Biology 12. Biochemistry. Water - a polar molecule Water (H 2 O) is held together by covalent bonds.

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1 Biology 12 Biochemistry Water - a polar molecule Water (H 2 O) is held together by covalent bonds. Electrons in these bonds spend more time circulating around the larger Oxygen atom than the smaller Hydrogen atoms. This causes a slight positive ( This makes water a POLAR molecule. Hydrogen Bonds The positive end (hydrogen) of 1 water molecule and the negative end of another water molecule attract each other. This attraction forms a weak hydrogen bond between water molecules. +- charge on the Hydrogen atoms and a slight negative ( - charge on the Oxygen atom) Diagram showing hydrogen bonding between water molecules Hydrogen bonds can form between any polar molecules. For example, the bond between nitrogenous bases in DNA is a weak hydrogen bond. Properties of Water - due to hydrogen bonding 1. Water is an excellent solvent (other materials) can dissolve in it easily. This is because polar molecules will be attracted to either the positive or negative ends of a water molecule. 2. Water is a good lubricant - ex. is found in joints of the body. This is because water molecules stick together due to hydrogen bonding. Therefore, water has surface tension. 3. Water acts as a good temperature regulator - ex. sweating. This is because water can absorb a lot of heat before its hydrogen bonds are broken, and water vapor (gas) is formed.

2 Acids and Bases Acids - dissociate to give up H + (hydrogen ions) - hydrogen ions can be called protons have a ph of less than 7 ex. hydrochloric acid (HCl) found in the stomach Bases -dissociate to give up OH - (hydroxide ions) have a ph of greater than 7 ex. NaHCO 3 (sodium bicarbonate) found in pancreatic juice. ph - a measure of the hydrogen ion concentration. Any ph below 7 is acidic and any ph above 7 is basic (alkaline). Human blood has a ph of 7.4 (slightly basic). A solution that has a ph of 2 is 10 times more acidic than a solution with a ph of 3. The kidneys aid in maintaining a constant ph by removing H+ from the blood. ph Scale ph = 7 = neutral [H + ] = [OH - ] Explain how the ph of the following solutions was determined. Buffers: A substance or compound that prevents large changes in ph. When an acid is added to a solution, a buffer takes up excess hydrogen ions. When a base is added to a solution, a buffer takes up excess hydroxide ions (OH - ) Therefore, in the presence of a buffer the ph value changes less (or ph does not change) Example: hemoglobin (Hb) acts as a buffer in the blood by taking up excess H + Neutralization Reaction Acid + Base Salt + Water Example: HCl + NaOH NaCl + H 2 O

3 Polymers A large molecule made up of many identical sub-units (unit molecules) Polymers can be broken down into sub-units by hydrolysis. Polymers can be put together (formed) by dehydration synthesis. Examples: Starch and glycogen are polymers of many glucose molecules. Proteins are polymers of many amino acids. DNA is a polymer of many nucleotides. Hydrolysis: Breaking a bond by using the elements of water to break a larger molecule into several smaller molecules. Examples: Starch can be broken down into smaller carbohydrates (eg. glucose)by adding water Proteins can be broken down into smaller peptides or amino acids by adding water. Dehydration Synthesis: Forming a polymer by removing water to link unit molecules together. Examples: Glucose linked together to form polysaccharides. Amino Acids linked together to form proteins. Use the following diagram as a summary of dehydration synthesis and hydrolysis.

4 Carbohydrates - (CH 2 0) n Consist of carbon, hydrogen & oxygen (2H to every O) Monomer is called a monosaccharide (ex: glucose) 2 monosaccharides joined together form a disaccharide (ex: glucose + glucose = maltose) more than 2 monosaccharides joined together form a polysaccharide Carbohydrates are the main source of energy in the body. Polysaccharides (or complex carbohydrates) serve as food (energy) storage. Monosaccharides simple sugars used by all organisms as energy source Disaccharides 2 monosaccharides joined together to form a molecule Dissacharides and polysaccharides are too large to enter the blood stream so they must be digested (Broken down) to monosaccharides. Monosaccharides like glucose can then be absorbed into the blood stream. Example - starch to maltose by enzyme amylase. (Amylase produced by salivary glands in mouth and by pancreas which empties into the duodenum. Example - maltose to 2 glucoses by enzyme maltase. (in small intestine) Polysaccharides Many monosaccharides joined together in long polymer chains. Three most common: starch, glycogen, cellulose Types of Polysaccharides 1. Starch: energy storage (glucose) in plants. Relatively straight chain of glucose molecules, has few side chains. Provides a reserve of glucose molecules to produce energy (ATP).

