Topic 1.1: Structure of water and hydrogen bonding

Properties of Water

Hydrogen Bonds + Polarity

• Polar: Oxygen has a partial negative charge, hydrogen has a positive charge

• Hydrogen bond: Weak bond between hydrogen in a polar molecule and a small electronegative atom, forms due to the two atoms’ opposite charges

  

• Cohesion: Hydrogen bonds hold a substance together

• Adhesion: Clinging of one substance to another-- especially between water and another polar substance

• Both adhesion and cohesion allow water to move against gravity

• Surface temperature: How difficult it is to break or stretch the surface of a liquid, water has a high surface tension due to hydrogen bonds

Temperature Moderation

• High specific heat: Water is able to absorb/release a lot of heat without its own temperature changing much, water absorbs warm air and releases it to cooler air. Allows climate moderation

• High heat of vaporization: Water has to absorb a lot of heat to change from a liquid to a gas and water cools when its molecules evaporate. Allows evaporative cooling

Ice Floats

• Water expands (becomes less dense) in its solid form, so ice floats

Floating ice insulates water below it

Solvent

• Solvent: The substance that dissolves other molecules in a solution

• H2O is a versatile solvent due to its polarity

• Water can carry many chemicals, nutrients, and minerals throughout an ecosystem and the organisms within it

Topic 1.2-1.6: Macromolecules and the elements of life

Carbon

• Carbon: Has 4 valence electrons so can form 4 covalent bonds, allowing it to be the backbone for many complex and diverse molecules

• Organic compounds: Compounds containing carbon

Functional Groups (not required course content but definitely helpful to know)

• Functional groups change function by being directly involved in chemical reactions

• Hydroxyl (OH-): Alcohol, make substance more basic (raises pH)

• Carboxyl (-COOH): Acid, contributes H+ (lowers pH)

• Amino group (-NH2)

• Phosphate group: Add negative charge to a molecule

Polymers and Monomers

• Polymer: A molecule made of similar building blocks

• Monomer: One of the units making up a polymer

• Dehydration reaction: Monomers connected and covalently bonded by removing a hydrogen from both molecules and an oxygen from one (making H2O)

Hydrolysis: Bond between monomers of a polymer is broken by adding H2O

Carbohydrates

• Contain elements: Carbon, hydrogen, and oxygen

• Monomer: Monosaccharide

• Polymer: Polysaccharides (chain of monosaccharides linked by covalent bonds called glycosidic linkages)

• Functions: Provide and store energy, provide structural support

Important polysaccharides (all are glucose polymers)

• Starch: Stores glucose in plants

• Glycogen: Glucose storage in animals

• Chitin: Structural polysaccharide in fungi cell wells and arthropod exoskeletons

• Cellulose: Cell wall component for plant cells

Lipids

• Elements: Carbon, hydrogen, oxygen (sometimes N or P)

• No true monomers of lipids

• Have little to no affinity for water (hydrophobic)

• Function: Energy storage and structure

• Saturated: No double bonds between carbon atoms, atoms tightly packed

• Unsaturated: Double bonds between some carbons creating a kink in the chain

Trigylcerol: 3 fatty acids attached to one glycerol, energy storage

Phospholipid: Form phospholipid bilayer, have a hydrophilic head and hydrophobic tail

Cholesterol: Steroid that contributes to cell membrane integrity

Nucleic Acids

• Elements: Carbon, hydrogen, oxygen, phosphorus

• Monomers: Nucleotides, consist of a 5 carbon sugar, a phosphate, and a nitrogenous base

  

• Polymers: Nucelic acids, linear sequences of nucleotides

• Nitrogenous base pairs: Adenine pairs with thymine (or uracil in RNA), and cytosine pairs with guanine

• Purines: Have a 2 ring structure (A and G)

• Pyrmidines: Have a 1 ring structure ( C and T/U)

  

• C and G are joined by 3 bonds, A and T are joined by 2

• Directionality: Determined by orientation of sugars (hydroxyl = 3´ and phosphate = 5´)

• Base pairs are joined by hydrogen bonds, nucleotides joined by covalent bonds

  

• DNA: Antiparallel double helix (2 strands running in opposite directions), has deoxyribose

• RNA: Single stranded, has ribose

Proteins

• Elements: Carbon, hydrogen, oxygen, nitrogen, sulfur

• Monomers: Amino acids, consist of carboxyl group + amino group + R group

• Different amino acids have different R groups

  

• Polymer: Polypeptide

  STRUCTURE

  • Primary: Linear sequence of covalently bonded amino acids

  • Secondary: Structure formed by interactions between polypeptide´s ¨Backbone¨ ( carboxyl and amino groups)

  • Tertiary: 3d structure formed by interactions ( hydrogen bonds, ionic bonds, disulfide bridge, hydrophobic, etc.) between R groups

  • Quaternary: More than one polypeptide chain joined together