BIOL150 Test 1 Review.pdf

BIOL150 REVIEW FOR TEST 1 TEST #1  Thursday September 26, 2024  Will include material from all lectures & self guided learning (on Blackboard)  Will consist of multiple choice and short answer questions.  Worth 20% of your final mark. Review  Matter: has vo...

BIOL150 REVIEW FOR TEST 1 TEST #1  Thursday September 26, 2024  Will include material from all lectures & self guided learning (on Blackboard)  Will consist of multiple choice and short answer questions.  Worth 20% of your final mark. Review  Matter: has volume and mass and is either a solid, liquid or gas  Element: something that can’t be broken down into a smaller substance by chemical reaction  Essential element: something that an organism needs to grow (C, H, O, N, P, S)  Trace element: an element in a sample that is present at less than 100 ppm, OR an element needed in minute quantities for the proper growth of an organism (micronutrient) Review  Atom: one unit of an element; smallest particle that retains properties  Compound: a pure chemical consisting of two or more elements bonded to each other; can be separated chemically  Molecule: one unit of a compound  Mixture: two or more substances mixed together but not chemically bonded to each other Review  Protons: positive charge in the nucleus  Neutrons: neutral particle in the nucleus  Electrons: fundamental particles with a negative charge  Atomic Number: tells you the number of protons in an atom  Mass Number: tells you the number of protons plus neutrons. Review  Ion: an atom that is either missing or has extra electrons  Isotope: an atom that is either missing or has extra neutrons  Radioactive decay: the loss of neutrons from an isotope  Review  Electron orbitals (shells): where the electrons are found. They are found in the following order…  1s orbital contains 2e  2s orbital contains 2e  2p(x,y,z) each contain 2e for a total of 6e  3s contains 2e  3p(x,y,z) each contain 2e for a total of 6e  Generally, atoms are most stable when they have 8e in their outermost shell.  Practice determining the electron orbitals for elements up to Argon on the periodic table Review  Types of intramolecular chemical bonds:  Covalent: atoms that share electrons, usually because they have similar electronegativity (H2O, ethanol, urea)  Can be characterized as single, double or triple bonds, depending on number of shared electrons.  Ionic: one atom “steals” an electron from another because it is much more electronegative, and the resulting positive/negative charges hold the two together (NaCl, NaF, KCl)  Weaker than covalent bonds, and typically form between a metal and a non-metal Review  Types of intermolecular chemical bonds:  Hydrogen bonds: when a partial positive charge of one molecule is attached to the partial negative charge of another  any molecule that has an H attached to an electronegative atom that has a lone e pair can H-bond  Which type of bond is better for cellular biology? Why? Review Organic molecules: contain C-H bonds; tend to be found in or produced by living things. Examples… Carbohydrates, such as glucose, cellulose, and fructose Lipids, such as wax, tallow, and detergent Proteins, such as collagen and enzymes Nucleotides, such as DNA and RNA Hydrocarbons, such as methane, benzene, and asphalt Other carbon-containing compounds, such as formic acid, caffeine, and penicillin Are generally larger and more complex Inorganic molecules: not normally found in living things, usually no C-H bonds Are generally simple. Examples… Salts, such as sodium chloride (NaCl), calcium oxide (CaO), and carbonates Metals and alloys, such as silver, brass, and iron Substances made from single elements, such as diamond, sulfur, and helium Carbon monoxide (CO), carbon dioxide (CO2), and ozone (O3)  Review  Special properties of water:  Most abundant compound on Earth’s surface.  Only common substance found naturally in all 3 states of matter.  55-78% of human body  Solid form less dense than liquid form. WHY?  High specific heat capacity and heat of vaporization! WHY? Examples of how these are used?  Specific heat: amount of energy required to change the temp. by a given amount  Heat of Vaporization: amount of heat required to transform water from liquid to gas Review  Special Properties of water cont’d:  Be able to draw a water molecule, showing where the charges are, and be able to show how many H-bonds can form with other water molecules.  Cohesion (water sticks to water) and adhesion (water sticks to other materials) WHY?  Water has highest surface tension (cohesion at surface) of all non- metallic liquids  Capillary action: water molecules adhere to straw molecules; cohesion pulls more water along and surface tension straightens out the surface  Temperature moderation of earth’s climate  pH of pure water is neutral; of rain is ~5.6 (know why rain is not pH = 7)  Water is a good solvent due to it’s polarity.  Hydrophobic (water hating) vs. hydrophilic (water loving)  Define: Polarity, electronegativity Review  Acids, Bases and pH:  Be familiar with the pH scale  Hydroxyl ion (OH-) is alkaline; pH above 7  Feel slippery, change litmus blue  Hydrogen ion (H+) is acidic; pH below 7  Taste sour, change litmus red, corrosive to metals  Salts and water are formed when acids and bases are mixed together (neutralization reaction)  Strong vs weak acids and bases (complete vs incomplete dissociation in water)  Buffer: a mixture of a weak acid and its base or a weak base and its acid; work by reacting with added acids or bases to maintain the pH in a solution (they mop up extra H+ or OH-)  Why is this important? Review  Organic chemistry:  4 major classes (carbohydrates, proteins, nucleic acids, lipids)  Know how to draw the principal functional groups: methyl, hydroxyl, carbonyl (aldehyde AND ketone), carboxyl, amino, sulfhydryl and phosphate  Where might you find these groups?  What do they do (in general)? Review  Monomers: atoms or molecules that can bind chemically to others  Polymers: many monomers bound together  How do they do this?  Hydrolysis: breaking up a polymer into smaller units; water is broken to add hydroxyl group to one and hydrogen ion to another  Condensation reaction (dehydration synthesis): monomers are joined together to form a polymer; water is produced. Review  Carbohydrates: carbon plus hydrogen…  Also called saccharides  Monosaccharide: single sugars (glucose, galactose, fructose)  Are either aldoses or ketoses. What’s the difference?  Disaccharide: double sugars (lactose, sucrose)  Linked by glycosidic bond (alpha vs beta)  Polysaccharides: several sugars (starch, cellulose, glycogen, chitin); ideal storage molecules  Linked by glycosidic bonds  We can’t digest cellulose. WHY? Review  Lipids: hydrophobic molecules, include fats, oils, waxes, phospholipids, steroids, etc.)  Non-polar (hydrophobic)  Fats and oils: made up of glycerol (3C alcohol) + 3 fatty acid tails(triglycerides)  Fatty acids are long (non-polar) hydrocarbon chains with a carboxyl group “head” (polar)  When attached to glycerol the head is no longer polar.  Saturated vs unsaturated  Fats are saturated  Oils are unsaturated  Can be monounsaturated or polyunsaturated Review  Phospholipids: consist of choline+phosphate group+ glycerol+fatty acid chains (2)  Hydrophobic tail + hydrophilic head  Steroids: rings system of 3 6C rings and 1 5C ring  Cholesterol- made in brain, nerve tissue, blood  Testosterone- responsible for dev. of male genitals, 2° sex characteristics; synthesized from cholesterol  Estrogen (synthesized from testosterone) and progesterone- control ovulation  Waxes: long chain alcohol (12-32 C) + fatty acid  Found coating leaves/stems Review  Proteins: very important molecules that are made up of chains of amino acids.  Structural (keratin)  Enzymes  Transport molecules (cell membrane channels)  Hormonal  Receptors on cell surfaces  Defense mechanisms (antibodies)  Storage  Contractile and movement  Proteins have 1°, 2°, 3° and 4° structure Review  Amino acids:  Contain an amino group, a carboxyl group, a hydrogen atom and a variable functional group, all attached to the central α-carbon  Are joined by (covalent) peptide bonds  There are 20 amino acids used by humans to build proteins (21 in some other organisms).  The variable functional group is what determines the amino acid. Review  Enzymes are proteins that act as catalysts in reactions; that is they make reactions happen more easily.  Three characteristics:  increase reaction rates;  act on specific substrate;  can go forward or backward  Substrates fit in a groove called the active site (think lock and key). Taxonomy and Cell Theory Which scientist in 300 BC classified living things into plants and animals Who was the first scientist to view a living cell Know what is binomial nomenclature (Genus species) How would you write a human? Know the order of the different classifications: Domain-Kingdom-Phylum-Class-Order-Family-Genus-Species Cell Theory  Know the 3 basic components of the original cell theory:  All organisms are composed of 1 or more cells  The cell is the basic unit of life in all living things  All cells are produced by the division of preexisting cells  Modern cell theory additions:  The cell contains DNA which is passed on during division  All cells are basically the same in chemical composition  All basic metabolic and physiological functions happen inside the cell  These activities depend on the activities of sub-cellular structures  Some organisms are unicellular, others are multicellular Some Definitions  Binomial nomenclature: organization of a scientific name into a two term system, Genus and species.  Eukaryotes: have a nucleus and other membrane bound organelles  Prokayotes: simpler organisms, lack organelles  Intercellular: between cells  Intracellular: inside a cell  Extracellular: outside a cell  Spontaneous Generation: the thought that organisms spontaneously arose from other things.  