ^^==separates== the DNA strands and ==synthesises== an RNA copy (no helicase).
• After transcription is complete, the RNA sequence is ==released,== and the DNA double helix ==reforms.==
• The RNA then moves to the cytoplasm for ^^translation^^.

Sense:

Translation:

• An ^^mRNA transcript^^ is organized into triplets of nucleotide bases known as ^^codons.^^

Cell division:

Cell cycle:

Interphase:

M phase:

Functions of Mitosic Division:

• Tissue repair.
• Organismal growth
• Asexual reproduction
• Development of embryos

Meiosis:

• The first division ==separates== the ^^homologous chromosomes^^, turning them from diploid to haploid.

• The second division ==separates== the ^^sister chromatids^^- a mitotic division of haploid cells.

  

  

Three ways meiosis promotes ^^genetic variation^^:

• ^^Crossing between^^ non-sister chromatids (prophase I)
• ^^Random assortment^^ of homologous chromosomes (metaphase I)
• Fusion of gametes from %%different parents.%%

Non-disjunction:

• Anaphase I: @@all four@@ daughter cells will be affected:
• Anaphase II: @@two@@ daughter cells will be affected.

Inheritance:

Pedigree:

Mutations:

Genetic disorders include:

• Single gene disorder: When a mutation to a single gene alters or abrogates protein function.

  

• Chromosomal abnormalities

• Mitochondrial diseases

• Multifactorial disorders

Sickle cell anemia: Caused by the change in nitrogenous base substitution in hemoglobin, altering the red blood cell shape into a sickle that can’t carry oxygen as effectively, leading to anemia.

Huntington’s disease: Autosomal dominant disorder caused by a mutation to the HTT gene (chromosome 4) and will cause neurodegeneration, leading to dementia.

Cystic fibrosis: Autosomal recessive disorder caused by a mutation to the CFTR gene (chromosome 7) that produces thick mucus that clogs the airways and digestive tracks.

Red-Green colour blindness: X-linked recessive condition caused by a mutation in the red-green photoreceptors.

Haemofilia: X-linked recessive condition that is caused by mutations in coagulation factors resulting in sustained bleeding.

Evolution:

Evolution requires a @@source@@ of change and a mechanism of change.

Sources for change (@@variation@@):

• Genetic mutations
• Sexual production
• Gene flow (^^migration^^)

Mechanisms of change (selective pressure):

• Genetic drift
• Natural selection
• Artificial selection

Genetic drift:

• Greater when the population is smaller.
• Enhanced by ^^population bottlenecks^^ or the ^^founder effect^^.

Natural selection:

• Survival of the fittest.

Genotype frequency:

• Better-adapted individuals live longer and reproduce more, and vice versa,
• Results in a change in allele frequency as certain genotypes become more important.

Classification:

Purpose:

• Collect, sort, and group information about organisms.
• Enable identification of organisms with a collective understanding
• Comparison of organisms.
• Show evolutionary links.

Taxon:

Binomial nomenclature system:

• The genus is written first and capitalized (e.g. Homo)
• Species follow in lowercase (e.g. sapiens)
• Organisms may have a sub-species designation.
• All species have a common name.

Speciation:

Three main types of natural selection:

Stabilizing selection:

• An intermediate phenotype is featured over the extremes.
• Removal of the %%extreme phenotypes.%%
• %%Distribution%% becomes ==centrally clustered==
• Operates if conditions are stable (%%competition%% is ==low==)

Directional selection:

• One phenotypic extreme is selected at the expense of another.
• This causes the %%distribution%% to clearly shift in one direction
• Operates in response to ==gradual or sustained changes== in %%environmental conditions.%%

Disruptive selection:

• Both extremes are selected over an intermediate phenotype.
• Results in a ^^bimodal spread^^ of the ==distribution==.
• Occurs when fluctuating %%environmental conditions%% favor the presence of ==two distinct phenotypes.==

As organisms evolve and begin to genetically diverge, reproductive barriers emerge to keep the two populations from interbreeding.

Speciation caveats:

• Certain organisms do not reproduce sexually. (e.g. bacteria)

• Breeding capacity may be impossible to ascertain from fossil records.

• May be impossible for certain members of the same species to mate

• Ring species involve interlinking breeding with incompatible ends.

  

Natural selection:

Three stages of natural selection:

• Variation

• Adaptation

• Selection

  

Evolutionary theories:

Lamarck:

• Organismal change via habitual use and disuse (1801)
• Excessive use causes features to develop, continued disuse causes atrophy.
• E.g. giraffes grow long necks to reach high leaves.

Darwin + Wallace:

• Theory of descent with modification (1859)
• Beneficial traits have an adaptive advantage, leading to higher reproduction.
• E.g. Long-necked giraffes have more offspring because of their competitive advantage.

Neo-Darwinism:

• Combines Darwinian theory with Mendelian genetics.

  

Adaptations:

• Structural: Physical differences (e.g. neck length in a giraffe)
• Behavioral: Differences in the pattern of activity (e.e. opossums feigning death)
• Physiological: Variations in response by vital organs. (e.g. homeothermy)
• Developmental: Changes that occur throughout a lifespan (e.g. senescence)

Evidence for evolution:

Paleontology:

Fossils: Preserved remains or traces of organisms from the remote past.

Fossil record: Totality of fossils discovered and undiscovered.

Law of fossil succession: Over time changes occur in ancestral organisms with different species appearing in the fossil records in a systematic order.

Transitional fossil: An intermediary form of an evolutionary pathway that connects species to its ancestor or predicted descendant.

Conditions for fossilisation:

• Preservation of remains.

• Exposed to high pressure to promote mineralization (e.g. rapid burial)

• Subjected to anoxic (low oxygen) conditions to prevent decomposition.

  

Comparative anatomy (homologous structure):

Homologous structures: Characteristics that share a common basic structure but used in different ways.

Adaptive radiation: A rapid increase in the number of species with a common ancestor when members occupy niches with different conditions.

Niche: The role an organism plays in a community

Vestigial organs: Reduced remnants of functional organs present in ancestors

Selective breeding:

• Humans breed animals with desirable characteristics
• Leading to the exaggeration of certain traits in domesticated animals.

Biogeography:

Biogeography: Distribution of life forms over different geological areas.

• Related species tend to be in close physical proximity.
• Exceptions can be explained by continental drift.