Biological Molecules

PLO C1 (32, 34, 38, 41, 55)

PLO C2 (31 – 42)

PLO C3 (not in text)

PLO C5 (32, 33)

The major categories of Biological molecules are:

Ø

These organic molecules all contain carbon (C) and hydrogen (H).

Carbohydrates

Ø Proteins

Ø Lipids (Fats)

Ø Nucleic Acids

· All of these molecules exist primarily as organic polymers in living things. A polymer is a molecule that is made up of small repeating units called monomers.

Polymer	Monomer
Carbohydrate	Monosaccharide
Protein	Amino acid
Nucleic Acid	Nucleotide

· Each of the above categories has different monomers however they all join together the same way through a condensation synthesis reaction.

· Furthermore, all of the polymers listed above can break down into their monomers through a hydrolysis reaction.

Carbohydrates

Functions

· for quick and short-term energy storage in all organisms. Glucose is a reactant for cellular respiration.

· have structural function in plants, bacteria and insects.

· have cell recognition role – the ‘glycoprotein’ cell markers on outside of membrane are referred to as the glycocalyx. These markers are individualized and this is the mechanism by which donor organs are rejected by recipients. These are the basis for the A, B, O blood groups

· The glycocalyx also help cells adhere to each other.

Structure

· All carbohydrates have approximately 2 hydrogen atoms and 1 oxygen atom (ie. water) for each carbon atom hence the name ‘hydrates of carbon’.

· Usually, the formula for carbohydrates is given as the molecular formula which gives clues about the structure of the molecule, however the empirical formula of a carbohydrate is sometimes used. ex: glucose molecular formula is C₆H₁₂O₆, whereas the empirical formula is CH₂O. Although easier to write, it happens to have the same empirical formula as fermaldehyde and can be therefore confusing.

· There exists two categories of carbohydrates: Simple and Complex

Simple carbohydrates include the monosaccharides and the disaccharides. A monosaccharide is a 3 to 7 carbon chain or ring. A dissaccharide is when two monosaccharides are joined through a condensation synthesis reaction.

Monosaccharides	Disaccharides
glucose	maltose (glucose + glucose)
fructose	sucrose (glucose + fructose)
galactose	lactose ( glucose + galactose)

Complex carbohydrates (Polysaccharides) are polymers and are made up of many monosaccharides joined together. Starch, glycogen and cellulose are three examples.

1. Starch is a storage form of glucose in plants. Up to 4000 glucose units per starch molecule. There is some side branching so, these 4000 are not all in a single line. Ingested starch gets broken down to glucose by digestive enzymes (both salivary and pancreatic amylase and maltase) and then the body stores it as…

2. Glycogen is a storage form of glucose in animals. Considerably more side branching than starch molecules. Glycogen storage is largely in the liver, and the liver slowly releases hydrolyzed glycogen (glucose) into the bloodstream between meals to maintain 0.1% glucose concentration.
3. Cellulose is a structural polysaccharide used in plant cell walls. Cellulose is also long chains of glucose monomers, but every second bond joining monomers is upside down. This alternation makes this molecule indigestible and is commonly referred to as fibre.

Biological Molecules - Lipids

PLO C7 (34)

PLO C8 (34, 35, 49, 53, 68, 69, 410, 388, 419)

Lipids (Fats and Oils, Phospholipids, and Steroids)

Functions

· Fats function as energy storage molecules, insulators against heat loss, and cushion tissue for organs.

· Oils are generally something in our diet, however they are converted to fats in our bodies and therefore only function as a nutrient.

· Phospholipids are the main component of membranes.

· Steroids generally act as hormones (messenger molecules) and are also components of cell membranes (cholesterol)

Structure

• All lipids are insoluble in water on their own. Emulsifiers allow lipids to mix into water. An emulsifier has a non-polar end that points towards the fat/oil and a polar end that allows it to be dissolved into water. Bile contains emulsifiers.
• Fats and oils OR triglycerides OR neutral fats

o All formed from one glycerol molecule reacted with three fatty acid molecules through a condensation synthesis reaction.

o Fatty acids come in two varieties:

§ Saturated: the carbon chain is completely surrounded by hydrogen; only single covalent bonds between the carbons. Solid at room temp.

§ Unsaturated: the carbon chain is partially surrounded by hydrogen because of some double bonds between the carbon atoms. Liquid at room temp. Often are hydrogenated in foods.

• Phospholipids

o These are similar to the triglycerides except there are only 2 fatty acids. Instead of a third, there is a phosphate/nitrogen group.

o The phosphate/Nitrogen group is charged and phospholipids therefore have non-polar hydrophobic regions (fatty acids and the glycerol) and polar hydrophilic regions (the phosphate/nitrogen group).

• Steroids

o Basic structure is 4 fused carbon rings with various functional groups around the outside.

o Cholesterol is the classic steroid and is the precursor for many other hormones in the body (ex. Testosterone, and estrogen).

o Cholesterol is a component of cell membranes.

Biological Molecules – Proteins

PLO C9 (37, 545)

PLO C10 (39)

Structure

The monomer of proteins is the amino acid.

Amino acids are made up of a central carbon atom attached to a hydrogen atom and 3 groups. Two of these groups are the same for all amino acids: the amine group and the carboxyl group. The last group is different for all of the amino acids; this is commonly referred to as the ‘R’ – group. The generic structure for all amino acids is then:

There are 21 amino acids that are required for building proteins in our bodies. They can be categorized in two ways:

• Essential vs. non-essential amino acids
• Essential amino acids must be ingested since our bodies do not manufacture these molecules
• Non-essential amino acids can be made by our bodies from other amino acids.

