Unit 1 Cell and Molecular Biology Section 4 Molecules.

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Unit 1Cell and Molecular

Biology

Section 4

Molecules

Structure and function of cell components

(i) Carbohydrates

(ii) Lipids

(iii) Proteins

(iv) Nucleic Acids

Carbohydrates

Carbohydrates are chemical structures containing C, H, and O in a ratio of 1:2:1

The general formula is (CH2O)n

Facts about monosaccharides

Monosaccharides are molecules with the general formula (CH2O)n.

The main example is glucose. Monosaccharides such as glucose are all

• of low molecular weight• sweet• soluble• crystalline.

Monosaccharides such as glucose are used as sources of energy.

Glucose chain structure Glucose is an example of an

aldose sugar as its terminal group C1 is an aldehyde (CHO).

Glucose is a reducing sugar due to the presence of the carbonyl group CO which can donate electrons.

It is possible for the atoms in a 6-carbon sugar to take up different positions on the carbon chain. This leads to structural isomers

Optical isomers of glucose

Since molecules are 3-dimensional in shape optical isomers can be formed which are structurally identical but are mirror images of each other.

D-glucose with OH on right of C6.

L-glucose with OH on left of C6.

Ring structure of Glucose

Since glucose is a relatively long molecule, groups within it can react and change the shape of the molecule to form a pyranose ring structure.

Glucose Reacting to form disaccharides

The monomer glucose reacts by condensation (or dehydration) to form disaccharides.

Water is removed in the process.

In the example below two molecules of a-D glucose react together to form maltose.

The bond holding the glucose molecules together (highlighted in red) is known as a glycosidic bond.

Maltose is linked by an (1-4) glycosidic bond.

If two β-D glucose join the result is cellobiose and the bond is at an angle (top to bottom)

glycosidic bond

Structure and function of polysaccharides

Polysaccharides are complex carbohydrates made up linked monosaccharide units.

When a polysaccharide is made up of one type of monosaccharide unit it is called a homopolysaccharide.

Starch and glycogen are polysaccharides used for energy storage.

Other polysaccharides such as cellulose and chitin may be structural in function.

Starch

Starch is a storage compound in plants, being insoluble in water.

It is a homopolysaccharide made up of two components: amylose and amylopectin.

Amylose – a straight chain structure formed by 1,4 glycosidic bonds between -D-glucose molecules.

Structure of Amylose Fraction of Starch

The amylose chain forms a helix.

This causes the blue/black colour change on reaction with iodine.

The structure of the Amylopectin Fraction of Starch

Amylopectin is a branched structure due to the formation of 1,6 glycosidic bonds.

C6H2OH

The cross linkages are formed by dehydration reactions between carbon 1 of one chain and carbon 6 of a parallel chain

Start of chain 2

End of chain 1

Amylopectin causes a red-violet colour change on reaction with iodine.

This change is usually masked by the much darker reaction of amylose to iodine.

Starch therefore consists of amylose helices entangled on branches of amylopectin.

Shows branching of amylopectin

Glycogen Glycogen is a homopolysaccharide made from

repeating -D-glucose units and is very similar in structure to amylopectin, i.e. it has a highly branched structure.

Glycogen is a storage compound in animals; including humans.

It causes a red-violet colour on addition of iodine (similar to amylopectin).

Cellulose

Cellulose is the most abundant organic material on earth.

Most animals however lack the enzyme cellulase required to break it down to its component monomers.

Cellulose is made up of long straight chains of -glucose molecules.

The -glucose molecules are joined by condensation, i.e. the removal of water, forming (1,4) glycosidic linkages.

Note however that every second -glucose molecule has to flip over to allow the bond to form. This produces a “heads-tails-heads” sequence.

The glucose units are linked into straight chains each 100-1000 units long.

Weak hydrogen bonds form between parallel chains binding them into cellulose microfibrils.

Cellulose microfibrils arrange themselves into thicker bundles called macrofibrils. (These are usually referred to as fibres.)

