1.5 – Biological Chemistry

Organic compounds – compounds containing C atoms bound to other elements• Main atoms found in the body: C, H, O, N

Functional group – a cluster of atoms that gives compounds specific chemical properties• Causes chemical reactions between organic

compounds

Functional Group Structural Formula

Hydroxyl

Carboxyl

Amino

Sulfhydryl

Phosphate

Biological Compounds

Macromolecules – large molecules sometimes composed of repeating subunits

There are 4 major classes:1. Carbohydrates2. Lipids3. Proteins4. Nucleic Acids

Carbohydrates

Contain C, H, and O atoms in a 1:2:1 ratio (Ex. Glucose C6H12O6)

Used as sources of energy, building materials, and cell surface markers for cell-to-cell identification and communication

Can be classified into 5 groups:

1. Monosaccharides – “simple sugars”• single chain of carbon atoms with hydroxyl

groups attached• identified by the carbonyl group and number

of carbons (pentose, hexose)• Ex. Ribose (DNA), glucose, fructose (fruit),

galactose (milk)

2. Disaccharides – two simple sugars attached to one another• Glycosidic linkages – covalent bonds holding

monosaccharides to one another • Ex. Maltose (2 glucose), sucrose (glucose,

fructose), lactose (glucose, galactose)

3. Polysaccharides – complex carbohydrates• Hundreds to thousands of monosaccharide

subunits held together by glycosidic bonds• Energy storage and structural support• Ex. Starch• Polymers – large molecules made of long

chains of repeating subunits• Monomers – the individual part of a polymer

4. Cellulose – glucose polymer found in plant cell walls• Humans can’t digest it b/c of the bonds it has• Cellulose passes through the human digestive

system undigested– Helps waste pass through

5. Chitin – modified form of cellulose that forms the tough exoskeleton of insects, fungi, and crustaceans • Used in contact lenses and stitches

LipidsMade of C, H, O; hydrophobic – contain more non-polar O-H bonds

Used for storing energy, building membranes and other cell parts, and as chemical signalling molecules

Can be divided into 4 types:1. Fats and OilsEnergy-storing molecules in living organisms; 1g fat = 9 calories

Animals convert excess carbohydrate into fat and store the fat molecules as droplets in the cells of adipose tissue

Triglycerides – lipids containing 3 fatty acids attached to a single molecule of glycerol • Glycerol – 3-C alcohol containing a hydroxyl

group attached to each carbon• Fatty Acid – long H-C chains containing a

hydroxyl group (COOH) at each end

Saturated triglyceride:• Has single bonds between carbons• Has the maximum number of hydrogens possible• Straight chains• Solid at room temp

– Ex. Butter

Unsaturated triglyceride: • Has double bonds between 2 or more carbons• Has less than the maximum number of H’s possible• Liquid at room temp• Monounsaturated – only 1 double bond• Polyunsaturated – more than 1 double bond

– Ex. Canola oil

2. PhospholipidsGlycerol attached to 2 fatty acids (hydrophobic tails) and a highly polar phosphate group (hydrophilic head)

Found in cell membranes as the phospholipid bilayer – 2 layers with the phosphate heads on the outside and the fatty acid tails on the inside • Water can’t pass through the bilayer because

it’s mainly non-polar

3. Sterols (steroids)• Compact hydrophobic molecules containing 4

fused hydrocarbon rings and many different functional groups. Ex. Cholesterol

4. Waxes• Long-chain FA’s linked to alcohols or carbon rings• Used for waterproof coatings on plants and

animal parts

Proteins

Polymers of amino acids

Amino acids – a protein building block• Has a central C, amino group, carboxyl group, H atom, and

side chain (different)• 20 different amino acids – 20 different functional groups• Essential – body can’t make them; must get them from

food (8/20)• Nonessential – your body can make them (12/20)

Used as structural building blocks, functional molecules, enzymes, immunoglobins, transportation devices