• Polar vs. non-polar: This designation has implications about the different levels of structure that can be achieved as we will note later.

Amino acids join together through condensation synthesis reactions to form peptides as shown below.

®

+

Dipeptides – two amino acids joined through condensation synthesis to form a peptide bond between them

Polypeptides – three or more amino acids joined through condensation synthesis

Proteins – when a peptide reaches has 50 or more amino acids then it is referred to as a protein.

Levels of protein structure (see text diagram)

Primary – the specific sequence or order of the amino acids in a protein.

Secondary – includes the tendency for amino acid chains to form alpha-helical shapes and beta-pleated sheets.

Tertiary – the folding of the amino acid chain and it’s secondary structures into a globular shape

Quaternary – the joining of two tertiary proteins determines a quaternary level of protein structure. Ex. hemoglobin

Biological Molecules – Protein Functions

PLO C11 (37, 58-59, 68-70, 74-77, 83, 84, 196, 200, 272-275, 244, 247, 253, 410)

Functions

· Structural roles

- keratin: makes up hair and nails

- collagen: support in ligaments, tendons, and skin

- actin and myosin: make up muscle fibres in muscle cells that allow contraction AND are a major component of the cytoskeleton of cells.

- tubulin: hollow cylinders of globular protein arranged in rows to make microtubules; also a major component of the cytoskeleton. They act as highways for organelle movement.

- kinesin: protein that moves vesicles/organelles along a microtubule

- dynein: protein that moves vesicles/organelles along a microtubule

- histones: protein associated with DNA to make chromosomes

- intercellular filaments: hold cells together

· Hormonal roles

- insulin: messenger molecule in blood from pancreas that signals for cells to absorb glucose.

- cyclin: messenger molecule in blood to signal cells to go into stages of mitosis.

· transportation roles

- hemoglobin: transports O2 in the blood.

· cell recognition roles

- complement system proteins: aid the immune response

- antibodies: used by immune system to help identify foreign material or specific antigens in the blood

- MHC proteins: mark cells as belonging to ‘self’

- glycoproteins: are cell markers that are a combination of protein and carbohydrate.

· Membrane proteins

- act as channels for specific molecules to cross membrane.

- act as carriers for specific molecules to cross membrane.

- act as receptors for very specific molecules (ex. there are receptor proteins for insulin) which can signal certain cellular functions.

- act structurally to shape cells

· enzyme proteins

- cytochrome c: involved in glucose metabolism.

- lactase: breaks lactose into it’s monosaccharides

- pepsin: breaks protein down into small peptides in the stomach.

- trypsin: breaks specific peptide bonds between amino acids in the small intestine.

Biological Molecules – Nucleic Acids

PLO C2 (31 – 42)

Overlap with PLO D1 (40, 41)

PLO C12 (41)

Overlap with PLO D5 (41, 488-490)

Structure

There are two main types of nucleic acids (DNA and RNA)

· DNA (Deoxyribonucleic Acid) has a double helix shape and is two strands (polymers) of nucleotides wound around each other.

Ø A nucleotide has three parts:

- A pentose sugar ring: deoxyribose

- A phosphate group: PO₄

- 1 of 4 nitrogenous bases (ie. they raise pH): purines & pyrimidines

v The purines, guanine (G) and adenine (A), are double ring bases

v The pyrimidines, thymine(T) and cytosine (C), are single ring bases

phosphate group
		deoxyribose sugar

Ø The polymer of nucleotides is NOT formed through a condensation synthesis reaction like polysaccharides, proteins and triglycerides; however hydrolysis of the polymer does occur.

Ø The deoxyribose and the phosphate group make up the sides of the ladder while the bases from each of the strands point towards each other to make up the rungs of the ladder.

Ø The bases on opposite strands always pair accordingly:

- G always pairs with C with three hydrogen bonds

- A always pairs with T with two hydrogen bonds

This is complimentary base pairing.

· RNA (Ribonucleic Acid) is also a sequence of nucleotides with the following differences from DNA (see table 2.3 pg. 41)

Ø it is usually single stranded

Ø it is not helical

Ø it uses ribose sugar instead of deoxyribose

Ø there is no thymine in RNA. Uracil is used instead

Functions

· The sequence of the bases in a DNA molecule provide the code for the amino acid sequences of all proteins made in cells.

· RNA is a copy of one strand of an unzipped DNA molecule and can have 1 of 3 different functions in eukaryotic cells.

Ø it becomes ribosomalRNA (rRNA) and becomes a ribosome subunit out in the cytoplasm

Ø it becomes messengerRNA (mRNA) and delivers the genetic code from nucleus to the ribosome

Ø it becomes transferRNA (tRNA) and picks up amino acids in the cytoplasm and brings them to ribosomes.

Adenosine Triphosphate (ATP)

· referred to as the “energy currency of cells”.

· a nucleotide with deoxyribose, adenine and THREE phosphate groups

· mitochondria makes ATP from glucose

· ATP has a much more useable amount of energy stored. Glucose has more energy stored than is needed for most cell processes.

· energy is stored between the 2^nd and the 3^rd phosphate groups; when hydrolyzed to make adenosine diphosphate and inorganic phosphate the energy released is used for many cell processes such as:

Ø macromolecule synthesis

Ø muscle contraction

Ø conduction of nerve impulses

Ø membrane channel operation