The cellulose fibres are often “glued” together by other compounds such as hemicelluloses and calcium pectate to form complex structures such as plant cell walls.

Other Polysaccharides

Chitin is the main structural component of the exoskeleton of arthropods (e.g. spiders, insects and crustaceans) and the walls of fungi such as yeast.

Chitin is structurally similar to cellulose but the monomer is an amino sugar called glucosamine.

• Glucosaminoglycans are complex heteropolysaccharides found in the connective tisues and skin of vertebrates.

Activity

Read Dart Pg 25-31

Scholar 4.2 carbohydrates

Practice drawing different molecular structures

Lipids

Lipids have a varied structure but all have the following properties in common:- Insoluble in water Soluble in organic solvents

The three main groups of lipids are:- Triglycerides Phospholipids Steroids

Lipids are important in cell membrane structure and also as energy storage molecules and hormones.

Structure of glycerol

Glycerol is a three carbon alcohol that contains 3 –OH (hydroxyl) groups

Structure of Fatty Acids

Fatty acids are hydrocarbon chains ending in a carboxyl group (COOH)

R is an abbreviation for any organic group About 30 different fatty acids are commonly found in

lipids (they nearly always have an even number of carbon atoms).

HO – C – R

Saturated fatty acids All available bonds are occupied by

hydrogens E.g

Palmitic acid CH3(CH2)14COOH

Stearic acid CH3(CH2)16COOH

OH – C – C – C – C – C – C – C – C – C – C – C – C – C – C – C – CH3

Unsaturated fatty acids Some carbon atoms are double bonded with one another,

therefore they are not fully saturated with hydrogen E.g. Oleic Acid CH3(CH2)7 CH = (CH2)7COOH

Note - this is monounsaturated (1 double bond)

E.g. Linoleic acid CH3(CH2CH=CH)3(CH2)7COOH

Note – this is polyunsaturated (more than 1 double bond)

Formation of Ester Linkages

Glycerol and fatty acids are joined together by dehydration (condensation) reactions

The bond linking glycerol and fatty acids is called an ester bond

HO – C – R

O – C – R

Ester bond

Triglycerides

Triglycerides consist of a single glycerol molecule and three fatty acids.

Glycerol

Glycerol (blue) is an alcohol derivative of glyceraldehyde and has three hydroxyl groups. It acts as the backbone of the structure.

Fatty acids (red) – there are more than 70 types of fatty acid but they all have long hydrocarbon tails and a terminal carboxyl group (COOH). The variety of fatty acids determine the properties of each triglyceride.

Formation of Triglycerides

Triglycerides form by condensation (dehydration) reactions between the hydroxyl (OH) groups of the glycerol and the carboxyl (COOH) group of three fatty acids.

Triglycerides are esters being derived from an alcohol and a fat.

Structure of triglycerides

Triglycerides in plants

Plants store their energy in triglycerides with low melting points which are liquid at room temperature.

These triglycerides are referred to as oils result from reaction between

glycerol and an unsaturated fatty acid e.g. oleic acid.

Triglycerides in Animals

Animals store their energy in triglycerides with high melting points which are solid at room temperature.

These triglycerides are referred to as fats. result from reaction between

glycerol and a saturated fatty acid e.g. stearic acid.

Triglycerides in cells

Triglycerides are insoluble in water because they have no charge i.e. they have covalent bonds. This causes them to form droplets in the cytoplasm

Functions of triglycerides

Energy storage - triglycerides contain twice the energy/gram of carbohydrates or proteins. During aerobic respiration triglyceride is broken into 2C portions which are fed into the Krebs cycle.

Source of metabolic water. water is released on the breakdown of triglycerides and this property is used efficiently is by desert mammals.

Insulation – triglycerides are found in the blubber of whales and other aquatic animals.

Buoyancy – aquatic animals use triglycerides to help them float as they are less dense than water.

Phospholipids

The structure of phospholipids is based on the structure of triglycerides but the third hydroxyl group of the glycerol is linked to phosphoric acid which is often linked to a large polar group.

The fatty acids which make up phospholipids have a consistent length of between 16 and 18 carbons. This allows them to form neat bilayers.

Phospholipids are said to be amphipathic, having two very different sides to their nature.

The ‘head’ containing the polar group and the phosphate group has polar covalent bonds. It is slightly charged and attracts water, i.e. it is hydrophilic.

The ‘tail’ containing the long hydrocarbon group which is non-polar covalent. It is not charged and repels water, i.e. it is hydrophobic.

Hydrophilic portion

Hydrophobic portion

The amphipathic nature of phospholipids is important in the formation of bilayers such as cell membranes.

The hydrophilic groups line up on the outside faces of the membrane. The hydrophobic portions are arranged within the membrane.

Phospholipids may have fatty acids which are saturated or unsaturated. This affects the properties of the resulting bilayer/cell membrane: Most membranes have phospholipids derived

from unsaturated fatty acids. Unsaturated fatty acids add fluidity to a bilayer

since ‘kinked’ tails do not pack tightly together. Phospholipids derived from unsaturated

phospholipids allow faster transport of substances across the bilayer.

Membranes exposed to the cold have a very high percentage of unsaturates e.g. bacteria grown at low temperature or the membranes of reindeer ears – remember unsaturates are liquid at much lower temperatures.

Membranes which are stiffer such as those in nerve cells contain a much higher percentage of phospholipids derived from saturated fatty acids.

They also contain high levels of cholesterol which stiffens membrane structure further.

Steroids

Steroids have a common four ring structure. Each unit within the four-ring structure is

known as an isoprene unit (C5H8).

Different steroids vary in the side chains attached to the rings.

Notice that cholesterol and testosterone are almost identical except for the side groups on C3 and C17.

Steroids are classified as lipids since they are soluble in organic compounds but not in water. They have a very powerful effect because of this as they can pass through cell membranes.

Steroids are hormonal in function and have a wide variety of functions.

Other examples of steroids are oestrogen, progesterone, cortisol, cholesterol and aldosterone.

Activity

Read and take notes from Dart Pg 32-37

Scholar section 4.3

Use the internet to familiarise yourself with different ways of presenting the chemical formulae / structures

Amino acids

Amino acids are the structural building blocks (monomers) of proteins.

There are twenty different kinds of amino acids used in proteins.

Proteins are referred to as heteropolymers due the variety of amino acids involved in their structure.

Structure of amino acids

Amino acids, like carbohydrates, show isomerism. Proteins are only made up of amino acids which are L-isomers.

L-isomerD-isomer

At neutral pH’s amino acids exist in an ionised form and have both acidic and basic properties. This is because the carboxylic group donates hydrogen ions to the solution (acidic) whereas the amino group (NH2) attracts hydrogen ions from the solution.

The repeating sequence of atoms along a proteins is referred to as the polypeptide backbone. Attached to this repetitive chain are the different amino acid side chains (R-groups) which are not involved in the peptide bond but which give each amino acid its unique property.

Amino acids are grouped according to whether their side chains are:-

acidicbasicuncharged polarnon polar

Acidic Amino acids

AsparticAcid asp Acidic

GlutamicAcid glu Acidic

Basic amino acids

Lysine lys Basic

Arginine arg Basic

Neutral polar amino acids

Glutamine gln NeutralPolar

Tyrosine tyr Neutral Polar

Non-polar amino acids

Isoleucine ile Neutral Non-polar

Methionine met Neutral

Non-polar

The type of side chain is very important as it affects the solubility of the amino acid.

Hydrophobic features include long non-polar (uncharged) chains or complex aromatic rings.

Hydrophilic features include additional carboxyl groups or amino groups not involved in peptide bonding which are ionised in solution.

Structure of proteins Primary structure

The sequence of amino acids in a given protein is known as its primary structure.

Secondary structure Simple proteins with regularly repeating amino acids often form a secondary

structure due to hydrogen bonds between the amino group ( NH) and carbonyl group ( CO ) of adjacent amino acids.

This additional bonding may twist the long protein chain into a helix known as an alpha helices

This secondary bonding gives rise to proteins which are structural e.g.

Collagen – 3 alpha helices twisted together Elastin Keratin -7 alpha helices twisted together

A second formation resulting from hydrogen bonds between adjacent peptide bonds is known as β- pleated sheets

An example of a protein made up of β- pleated sheets is fibroin found in spiders webs which is extremely strong.

Tertiary structure The third type of structure found in proteins is called tertiary protein structure.

The tertiary structure is the final specific shape that a protein assumes.

This final shape is determined by a variety of bonding interactions between the "side chains" on the amino acids. These bonding interactions may be stronger than the hydrogen bonds between amide groups holding the helical structure.

Bonding interactions between "side chains" may cause a number of folds, bends, and loops in the protein chain. Different fragments of the same chain may become bonded together.

There are four types of bonding interactions between "side chains" including: hydrogen bonding, salt bridges, disulfide bonds, non-polar hydrophobic interactions.

Globular proteins such as enzymes, antibodies, and cell membrane proteins all show tertiary structure

The hydrophobic interactions of non-polar side chains are believed to contribute significantly to the stabilizing of the tertiary structures in proteins.

Non groups such as benzene rings repel water and other polar groups and results in a net attraction of the non-polar groups for each other

Quaternary Structure The quaternary protein structure involves the clustering of several

individual peptide or protein chains into a final specific shape.

A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry.

There are two major categories of proteins with quaternary structure - fibrous and globular.

Fibrous Proteins:

Fibrous proteins such as the keratins in wool and hair are composed of coiled alpha helical protein chains with other various coils analogous to those found in a rope. Other keratins are found in skin, fur, hair, wool, claws, nails, hooves, horns, scales, beaks, feathers, actin and mysin in muscle tissues and fibrinogen needed for blood clots.

Globular Proteins On the other hand, globular proteins may have a combination of

various individual units of various shapes which are mostly clumped into a shape of a ball. Major examples include insulin, hemoglobin, and most enzymes.

Nucleotide structures

The building block of a nucleic acid is a nucleotide.

Nucleotides consist of A pentose sugar A nitrogenous base A phosphate group

Pentose Sugars

Deoxyribose and ribose differ by the group attachment at the 2’C.

There are 5 bases These can be classified into two types

Purines Double ringed Adenine and Guanine

Pyrimidines Single ringed Cytosine, Thymine and Uracil

Formation of a nucleotide

A condensation reaction occurs between the OH group on the 5’ C and phosphate group to form a strong phosphodiester bond.

A condensation reaction occurs between the base and the 1’ C to form a strong glycosidic bond

Formation of nucleic acid

A phosphodiester bond also forms between the 3’ C and the phosphate group of the next nucleotide to form the sugar phosphate backbone.

Base Pairing in DNA

A and T join by two weak hydrogen bonds G and C join by three weak hydrogen bonds

DNA strands

DNA strands are antiparallel

Enzymes

DNA polymerase Catalyses the linking together of DNA nucleotides

during replication DNA polymerase can only add a nucleotide to the

3’ end of the previous nucleotide. RNA polymerase

Catalyses the linking of RNA nucleotides during transcription (and in the replication of the lagging strand during DNA replication)

DNA ligase Joins short sections of DNA together

DNA replication animation:

http://207.207.4.198/pub/flash/24/menu.swf

Activity

Read DART pg 48 – 53 and take notes Scholar 4.5 http://www.maxanim.com/genetics/index.htm

Look at Replication fork DNA replication Meselson-Stahl experiment

Make notes on DNA and RNA structure Make notes on replication and transcription Think about how you will remember which bases are purines and

which are pyrimidines Write a summary of all the different bonds formed between

molecules by dehydration reactions.

Unit 1 Cell and Molecular Biology Section 4 Molecules.

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