1 ZOO 1 Notes by F5XS Zoology as a Science science (Latin scientia, knowledge) exact knowledge tested and verified by human

an experience facts real state of things data accumulated facts scientific method making careful observations; gathering data for formulating principles observation arouse speculation for explanation hypothesis tentative explanation; requires experimental support Specialized Fields of Science Fields of Zoology According to Discipline morphology (morphe, form) structure histology (histos, tissue) tissue microstructure cytology (kytos, hollow) cell structure and function physiology (physis, nature) living processes nutrition (nutrio, feed) use and conversion of food substances embryology (formerly developmental biology; en, in + bryo, swell) growth and development within the egg or mother genetics (genesis, origin) heredity and variation natural history animal life and behavior in the natural environment ethology (ethos, character) animal behaviour ecology (oikos, house) relationship of the animal to its environment zoogeography (zon, animal) animal distribution in space and time paleontology (palaeos, ancient + ont, being) fossilized animals evolution (e, out + volvo, roll) origin and differentiation of animals taxonomy (taxis, arrangement + nomos, law) animal classification Fields of Zoology According to Animal Groups Protozoology Protozoans Spongiology Sponges Round Worms Helminthology Worms Nematology Nematodes Mollusks Malacology Acarology Mites and Ticks Snails Entomology Insects Parasitology Parasites Ichthyology Fishes Herpetology Amphibians and Reptiles Orinthology Birds Mammalogy Mammals Characteristics of Living Things metabolism consists of a complex series of essential chemical processes occurring in living things anabolic (building-up) catabolic (breakdown) growth by intussuception new parts develop between or within older ones irritability ability to respond to environmental stimulus reproduction perpetuation of species definite form and characteristic size (range) chemical composition (mostly carbon, hydrogen, oxygen and nitrogen)

2 ZOO 1 Notes by F5XS Animals vs. Plants Criteria Animals Form rather invariable Organs mostly internal Cell Membrane delicate Body Fluid with NaCl Metabolism consumers Nervous present; react quickly System stimulus

to

Plants variable added externally with external cell wall NaCl is toxic to most plants producers absent; react slowly to stimulus

Manifestations of Life protoplasm (protos, first + plasma, form) colloidal complex of chemicals comprising the living substance of the cell colloid (kolla, glue) particles (10-5 to 10-7 mm diameter) suspended indefinitely particles too large to enter a solution (i.e. to be dissolved) particles too small to settle out of a solution (i.e. to precipitate) colloidal system a semi-rigid gel or a more fluid sol sol-gel reversals occur as consequences of metabolic processes Physical and Chemical Basis of Life Laws of Thermodynamics first law in any closed system, the total quantity of energy remains unchanged second law physical systems to proceed towards a state of greater disorder (entropy). The ultimate fate of materials in the cells is degradation and dissipation of their chemical bond energy as heat. Heat is the end form of all energy transformations. All energy forms may be transformed into heat, but heat cannot be completely transformed into other energy forms third law Chemical Constituents of Living Matter 95% of an organism is composed of C, H, O and N Inorganic Molecules: Water makes up 80% of the cell molecular shape looks like an isosceles triangle intermolecular distance: 0.099nm bond angle: 105 each water molecule has four neighboring water molecules 75% of the surface of the earth is covered by water makes up 0.06% of the mass of the earth gas giants may be as much as 50% water by mass water molecules cling together because of the hydrogen bonds between water molecules at water-air interference; a high surface tension is created when a crystal of NaCl dissolves in water, the negative ends of the dipolar molecules of water surround the Na+ ions, while the positive ends of water molecules face the Cl- ions; ions are this separated and do not reenter the salt lattice

3 ZOO 1 Notes by F5XS Inorganic Molecules: Oxygen constitutes 20.99% of the earths atmosphere much less soluble and diffuses slower in water than carbon dioxide solubility falls with increasing temperature and salinity Inorganic Molecules: Carbon Dioxide difficult to displace carbon dioxide from water solubility falls with increasing temperature and salinity forms an acid if dissolved in water increases the solvent powers of water forms one of the primary buffers CO2 + H2O [ H+ + CO3- ] H2CO3 this reaction is catalyzed by carbonic anhydrase Organic Molecules: Carbohydrates monosaccharides are aldehydes or ketones with two or more hydroxyl groups general formula is (CH2O)n disaccharides are two sugar molecules connected together by a glycosidic link oligosaccharides are short chain of sugars polysaccharides are long chain of sugars Organic Molecules: Lipids usually are fatty acids, sterols and phospholipids fatty acids are carboxylic acids with long hydrocarbon tails usually stored as an energy reserve or fat through the linkage with glycerol to form triglycerides sterols are complex molecules with three 6-carbon rings, one 5-carbon ring, and at least one OH-radical phospholipids are formed by triglycerides connected to a polar head by a phosphate makes up the bilipid layer of the cell membrane with the hydrophobic end in the middle of the layer and the hydrophilic end on the outer part of the layer a fatty acid is usually linked to other groups to form esters and amides Organic Molecules: Nucleic Acids polymers of nucleotides for protein synthesis and heredity the deoxyribonucleic acids (DNA) is the central information storage molecule there are three types of ribonucleic acid, the messenger (mRNA), transfer (tRNA), and ribosomal (rRNA) a nucleotide consists a sugar, a base and a phosphate the sugar base may either be D-deoxyribose or D-ribose, depending on the genetic material the base may either be purine or pyrimidine the purine bases are adenine and guanine the pyrimidine bases are cytosine and thymine the orientation of a DNA/RNA strand from left to right is described as 3-5 since the phosphate is bonded to the C-3 carbon of deoxy/ribose on the left and to the C-5 on the right a single turn of a double-helix strand has ten base pairs measuring 3.4nm

