Science: Biology

SCIENCE: BIOLOGY Biology the study of living organisms, divided into many specialized fields that cover their morphology, physiology, anatomy, behavior, origin, and distribution. • Principal branches of biology • Morphology – deals with both the external and internal structures of organisms. Subject concerning internal structures is also known as anatomy. • Cytology – deals with the structures and functions of cells. • Histology – deals with the structure, location and function of different tissues. Physiology – includes all the • activities of living things (e.g growth respiration, excretion, photosynthesis, etc.) Taxonomy – discussion is made • on identification nomenclature, and classification of plants and animals into groups and subgroups. • Genetics – talks about how different characters are inherited from parents to offspring, and how the processes can be controlled and improved. • Ecology – considers the effects of the environment on living organisms or living communities and interaction between them. • Evolution – deals with the origin and successive transformations of living organisms. • Some special branches of biology have been created based on different types of living organisms: • Phycology – algae • Mycology – fungi Virology – viruses • • Bacteriology – bacteria Helminthology – worms • • Entomology - insects Aristotle – father of biology and zoology Theophrastus – father of botany Carolus Linnaeus – father of modern taxonomy Gregor Johan Mendel – father of genetics • • Characteristics of Plants and Animals • Size and shape – Plants have no definite size and shape while animals have definite size and shape. • Lifetime – Lifetime is not limited to plants and under suitable conditions they live for a long period. But animals live up to a certain length of time under • • • • • • suitable conditions. Growth – In a suitable environment growth of many plants continues for a long period. Growth in animals takes place up to a certain stage of life and growth ceases after that. Movement – Most land plants remain fixed in soil with the help of roots and as a result they cannot move, some organs of plants may show some movement. A few animals (Such as Sponge) are not capable of movement. Most of the animals can move freely. Nature of Food – Plants cannot take solid food Animals can take solid and liquid types of food. Nutrition – Plants are autotrophic, it can prepare food through photosynthesis. Animals cannot prepare their own food. For food they are to depend on plants and other animals. Structure of Cell – A Plant cell has dead cell wall. Most of the mature cells have a large vacuole and plastids. The animal cell has no cell wall, and it contains small vacuoles and centrioles. Reproduction – Plants reproduce by vegetative, asexual, and sexual methods. Reproduction in animals mainly takes place by sexual method. Vegetative and asexual reproduction may be found in some animals. There are different systems in the animal body. But plants have no body system. Organizational levels of life (lowest to highest) • Biomolecules & biomolecular complexes include proteins, RNA/DNA, lipids, and carbohydrates. • Organelles are functional groups of biomolecules and are sites of biochemical reactions. Cell is the basic unit of all life and • is made up of organelles. • Tissues are groups of cells that perform the same function. • Organs are groups of tissues that perform the same function. Organ system is a group of • organs that perform the same function or are involved in the same process, e.g. digestion • Organism or a life form refers to any individual entity that exhibits the properties of its species/kind. • Populations are groups of organisms of the same species. • • • Communities are groups of interacting populations existing in one common place and time. Ecosystems include both living factors (communities) and abiotic factors (environment: air, water, soil, etc). Biome is made up of communities of flora and fauna that span climatically and geographically contiguous areas with similar climatic conditions. Biosphere is the sum of all ecosystems on the planet. Taxonomic Ranking Taxonomic Example rank (modern (general to human) specific) Domain Eukarya Kingdom Animalia Phylum Chordata Class Mammalia Order Family Carnivora Hominidae Genus Species Homo Homo sapiens The cell Commonly used suffixes Plants: -phyta Plants: -phyceae, -opsida, -ae Plants: -ales Plants: -aceae Animals: -idae - Species to remember Found in the Philippines • Pithecophaga jefferyi (Philippine eagle) • Bubalus mindorensis (tamaraw) • Bubalus bubalis (carabao / water buffalo) • Jasminum sambac (sampaguita) • Musa textilis (abaca) • Musa squamosa (banana) • Passer montanus (maya bird) • Chanos chanos (bangus) • Mangifera indica (mango) • Pterocarpus indicus (narra) • Macaca fascicularis (Philippine macaque) • Oryza sativa (rice) Model organisms • Drosophila melanogaster (fruit fly) • Escherichia coli • Saccharomyces cerevisiae (baker’s yeast) • Danio rerio (zebrafish) • Mus musculus (house mouse) Animal cell Plant cell Nucleus Nuclear envelope – perforated; continuous with ER Nucleolus – nonmembranous; ribosome production; 1 or more; rRNA synthesis Chromatin – consists of DNA and proteins Synthesis organelles Endoplasmic reticulum (ER) – membrane synthesis and metabolisms Rough ER – with ribosomes Smooth ER – lipid synthesis Ribosome – protein synthesis; can be free (in cytosol) or bound (to rough ER or nuclear envelope) Golgi apparatus – synthesis, modification, sorting, & secretion of products Structure Cytoskeleton – cell shapes and movement Microfilaments – structure Intermediate filaments – spread from the nuclear envelope to the plasma membrane. Microtubules – movement in animal cells; structure in plant cells Centrosome – microtubule initiation; has a pair of centrioles Peroxisome – produce hydrogen peroxide then converts to water Mitochondrion – site of cell respiration and ATP generation Lysosome – digestion of macromolecules through hydrolysis Central Vacuole – storage and breakdown of waste, hydrolysis of macromolecules Chloroplast – converts light energy to chemical energy in the form of sugar Plasmodesmata – cytoplasmic channels through cell walls of adjacent cells • Tonicity • The ability of an extracellular solution to make water move into or out of a cell by osmosis, The cell cycle Terminology • Chromatin contains uncondensed genetic material. • Chromosome contains condensed genetic material. • Sister chromatids - joined copies of the originalchromosome. • Centromere - a region made up of repetitive sequences in the chromosomal DNA where the chromatid is attached most closely to its sister chromatid. • Centrosome - a subcellular region containing material that functions throughout the cell cycle to organize the cell’s microtubules; with 2 centriole pairs. Nonkinetochore microtubules elongate the cell. • Telophase • Nuclear envelopes arise and nucleoli reappear. Cytokinesis • Separation of daughter cells Cleavage furrow - animal cell • • Cell plate - plant cell Meiosis • • • • • Nonkinetochore microtubules lengthen at the sides. Metaphase • Centrosomes are now opposite poles of the cell. at Interphase - DNA replication Meiosis I - separation only occur in diploid cells. • Prophase I • Crossing over of genes duplicated homologous chromosomes pair up and exchange segments. • Metaphase I - Chromosomes line up by homologouspairs. • • • of homologous chromosomes; can • MITOTIC PHASE (M) Mitosis • the division of one nucleus into two genetically identicalnuclei. Prophase • DNA replicates • Mitotic spindle forms • Nucleolus disappears. Prometaphase • Nuclear envelope fragments. • Kinetochore forms at the centromeres (2 per chromosome) for kinetochore microtubules. Chromosomes align at metaphase plate (imaginary plate) Anaphase • Shortest stage (few minutes). • Cohesin proteins are cleaved by separase enzyme which separates the sister chromatids. • INTERPHASE (I) • Growth 1 (G1) - first gap • G0 - the cell exits the cell cycle; optional. • Synthesis (S) copies chromosomes • Growth 1 (G2) - second gap • • Anaphase I - homologs separate. Telophase I - Two haploid (n) cells form; each chromosome. still consists of two sister chromatids. Cytokinesis Meiosis II - separation of sister chromatids • Prophase II • Metaphase II • Anaphase II • Telophase II • • Cytokinesis 4 haploid daughter cells Gametogenesis • Process by which gametes, or germ cells, are produced in an organism. • Oogenesis • The formation of egg cells or ova • Spermatogenesis • The formation of sperm cells or spermatozoa The Central Dogma Replication • Occurs in the nucleus (for eukaryotes) or the cytoplasm (for prokaryotes). • • • • Make copies of DNA • Guanine pairs with Cytosine • Adenine pairs with Thymine Involves a leading strand (replicated from 5’ to 3’) and a lagging strand (replicated from 3’ to 5’). Enzymes involved in DNA Replication • Helicase: Unzips your genes (literally!) • Primer: Starting point for replication • DNA polymerase: Replicates DNA Ligase: Glues DNA segments • together Okazaki fragments are segments of replicated DNA in lagging strand. Transcription • Occurs in the nucleus (for eukaryotes) or the cytoplasm (for prokaryotes). • • A segment of DNA is copied out to make RNA. Thymine becomes uracil, so Adenine pairs with Uracil instead. • Performed by RNA polymerase. • • • • • • Translation • Occurs in the cytoplasm. happen alongside • Can transcription in prokaryotes. • A segment of RNA is translated per codon (groups of three base pairs) into amino