Bio 104 Final Review Notes

Chapter 2.1-2.3 Molecular Structures and Properties

• Matter: anything that takes up space and has mass (in the form of gas, solid, liquid).
• Elements: cannot be broken down into substances with different properties - has only 1 type of atom.
• Atom: smallest part of an element that displays the properties of an element - made of subatomic particles.
• Atomic number = protons
• Mass number = protons + electrons
• 6 elements basic to life = carbon, hydrogen, sulfur, nitrogen, oxygen, phosphorus.
• Atomic mass = number on periodic table.
• Radioactive isotopes = release various types of energy as they decay.
  • Low levels of radiation: can help tumors show up on scans.
  • High levels of radiation: can cause cancer and harm cells.

Bonds

• Molecule: 2+ atoms bonded together ($O_2$)
• Compounds: 2+ elements bond together ($H_2O$)
• Covalent bonds: atoms that share electrons so they have 8 in the outer shell.
  • 2 Types of covalent bonds:
    • Nonpolar - atoms share electrons equally.
    • Polar - one atom is more electronegative, pulling more electrons so the share isn’t equal.
      • High electronegativity = Nitrogen and oxygen
      • Low Electronegativity = Hydrogen and carbon
• Hydrogen Bonds: weak bond that arises between a slightly positive hydrogen atom of 1 molecule and a slightly negative atom of another molecule.
  • Partial opposite charges in different molecules attract each other.

Acids and Bases

• Acids: substances that release hydrogen atoms.
• Bases: release hydroxide ion.
• Polarity: something that has 2 sides with opposite charges (like a battery).
  • One side pulls electrons stronger (slightly -) and the other side has a weaker pull (slightly +).
  • Water is polar because the oxygen is slightly negative and the hydrogen sides are positive.
  • Polar bonds = O-H, N-H, O-C

Properties of Water

• Water has a high heat capacity
  • Important to all organisms because water temperature rises and falls slowly, organisms are better able to maintain their normal temperature and are protected from rapid temperature change
    • When heat is absorbed, hydrogen bonds are broken and water molecules can move freely
    • When water gets cold, hydrogen bonds form and release energy
• Water has a high heat vaporization
  • Hydrogen bonds hold the water molecules tightly together, so it takes a lot of heat to break them apart and let the water molecules escape as a vapor
  • Takes a lot of energy to turn water from a liquid to a gas
• Water is a solvent
  • It dissolves lots of substances
  • Due to waters polarity, it can surround itself around particles and pull them apart
• Water molecules are cohesive/adhesive
  • Cohesive = water molecules stick together because of hydrogen bonding (allows water to flow)
  • Adhesive = water molecules can cling to other polar surfaces (allows nutrients to stick to it when flowing through plants)
• Ice is less dense than liquid
  • Ice - molecules lock into a pattern leaving empty spaces
  • When ice floats it forms a layer on top of water which prevents the water from freezing solid and protects marine life

2.4 - Inorganic Molecules

• Organic Molecules: contain carbon and hydrogen (molecules of life)
• Inorganic molecules: does not contain carbon+hydrogen together
• Isomers: same chemical formula but different structure
• Functional groups: clusters of atoms attached to carbon skeleton of organic molecules
  • Determines how that molecule behaves and reacts
  • Always has the same chemical properties
  • How functional groups are positioned determine the chemical properties
• Polymers: macromolecules made up of repeating units called monomers that are linked together by covalent bonds
  • Carbohydrates, proteins, nucleic acids
  • Lipids contain 2 different subunits (glycerol and fatty acids) so they aren’t polymers
• Dehydration reaction: $H_2O$ is released to form polymers
• Hydrolysis reaction: $H_2O$ is added to break a polymer

Carbohydrates

• Monomer: saccharides
• Polymers: polysaccharides
• Function: short term energy source for living organisms, also structural role in plants
• Monosaccharides - simple sugar that can’t be broken down by hydrolysis
  • Simplest form of carbs
  • Basic building blocks
  • Classified based on number of carbon atoms they have (triose is 3 carbons, pentose is 5 carbons, etc)
  • OH group makes them soluble in water
• Examples of monosaccharides: (All isomers with molecular formula $C<em>6H</em>{12}O_6$)
  • Glucose - hexose sugar that acts as the primary energy source for cells
  • Fructose - fruits
  • Galactose - milk
• Disaccharide - composed of 2 monosaccharide molecules that joined together during dehydration reaction, linked by glycosidic bond
• Examples:
  • Sucrose ( glucose + fructose)
  • Lactose ( glucose + galactose)
  • Maltose ( glucose + glucose)
• Polysaccharides - complex carbs composed of long monosaccharide chains linked by glycosidic bonds ( insoluble in water)
• Types:
  • Energy storage
    • Starch - main energy storage in plants
    • Glycogen - in animals
  • Structural - provides support and protection
    • Cellulose - found in plant cell walls, humans cant digest