4 ZOO 1 Notes by F5XS Organic Molecules: Proteins biomolecules made up of amino acids an amino acid is composed of an amino group, a carboxyl group and the R group monomers of amino acids are joined by peptide bond carbon from the carboxyl group bonds with the nitrogen in the amino group forming water as a by-product the primary structure is determined by the type (of sequence), position and number of amino acids of a polypeptide chain the secondary structure may either by a pleated sheet or an -helix which are stabilized by hydrogen bonds a loop of the -helix has 13 atoms the tertiary structure is formed by folding, refolding and superfolding of the chain the quaternary structure describes the manner in which two or more polypeptides of a protein fit into each other

1665 1808 1809 1833 1838 1839 1848

Robert Hooke described in thin slices of cork and other plant materials minute partitions separating cavities he named as cells. Mirbel suggested that plants are made up of membranous cellular tissue Lamarck stated that any living body must have its parts of cellular tissue. Robert Brown described the nucleus as the central feature in plant cells. Matthias Jakob Schleiden stated that cells were the unit of structure in plants. Purkinje gave the name protoplasm to refer to the cells contents. Rudolph Virchow postulated the accepted form of the cell theory which states that, every animal appears as a sum of vital units, each of which bears in itself the complete characteristics of life..

The modern cell theory states that all animals and plants are composed of cells and cell products. Cytology (cell biology) is the study of cell structure and function. site of chromosomes site of DNA directed RNA synthesis RNA and protein synthesis protein synthesis membrane bound ribosomes (of RER) are major sites of protein synthesis synthesis of various lipids oxidation of many antibiotics defense site of many hydrolases

Nucleus Nucleoli Ribosomes

nucleic acids, proteins, lipids RNA, proteins RNA, proteins

Endoplasmic Reticulum

nucleic acids, proteins, lipids, carbohydrates

Lysosomes

enzymes

5 ZOO 1 Notes by F5XS degradation of fatty acids and amino acids production and degradation of H2O2 involved in changing shape of eukaryotic cells repositioning of internal organelles site of intermediary metabolism site of enzymes of glycolisis, gluconeogenesis, biosynthesis of fatty, amino and nucleic acids transport of molecules in and out of cells intercellular adhesion of communication intracellular storing of proteins glycosylation reactions sulfation reactions citric acid cycle oxidative phosphorylation (electron transport chain)

Peroxisomes

enzymes proteins, microtubules (25nm), intermediate filaments (10 nm), microfilaments (7nm)

Cytoskeleton

Cytosol

lipids, proteins

Plasma Membrane

lipids, (transmembrane) proteins, carbohydrates

Golgi Apparatus

proteins, lipids, carbohydrates proteins, lipids, carbohydrates, nucleic acids, coenzymes, inorganic ions, energy-rich systems

Mitochondrion

Plasma Membrane Note: a fold in the inner membrane selectively permeable fluid mosaic of the mitochondrion is called a made out of proteins and a lipid crista bilayer Note: a nuclear pore is octagonal the diffusion rate of transfer between with eight embedded proteins the lipid bilayer depends on the size of the molecule and its relative solubility in lipid hydrophobic molecules and small uncharged polar molecules go through large uncharged polar molecules and ions takes time to go through membrane transport proteins embedded on the protein aid molecules pass through the cell types of diffusion simple (passive) diffusion random movement of molecules from a higher to a lower concentration facilitated diffusion transport of molecules with the aid of a (protein) carrier active transport transport of molecules with the aid of a carrier at an expense of energy osmosis is the diffusion of water across the plasma membrane from low concentration to high concentration Cell Cycle and Mitosis total of 16 hours, M is 1 hour, G1 is 5 hours, S is 7 hours, G2 is 3 hours

6 ZOO 1 Notes by F5XS G1 growth phase after mitosis S DNA replication G2 protein production for cell division Mitosis division of the somatic cell Enzymes binds the substrate at its active sites, forming a temporary enzyme-substrate complex an allosteric site is a site other than the active site that inhibits the activity of the active site cooperative interaction is the speeding up of enzyme activity by inserting a substrate that induces higher enzymatic activity the rate of enzymatic activity is influenced by the substrate concentration, temperature, and pH Cell Respiration Notable Compound aerobic pyruvic acid (product) anaerobic acetyl-CoA (central molecule C6H12O2 6CO2 + 6H2O + 36ATP

Process Glycolysis Krebs Cycle

Place cytoplasm mitochondrion

Glycolysis: 6C (Glucose) 3C + 3C (two pyruvic acids) + 6ATP Krebs cycle; lactic acid is produced if not enough oxygen is present Krebs Cycle: 36 ATPs are produced from each molecule of glucose from glycolysis and Krebs cycle -oxidation: Stearic acid (18C) is broken down to two carbon pairs which combines to form acetyl-CoA to make a total of 147 ATP per stearic acid Amino acids are also used as energy source. Alanine, cysteine, cystine, glycine, hydroxyproline, serine and threonine converted into pyruvate which is then converted into acetyl-CoA. Phenylalanine, tyrosine, tryptophan, lysine, leucine are converted into acetyl-CoA without being converted into pyruvate. DNA Replication DNA polymerase is an enzyme that duplicates the DNA strands Okazaki fragments are fragments of the daughter DNA strand produced by not continuous duplication DNA duplication follows the 5-3 path three bases of the strand make up a codon which stand for an amino acid when transcribing