The Chemistry of Life IB Biology

Biochemistry Elements of life Most common elements of living things: (3.1.1) Carbon (C) Hydrogen (H) Oxygen (O) Other elements both plants and animals have: (3.1.2 & 3.1.3) Nitrogen (N) DNA and RNA Amino acids (proteins) Calcium (Ca) Component of cell walls Component of bones and teeth

Phosphorus (P) ATP Adenosine triphosphate stores energy in both plants and animals DNA and RNA Iron (Fe) In hemoglobin (animals) In cytochromes Molecules in the electron transport chain (ETC) of: –Photosynthesis (in plants) –Cellular respiration (in plants and animals) Sodium (Na) Ion used for osmosis – “salty roots” Ion used for nerve transmission in animals

Atom vs. Ion Ex: Hydrogen Atom Ion – charged particle 1 p + 1 n 0 1e - 1 p+ 1 n 0 (no electron orbiting) H H+H+

Water (3.1.4) 1. Structure - OH + water is polar (has a positive and + H negative end) Hydrogen Bond OH 1. alone they are weak 2. together they are strong Hex: slide on a desk OHOH H Oxygen is very electronegative, which means it has an affinity for the electrons it is “sharing” in the covalent bond with hydrogen. The hydrogen bond is the attraction between the slightly positive H and the slightly negative O

2. Thermal Properties of Water (3.1.5, 3.1.6) a)Water has a high heat of vaporization Takes a lot of heat to change the state of water from a liquid to a gas 60 times more energy to vaporize water than alcohol Because energy (heat) is required to vaporize water (even when it’s at its boiling point), evaporation of water cools down surfaces (SKIN, LEAVES)

a) b)Water has a high specific heat 2X that of alcohol 4X that of air 1 calorie raises 1 gram of water 1 o C Keeps temperature of water constant c) Water changes density as it freezes 10 o C4 o C 0 o C Less dense Most dense Least dense (sinks) (ice floats)

3. Cohesive properties of water (3.1.5, 3.1.6) Molecules stick together (hydrogen bonds) Due to polarity Water moves up the xylem in plant stems –Capillary action –Cohesion and adhesion »Adhesion occurs when water clings to xylem tissue during plant transpiration

Solvent properties of water (3.1.5, 3.1.6) Salt (ionic-ally bonded) is dissolved in water (because it’s polar) and carried by blood Na+ -O H+ + H Cl - Hydrophilic – has an affinity for water; “water-loving” ex: glucose in blood sucrose in plants Hydrophobic – water fearing ex:oil, grease Question: When is it beneficial to have lipids be hydrophobic?

5. Significance of water to living organisms (3.1.6) PLANTSANIMALS A. Coolantevaporationevaporation -use of heat foron leaf causesof sweat causes evaporationcoolingcooling (high heat of Vaporization) B. Transportcarries carries mediumsucroseglucose -because its polarity causes it to be a good solvent

PLANTSANIMALS C. Good habitat- water stays at a constant -due to temperature high specific heat 1.Keeps temperature constant 2.Transparency -photosynthesis-see prey

Organic – contains carbon (and usually hydrogen), and is found in a living organism -ex: C 6 H 12 O 6 glucose Exceptions: Hydrogencarbonates – (a.k.a. bicarbonate) the anion HCO 3 - Carbonates – the anion CO 3 - Oxides of carbon – carbon monoxide (CO), carbon dioxide (CO 2 ) (3.2.1) (continuing… NOT talking about water anymore!)

4 Biological Molecules: 1. Carbohydrates (sugars) Monosaccharides – major nutrients for cells glucose, galactose, fructose, ribose Glucose circulates in animal blood and is used by cells for energy (3.2.4) Fructose is the sugar in the fruit of plants Disaccharides glucose + glucose  maltose glucose + fructose  sucrose glucose + galactose  lactose Lactose is the sugar in milk – gives energy (3.2.4) Sugar is transported as sucrose through the vascular tissue of plants (3.2.4) (3.2.3)

Polysaccharides (3.2.3.& 3.2.4) Energy-storing in plants: starch Energy-storing in animals: glycogen Structural in plants: cellulose Structural in animals: chitin All of these are made of chains of glucose molecules

2. Proteins (structure, enzymes) Amino acids are the building blocks 2 amino acids – a dipeptide Peptide Bonds R R R R H 2 N – C – C – N – C – C – N – C – C – N – C – C – OH || || || || H O H H O H H O H H O Amino Carboxyl This is a ‘polypeptide’

3.2.5 Condensation & Hydrolysis Reactions When are joining subunits (monomers) of molecules together to make polymers, a water molecule is given off. This is a condensation synthesis. When a polymer is broken into monomers, a water molecule is used. This is hydrolysis. NH 2 -–C—COOH + NH 2 —C—COOH  NH 2 —C—CO—NH—C—COOH + H 2 O RRRR H HHH Mono Polymer Water

3. Lipids (fats; mainly for energy storage, thermal insulation, and structure) HGLYCEROL O3 FATTY ACIDS | || HCOHHO C (CH 2 ) n CH 3 O || HCOHHO C (CH 2 ) n CH 3 O || HCOHHO C (CH 2 ) n CH 3 | H Hydrolysisvs. Condensation Synthesis(3.2.5, 3.2.6) H O | || HCO C (CH 2 ) n CH 3 O || HCO C (CH 2 ) n CH 3 O || HCO C (CH 2 ) n CH 3 | H +3 H 2 OLipid + Water

Phospholipid O - | R – O – P – O – CH 2 || | O H – C – O – C – (CH 2 ) n – CH 3 | H – C – O – C – (CH 2 ) n – CH 3 | H POLAR HEAD (hydrophilic) NON-POLAR TAIL (hydrophobic) OOOO This negative oxygen makes this part of the molecule hydrophilic

Energy Storage (3.2.7) Carbohydrates vs.Lipids Soluble in water,Insoluble in water, do not easily transported in bloodcause problems with osmosis Broken downquicklyBroken down for energy for energymore slowly Less energy per gramTwice as much energy per gram

4. Nucleic Acids (DNA & RNA) (3.3.1, 3.3.2) Made of nucleotides (these are the monomers) Phosphate Sugar Nitrogen Base Nitrogen Bases Adenine Guanine Cytosine Thymine (*DNA only) Uracil (*RNA only) Ribose or Deoxyribose sugar

DNA (3.3.3, 3.3.4, 3.3.5) P DATDDATD DGCDDGCD DCGDDCGD DGCDDGCD -double stranded -Helix (twisted) -A-T and G-C are complementary (weak) hydrogen bond One nucleotide Covalent bond

RNA P R U P R A P R C P-single strand R G-U instead of T

You MUST be able to recognize the following molecules from diagrams showing their structure: (3.2.2) Amino acids Glucose Ribose Fatty acids