Peptide bond – bond between amino acids in a protein molecule

Polypeptide – a short chain of amino acids

Protein Synthesis – amino acids get joined together to make a protein• As the amino acid chain grows, it folds (due to

attraction/repulsion forces)• If the protein doesn’t fold properly, it won’t

work properly (won’t fold properly due to a change in just one amino acid)

A protein has 4 structures:

1. Primary – the sequence of amino acids in the polypeptide

2. Secondary – the way that the polypeptide is shaped (α-helix, β-sheets)

3. Tertiary – the way that the polypeptide is folded

4. Quaternary – 2 or more polypeptides attached together (making a functional protein)

Protein DenaturationA change in the 3D shape of a protein• Caused by high temperatures (>40 deg) or

acidic, basic, or salty environments

Causes the protein to not work properly due to bent or broken peptide bonds

Will return to its normal shape once it is out of the harsh environment, as long as the peptide bonds aren’t broken

Fever above 39 degrees can denature enzymes in the brain leading to seizures or death

Curing meats with lots of salt, or picking preserves food by denaturing the enzymes in bacteria that causes food to go bad

Heat denatures proteins in hair so people can curl or straighten it

Coagulation – permanent change in a protein’s shape due to the breaking of bonds between amino acids

Nucleic Acids

Stores hereditary information that determines structural and functional characteristics

Nucleic acids are made of strands of nucleotides

Nucleotides are made of 3 components:1. A 5-C sugar (ribose in RNA, deoxyribose in

DNA)2. A phosphate group3. A nitrogenous base

• There are 4 types of nitrogenous bases: adenine (A), guanine (G), cytosine (C), thymine (T)

• A and G are purines• T and C are pyrimidines

Deoxyribonucleic Acid – double-stranded

Ribonucleic Acid – single-straned

DNA

• The sugars and phosphate groups for the backbone of the DNA or RNA

• The sugars and phosphates join together through a phosphodiester bond and the nitrogenous-bases face each other forming a “double helix”

A complimentary strand of DNA is made such that the N-bases bind as follows: A with TC with G

• A binds with T because 2 hydrogen bonds can form between them

• G binds with C because 3 hydrogen bonds can form between them

RNA• Single strand of NTs (mRNA and tRNA)• Contains uracil U, instead of thymine T• Codes for protein

The Central Dogma

DNA → RNA → protein

All of the features of our body are made of protein, which is coded for by DNA

Gene – a sequence of nucleotide bases in DNA• Each gene codes for 1 protein → 1 gene, 1 protein hypothesis

TranscriptionA section of DNA that codes for the protein to be made is unwound and unzipped, exposing the N-bases

Nucleotides come together and form a “complimentary” strand to the DNA• This strand is called messenger RNA (mRNA) and

has uracil (U) binding to A (no T)

The mRNA strand detaches from the DNA → single strand → leaves the nucleus, goes to the cytoplasm, and the ribosome subunits bind to it

TranslationThe ribosome that is attached to the mRNA moves over a sequence of 3 nucleotides → codon• A codon codes for a certain amino acid

When the ribosome is over the codon, it sends a signal to the complimentary tRNA codon (anticodon) to bind to the mRNA codon• The tRNA will be holding the proper amino acid, coded for by

the mRNA

• Once the tRNA and amino acid are in place, the ribosome moves over to the next codon

• The complimentary tRNA comes in and holds the aa in place and a peptide bond is formed between the 1st and 2nd amino acid

• Once the bond is formed, the first tRNA goes to get another amino acid in case it is needed again

• This process keeps happening until a chain of amino acids is formed

• Once the chain is formed, the ribosome subunits fall off the mRNA and the mRNA is recycled

• Depending on the sequence of amino acids, the protein will fold in certain ways, attaining its secondary and tertiary structure, and will bind to other proteins, attaining its quaternary structure– Then, the protein is functional

• The structure of the protein is important → change the structure, change the function

Homework

• Pg. 35 # 1, 2, 5-13