Prokaryotes vs Eukaryotes  Prokaryote = no nucleus, no membrane bound organelles, includes bacteria and archaea, small (0.3-2μm), simple organisms, arose ~3.5 billion years ago  Eukaryote = nucleus, and all other organelles, much larger (2-20μm, much more complex, arose 1.5 billion years ago  Common features: cell membrane, cytoplasm, DNA (although prokaryotic DNA is “naked”), ribosomes  Why do eukaryotes have organelles? (Eukaryotic) Cell Anatomy Make sure you can label the main structures of a plant and an animal cell! Cell Membrane  Semi-permeable, made mostly of phospholipids (in a bilayer) and proteins (forming pores, acting as binding sites)  How do substances enter the cell?  Things like O2 and CO2 dissolve in the lipid portion  Charged things have to go through the pores  Large molecules like glucose can’t pass through on their own, they have to cross in a vesicle The Nucleus  2 main functions:  To contain cell’s hereditary info (DNA)  Coordinate cells activities (growth, metabolism, protein synthesis, division)  Know the structure:  Nuclear membrane (envelope)-- phospholipid bilayer with protein lining called the lamina  Also connects to ER  Nuclear pores allow things in and out  mRNA needs to get out  Nucleoplasm is the liquid matrix inside, where the chromatin is  Nucleolus: has no membrane, makes ribosomes Cytoplasm  Made up of water, electrolytes and nutrients, as well as enzymes  Contains organelles and temporary structures (proteins, water vacuoles, vesicles, granules)  Endocytosis (the cell engulfs something and brings it in)  Exocytosis (the cell expels the contents of a vacuole outside of the cell) Mitochondria  Main role is ATP (energy) production  Cells that do a lot of work (muscle cells, liver cells) have a lot of mitochondria  Mitochondria have their own DNA, inherited maternally  Know the structure:  Outer membrane with a lot of transport proteins  Inner convoluted membrane (to increase surface area) Ribosomes  Made up protein and RNA together  Made in the nucleolus  Can either be free-floating or embedded in ER; singular or in chains (polyribosomes)  Ribosomes translate mRNA into protein Endoplasmic Reticulum  A single, continuous membrane that is folded into flattened sacs extending from the nucleus into the cytoplasm  Provides a channel through which substances can travel (cisternal space)  Rough ER manufactures and packages proteins  “Packaging” includes folding proteins into their appropriate shape, or adding modifications (sugars, methyl groups)  Smooth ER mainly produces lipids  Is also involved in detox and calcium storage and metabolism  Brain, muscle and liver cells have lots of SER  Finished products are sent via vesicles to their destination in the cell or more often to the Golgi apparatus for further processing Golgi Apparatus  The “post office” of the cell– sorts, packages and transports products received from the ER  Vesicles enter at cis face and deposit their contents into the membrane. Molecules move through the stacks, are modified (glycosylation, phosphorylation, signal sequence) by enzymes, and exit at the trans face in another vesicle. Lysosomes  Membrane bound, heterogenous vesicles filled with enzymes that break down cellular debris (worn out organelles, ingested cells, nucleotides, lipids etc.)  Lysosomal enzymes are active only at low pH (4.5-4.8)  Referred to as cells garbage disposal The Cytoskeleton  Only found in EUKARYOTES  Provides attachment sites for organelles and other structures, gives structure and stability to the cell, allows cellular movement  Composed of a network of protein fibres: Microvilli, Cilia and Flagella  Not present in all cells  Microvilli: small, finger-like projections on cells that  surface area of cells, provide structure and help with movement, microfilaments provide structure  Cilia: (think of little hairs) bigger than microvilli but smaller than flagella, numerous, help move mucous in resp. tract, microtubule cylinders at core  Flagella: longer and whip-like, singular, microtubule cylinders at core, only one type of human cell has them Plants vs Animals  Plant cells have cell walls, plastids, and one large vacuole.  Plant cells have a centrosome but not centrioles.  Intercellular Cell Junctions  Link cells together (intercellular)  Tight junctions: seal the space between cells so that nothing can pass through; (think intestinal epithelial cells, bladder cells to contain urine)  Gap junctions: use channels to connect the cytoplasm of neighboring cells to allow for fast communication (think of heart muscle cell contractions) Transport of Large Molecules  Exocytosis – movement out of cell via intracellular vesicle  Endocytosis – cell engulfs extracellular fluid and material in creates a vesicle called an endosome  Phagocytosis – cell ‘eating’; endosome very large and called a phagosome or vacuole  Pinocytosis – cell ‘drinking’; ingestion of dissolved materials by endocytosis