Lipids

• Monomers: fatty acid + glycerol
• Polymers: triglycerides and phospholipids
• Function - long term energy + fat storage
  • Hydrophobic
• Emulsifiers = molecules with a polar and nonpolar end
  • Nonpolar end surrounds fat/oils, polar ends bond with water
• Types:
  • Fats and oils (triglycerides) - long term energy storage
    • Composed of glycerol + 3 fatty acids
    • Saturated fats = solid
    • Unsaturated fats = liquid
  • Fatty acid - hydrocarbon chain that ends with a carboxyl group (COOH)
  • Saturated fatty acids - single bonds between carbon atoms
  • Unsaturated fatty acids - double bonds between carbon atoms
  • Trans fat - oils hydrogenated to make them solid
  • Phospholipids - glycerol + 2 fatty acids + phosphate group
    • forms the fundamental structure of cell membranes
    • Polar/hydrophilic head and hydrophobic tails
  • Steroids - have a backbone of 4 fixed carbon rings
    • Ex - cholesterol

Proteins

• Monomers = amino acids
• Polymers = polypeptides
• Function: structure and function of cells
• Amino acids:
  • Building blocks of proteins - composed of an amino group and an acid group
  • R group determined uniqueness of each amino acid
• Peptide Bonds:
  • From from dehydration synthesis
  • Remove $H_2O$ from carboxyl group and amino acid
• Levels of Protein Organization:
  • Primary structure
    • Linear sequence of amino acids joined together by peptide bonds, determines the proteins identity and shape
  • Secondary structure
    • Folding of the polypeptide chain into specific shapes due to hydrogen bonding between backbone atoms
  • Tertiary Structure
    • 3D shape of a single polypeptide chain formed by r group and amino acid, responsible for functional shape and stability
  • Quaternary Structure
    • 2+ polypeptide chains into a functional protein complex
    • Allows proteins to perform complex tasks

Nucleic Acids

• Polymer: DNA, RNA
• Monomer: nucleotides
• Function: genetic info
• 2 types:
  • DNA - deoxyribonucleic acid
    • Makes up genes and controls cell activities
    • Double stranded
  • RNA - ribonucleic acid
    • Directs protein synthesis
    • Single stranded
• Formation:
  • Nucleotides are joined together into a DNA or RNA polymer by a series of dehydration synthesis
  • - backbone is made of alternating sugar-phosphate molecules
  • The bases project to 1 side of the backbone
• Nucleotides: monomers of nucleic acids
  • Phosphate + nitrogen base + pentose (5 carbon) sugar

Cellular Organization

• Cells - basic units of life in living organisms
• 2 Types:
  • Prokaryotic - lack a membrane bound nucleus
    • Found in bacteria and archae
  • Eukaryotic - possess a membrane bound nucleus and complex internal organelles
    • Plants, fungi, animals, protists
• Cell theory:
  • All organisms are composed of 1+ cells
  • Cells are the basic living structure and function in organisms
  • All cells come only from other cells
• 3 Domains of Life
  • Bacteria (prokaryotes)
  • Archaea (prokaryotes)
  • Eukarya (fungi, plants, animals)

Prokaryotic Cells

• Simple cells
• No nucleus
• No membrane bound organelles
• 2 Types:
  • Bacteria-
  • Archaea
• Structure:
  • Capsule - shield that surrounds the cell wall of some bacteria
  • Cell wall - outside of plasma membrane consisting of peptidoglycan (only in bacteria)
  • Plasma membrane - phospholipid bilayer, protein embedded deeply or on surface
  • Flagellum - long/thin appendage used for movement
  • Fimbriae - short appendages that help attach to surfaces
  • Nucleoid - region of cytoplasm where a single bacteria chromosome is located
  • Ribosomes - used for protein synthesis
  • PRO=NO NUCLEUS/MEMBRANE BOUND ORGANELLES

Cell Envelope

• What is it?
  • The capsule, cell wall, and plasma membrane
• Glycocalyx = coating outside the cell wall
  • Provides resistance against a hosts immune system
  • Helps bacteria attack surfaces

Eukaryotic Cell

• Larger
• Has nucleus and membrane bound organelles
• Plants, fungi, animals
• Plant cells have a primary and secondary cell wall
  • Primary - composed of cellulose and provides strength
  • Secondary - inside the primary, composed of lignin, structure support
• Structures: