Biology - Section 2: Carbon and the molecular diversity of life

Isomers

molecules with same chemical formula but different structures and properties

Types of isomers

Structural isomers: differ in covalent arrangement of atoms

✘ Number of possible structural isomers increases with size of carbon skeleton

Cis-trans isomers: differ in arrangement around a double bond

✘ Inflexibility of double bond

✘ Affects biological activity of organic molecules

✘ Vision involves a light-induced change of retinal from cis to trans isomer

✘ Trans fats

Enantiomers: Differ in arrangement of atoms around an asymmetric carbon. C that bonds to 4 different groups

✘ Mirror images

✘ ‘Left’ and ‘right’ handed versions of the same molecule

✘ Non-superimposable

✘ Usually only one enantiomer is biologically active

Pharmacological Importance of Enantiomers

✘ The two enantiomers of a drug may not be equally effective

✘ An emergent property of molecules

Hydrocarbons

Molecule containing only C and H

✘ C-H are single non-polar covalent bonds

✘ Hydrophobic – not soluble in water

• H-O bonds of water are polar

✘ Hydrocarbons store energy

• Major components of petroleum fossil fuel

✘ Fats in organisms have long hydrocarbon chains – store fuel

Functional groups

Chemical groups directly involved in chemical reactions.

Ex: Chemical groups in place of Hs contribute to properties and function

• Shape

• Chemical reactivity

7 most important functional groups

hydroxyl (–OH), carbonyl (C=O), carboxyl (–COOH), amino (–NH₂), sulfhydryl (–SH), phosphate (–PO₄), methyl (–CH₃).

✗ All except methyl and sulfhydryl are hydrophilic – increase solubility in water

✗ Methyl group not chemically reactive – serves as a tag

Adenosine triphosphate - ATP

Very important to cell function

✘ Contains adenosine (adenine and ribose) attached to 3 phosphate groups

✘ ATP reacts with water to release ADP, inorganic phosphate, and energy

• HOPO₃^2-

✘ ATP provides energy currency of cells

Macromolecules

Polymers built from monomers.

Polymer – long molecule consisting of many similar or identical monomers linked together by covalent bonds (train with similar carts)

• Polys – many; Meros - part

Monomer – repeating subunit that serves as building block of polymer (one single cart on the train)

• Monos – single

• Monomers may have own functions

The Synthesis and Breakdown of Polymers

Dehydration reaction: chemical reaction in which two molecules become covalently bonded to each other with the removal of a water molecule

✗ Assembly of polymer from monomers - polymerization

Hydrolysis: chemical reaction that breaks bond between two molecules by the addition of water

✗ Disassembly of polymer to monomers

✗ Hydro - water

✗ Lysis – break

The Diversity of Polymers

✘ Each cell has 1000s of different macromolecules

✘ Diversity among organisms is vast

✘ Number of different monomers of each type of macromolecule

✘ Length – number of subunit

✘ Arrangement – particular linear order of subunits - is key –

unique molecules from common subunits

• Emergent property

Carbohydrate

A sugar (monosaccharide) or one of their dimers (disaccharides) or polymers (polysaccharides)

Monosaccharide – simple sugars and the monomers of more complex carbohydrates [mono=single; sacchar=sugar ]

Disaccharide – double sugars, two monosaccharides joined by a glycosidic linkage by a dehydration reaction [di=two]

Polysaccharide – polymer composed of many monosaccharides joined by glycosidic linkages [poly=many]

Sugars: Monosaccharides

Monosaccharides have molecular formulas that are a multiple of CH2O

✘ Contain carbonyl group and >1 hydroxyl groups

• Aldoses or ketoses, depending on position of carbonyl group

✘ 3 to 7 carbons in carbon skeleton (Sugar names end in 'ose’)

• 3 = triose

• 5 = pentose

• 6 = hexose

✘ Glucose and galactose are aldoses and hexoses

✘ Fructose is a ketose and a hexose

Benefits of monosaccharides

• Source of energy in cellular respiration

• C skeletons serve as raw materials for the synthesis of other

organic molecules – eg amino acids or fatty acids

• Monomers of di- and polysaccharides

Sugars: Disaccharides

Two monosaccharides joined by glycosidic linkage

• Glycosidic linkage – covalent bond between two monosaccharides formed by a dehydration reaction

• Maltose – two monomers of glucose

• Sucrose – a glucose and a fructose

• Lactose – glucose and galactose

Sugars: Polysaccharides

Macromolecules - 100s to 1000s of monosaccharides joined by glycosidic linkages formed by dehydration reactions

• Functions: storage or structural

• Determined by sugar monomers and position of glycosidic linkages

Storage Polysaccharides: Starch

Polymer of glucose monomers

• Energy storage carbohydrate in plants

• Hydrolysis breaks the bonds to release glucose monomers (when they use it)

• Used by plants and animals as a source of energy

Storage Polysaccharides: Glycogen

Polymer of glucose monomers

• Energy storage carbohydrate in animals

• Stored in liver and muscle

• Hydrolysis converts to glucose for fuel (when they need it)

• Readily depleted unless replenished by eating

• Similar in structure to starch but more branched

• More free ends available for hydrolysis

Structural Polysaccharides

Strong materials made by organisms

• Cellulose – component of the tough cell walls of plant cells

• Polymer of glucose like starch but with β isomer

• Hydrogen bonds between chains

Structural Polysaccharides: Chitin

• Arthropods in exoskeleton

• Fungi cell walls

• Glucose monomer has a nitrogen-containing chemical group

• Like cellulose in linkages

Lipids

Large biological molecules, but not polymers or macromolecules

• Grouped together because all are hydrophobic – mostly insoluble.

-Consist largely of hydrocarbons

• Fats, phospholipids, and steroids

Fats

Constructed from two types of smaller molecules:

1. Glycerol (an alcohol)

2. Fatty acids

• Fatty acids: long hydrocarbon chains with acidic carboxyl group at one end

• Triacylglycerols, triglycerides:Three fatty acids join to glycerol by ester linkages.

Ester linkages

Bond between carboxyl and hydroxyl groups formed by dehydration

Saturated fats

contain saturated fatty acids

• Fatty acids with only single C-C bonds in the hydrocarbon

• Solid at room temperature

• Found in animals

Unsaturated fats

contain unsaturated fatty acids. Function is for energy storage

• Contain one or more double bonds in the hydrocarbon

• Most are cis double bonds

• Causes branching

• Liquid at room temperature

• Found in plant seeds and fish

Phospholipids

• Like fats, but two fatty acids

• Third hydroxyl joined to a phosphate group, negative charge

• Small charged or polar group attached to phosphate eg. choline

• Hydrocarbon ‘tails’ are hydrophobic – water insoluble

• Phosphate heads are hydrophilic – water soluble

• Form a bilayer in aqueous solution with heads pointed out, tails in

• Major component of cell membranes - boundary between the cell and its environment

Steroids

lipids where C skeleton consists of 4 rings

• Different chemical groups in different steroids

Cholesterol

Steroid found in animal cell membranes

• Precursor for other steroids eg. sex hormones

Proteins

One or more polypeptides, folded and coiled into a specific 3-dimensional structure.

• Proteios – first or primary

• 50% of dry mass of cell

• Most functions of living organisms depend on proteins

• Enzymes, defence, storage, transport, cellular communication,

movement, structural support ...

• 10000s of different proteins, each with different structure and

function

Amino acids

20 amino acids are the monomer subunits

• Polypeptide – polymer of amino acids joined by peptide bonds

Amino Acid Monomers

Organic molecules with a central (α) carbon covalently bonded to

1. amino group

2. carboxyl group

3. hydrogen

4. R – side chain, varies among the 20 amino acids

R - Chain

• R can be as simple as an H, or a C skeleton with other functional groups

• Physical and chemical properties of R determine characteristics of amino acid and functional role in polypeptide

• Grouped into categories:

1. Nonpolar (hydrophobic)

2. Polar (hydrophilic)

3. Acidic (negatively charged)

4. Basic (positively charged)

Polypeptides (Amino Acid Polymers)

• Amino acid monomers are joined into polymers – polypeptides – by a dehydration reaction

• Covalent peptide bonds formed between COOH on one amino acid and NH2 on the next

• Polypeptide backbone

• Free NH2 group at one end defines the N-terminus

• Free carboxyl group at the other end defines the C-terminus

• Each polypeptide has a unique number/sequence of amino acids

– determines structure/function

Protein Structure and Function

A protein’s function results from its 3-D structure and chemistry of side chains.

• 3D structure partially determined by amino acid sequence of polypeptide – bonds between different parts of the chain

       -globular, fibrous

• Functional protein is folded, coiled polypeptide or polypeptides

• Function of a protein often involves recognizing and binding other molecules

Four Levels of Protein Structure - Primary Structure

• Amino acid sequence of polypeptide

• Determined genetically

• Dictates secondary and tertiary structure

Four Levels of Protein Structure - Secondary Structure

Hydrogen bonds between repeating components of polypeptide backbone

• α helix (carbonyl and amino)

• β pleated sheet

Four Levels of Protein Structure - Tertiary Structure

Overall shape of polypeptide resulting from interactions between side chains (R-chains)

• Hydrogen bonds

• Ionic bonds

• Disulphide bridges

          - Covalent bonds formed between SH groups of two cysteine amino acids

• Hydrophobic interactions – hydrophobic components of molecules associate

Four Levels of Protein Structure - Quaternary Structure

• Exhibited by some proteins

• The functional protein consists of 2 or more polypeptides aggregated together

• Polypeptide subunits can be the same or different

What Determines Protein Structure?

• Proteins may become denatured if conditions change

• May renature when conditions return to original

Protein Folding in the Cell

• Amino acid sequences known for > 65 million proteins

• ‘Rules’ of folding are hard to establish

• X-ray diffraction – technique used to determine 3D structure of a folded protein

• Misfolding of polypeptides is associated with many diseases

1. Parkinson

2. Cystic fibrosis

3. Alzheimer and other dementia

4. Mad cow disease Protein Folding in the Cell

5. Sickle Cell Disease

The Roles of Nucleic Acids

Inheritance

• DNA directs its own replication and is transmitted from parent to offspring and cell to cell

• Carries genetic information for all cell activities

Gene expression

• DNA directs the synthesis of messenger RNA within a cell (transcription)

• mRNA is translated to a polypeptide with a specific amino acid sequence (translation)

• Polypeptides form proteins which do the cell’s work

Components of Nucleic Acids (polynucleotides)

Nucleotide monomers contain: nitrogenous base, pentose sugar, phosphate group.

Nitrogenous bases:

• cytosine (C), adenine (A), guanine (G), and thymine (T) in DNA or uracil (U) in RNA

pyrimidines - C,T, and U (1 ring)

purines - A and G are purines (2 rings)

One of two pentose sugars:

• Deoxyribose in DNA

• Ribose in RNA

• Ribose contains OH group on 2’, deoxyribose does not

Nucleoside Vs. Nucleotide

Nucleoside: Combination of base and sugar is a nucleoside

Nucleotide: Addition of phosphate group to nucleoside

Phosphodiester linkage

Makes nucleotide polymers. 3’OH of one nucleotide joined to 5’PO4 of next by dehydration

Nucleotide Polymers Directionality

• free 5’PO4 at one end (5’ end)

• free 3’OH at the other end (3’ end)

• 5’-CCGGT-3’ different from 3’-CCGGT-5’

• Exact linear order of bases – DNA sequence - specifies amino acid sequence

• 5’-AGGGAACTT-3’ vs 5’-CGGGAAATT-3’

The Structures of DNA

DNA molecules have two polynucleotide strands winding around an imaginary axis - a double helix

• Strands run in opposite directions to each other – antiparallel

• Sugar-phosphate backbone is outside, bases project inward

• Held together by H-bonds between bases on opposite strands - base pairs

The Structures RNA Molecules

RNA molecules are single-stranded

• Complementary base-pairing can occur between bases in different parts of the molecule

• RNA molecules often 3 dimensional [Eg. transfer RNA (tRNA)]

• A pairs with U vs T