acids. • • Start codon: AUG (becomes Methionine) Stop codons: UAA, UAG, UGA Genetics terminologies • Genes - hereditary units • Locus - a gene’s specific location along the length of a chromosome. • • • • • • • • • • Somatic cells - all cells of the body except the gametes and their precursors; can not undergo meiosis. • • Germ cells - sex cells; produces • • Karyotype - ordered display of chromosomes. Homologous pair/homologs - • • • • • gametes; can undergo both mitosis and meiosis. same length, centromere position, and staining pattern. Sex chromosomes - refer to the X and Y chromosomes. Autosomes - chromosomes other than X and Y Diploid cell - usually denoted as 2n; any cell with two chromosome sets. Haploid cell - usually denoted as n; contains a single set of • chromosomes (i.e. gametes). Character - a heritable feature that varies among individuals, e.g. flower color. Trait - each variant for a character, e.g. purple or white color for flowers. True-breeding - had produced only the same variety as the parent. Hybridization - crossing, of two true-breeding varieties. P generation – parent F1 generation - from Latin filial, meaning son; first filial. Allele - alternative versions of a gene. Dominant - determines the organism’s appearance. Recessive - no noticeable effect on the organism’s appearance. Homozygous - gene that has a pair of identical alleles. Heterozygous - gene that has two different alleles. Phenotype an organism’s appearance or observable traits. Genotype - genetic makeup. Monohybrids - heterozygous for the one character being followed in a cross. Dihybrids - heterozygous for the two characters being followed in a cross. Pleiotropy - from the Greek pleion, more; having multiple phenotypic effects, especially in alleles (e.g. sickle cell anemia, albinism, autism). Epistasis - Greek for standing upon; the phenotypic expression of a gene at one locus alters that of a gene at a second locus (e.g. golden fur in Labradors). Quantitative characters - vary in the population in gradations along a continuum (e.g. hair color & height in humans). • Usually indicates polygenic inheritance - additive effect of two or more genes on a single phenotypic character. Laws of genetics Law of segregation • The two alleles for a heritable character segregate (separate from each other) during gamete formation and end up in different gametes. twoparental varieties. Codominance • The alleles each phenotype Law of independent assortment • Two or more genes Example: Human blood genotypes • alleles segregates independently of Phenotype Genotype A gamete formation. IAIA, IAiO B AB IBIB, IBiO IAIB O iOiO heterozygous (Aa) two organisms, what is the probability that they will have a homozygous recessive (aa) offspring? • To get an aa organism, each parent must contribute a recessive gamete. • Each heterozygous (Aa) parent has 1/2 chance of contributing a recessive gamete. • Therefore, the chance of an aa offspring = (1/2) x (1/2) = 1/4. Addition rule “either/or” situation mutually exclusive events Example: Given two heterozygous (Aa) organisms, what is the probability that they will have offspring with dominant phenotypes? • From a Punnett square: a cross between heterozygotes will yield the genotypes AA, Aa, Aa, and aa. • Therefore, the chance of a dominant offspring = 3/4. Degrees of dominance Complete dominance F1 offspring always resemble only • one of the two parental varieties. Incomplete dominance F1 hybrids have a phenotype • somewhere between those of the the separate, any other pair of alleles- during Probabilities in genetics Multiplication rule • “and” situation • mutually inclusive events Given • Example: • • • affect distinguishable ways. assort independently- that is, each pair of in Pedigree Conventions • box = male • circle = female • shaded shapes = carriers Types of genes • Autosomal genes - affect both male and female equally. • Sex-linked genes • Affects all males due to them being hemizygous, i.e. have only one X chromosome. Skips generations (crisscross inheritance passed through female child) • • • If the gene is dominant, more females are affected. Dominant genes • Present in every generation. • Common in pedigree charts. • Affects half the children. Recessive genes • Affected child is born to unaffected parents (skips generation). • • Rare in pedigree charts Genotypes are always homozygous. • Holandric (Y-linked) genes • Males only • Passed from father to son. • Does not skip generations. • Cytoplasmic genes • Mother transfers genes to all children. Cladograms • Used in phylogenetic systematics; shows organisms. relation between • Monophyletic – group contains ancestor and all descendants. • Paraphyletic – group contains ancestor and some descendants. • Polyphyletic – common ancestor. group without