5 2. Glycogen: energy storage (glucose) in animals. Highly branched polymer of glucose molecules. Liver and muscles store glucose as glycogen. Insulin promotes the storage of glucose as glycogen by liver. Provides a reserve of glucose molecules for use in cellular respiration to produce energy (ATP). The wall experienced by marathon a runner occurs when glycogen reserves in muscles have been used up. 3. Cellulose: forms cell wall of plants, used for strength not a food store. Contains a slightly different linkage between glucose molecules. Herbivores can digest this with the help of micro-organisms in their intestines. Example. rabbits have enlarged caecums full of cellulose digesters. Cellulose cannot be digested by humans - called roughage or fiber

6 Proteins: Polymers made up of amino acids - amino acids are the unit molecules or subunits of proteins. Uses of Proteins: 1. Structural - ex. collagen 2. Enzymes catalysts (speed up chemical reactions) 3. Hormones - chemical messengers that travel through blood stream 4. Transport - ex. hemoglobin 5. Storage - albumin 6. Contractile - muscle proteins 7. Antibodies - produced by white blood cells Amino Acids - monomer of proteins Deamination - the removal of the amine group from an amino acid. The functional or R group is different for each amino acid and gives each its I.D. There are 20 different amino acids.

7 Peptide Bonds - formed by dehydration synthesis join amino acids together Formation of a peptide bond Dipeptide - contains 2 amino acids, the beginning of a polypeptide Polypeptide - many amino acids joined together in a chain R groups extend from the chain A very long polymer of amino acids is called a protein if it has a function in the body.

8 Primary Structure of Protein Straight chain of many amino acids forming a polypeptide Proteins do not usually exist in this state for long because of polar and Hydrogen bonds that form between amino acids. This turns the chain into a spiral form called the secondary structure. Denaturation When a protein loses its normal shape or configuration. Normal bonding between the R groups has been disturbed. This affects the proteins ability to work properly. Factors that cause denaturation: 1. Excessive heat in the human body that would be temperatures above 37 C 2. Extremes of ph this depends on the ph range of that particular area of the body Example: the blood ph = approximately 7.4. Extremes would be any ph above or below 7.4 Example: the stomach has a ph = approximately 2 or 3. Extremes would be any ph above or below 2 or 3 3. Heavy metals (mercury - Hg, lead - Pb)

9 Lipids - not soluble in water (insoluble in water) 1. Neutral fats triglycerides Contain 3 fatty acids in this polymer Used for longer term energy, insulation and cushioning around organs Fatty acid types: a. saturated fatty acids 3 fatty acids Filled with Hydrogen No double bonds between carbon atoms b. monounsaturated fatty acids Not filled with Hydrogen One double bond between carbon atoms more Hydrogenated c. polyunsaturated fatty acids Not filled with Hydrogen Many double bonds between carbon atoms Unsaturated fatty acid types: a. Omega 3 fatty acids anti-inflammatory Food sources: Fish (brain food), flax seeds, walnuts, virgin olive oil b. Omega 6 fatty acids Food sources: meat, eggs, dairy c. Trans fatty acids from hydrogenated fats Straight, rigid chain fatty acids (normal cis fatty acid is bent and flexible) Lowers HDL, raise LDL can lead to cardiovascular disease, cancer, diabetes, obesity, liver dysfunction, depression 2. Phospholipids Contain 2 fatty acids in this polymer Used to form cell membranes Phospholipid structure: Polar head (hydrophilic) 2 non-polar tails (fatty acids) (hydrophobic) Phospholipid bilayer: cell membrane structure 3. Steroids and cholesterol Belong to lipid group because they are not soluble in water Include many hormones like the sex hormones (testosterone, estrogen and progesterone) Cholesterol found in cell membranes + can be converted to steroid hormones Cholesterol has many other functions in the body

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