2- Organic Molecules in Living Things

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Edexcel AS Biology Topic 1 Lifestyle, health and risk

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Organic molecules in living things

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What are organic compounds?

Organic compounds are compounds that contain carbon atoms and at least one hydrogen atom;

they may also contain oxygen and, less frequently nitrogen, sulfur and phosphorus.

Properties of Carbon as an element:

Each Carbon atom can form four covalent bonds --> it can join up with four other atoms:so Carbon is highly reactive.

Carbon atoms bond strongly to other Carbon atoms to make long chains. Carbon chains can be straight, branched, form rings or 3D shapes. In some Carbon compounds small molecules (monomers) bond with repeated similar units

to form a very large molecule called a polymer.

Importance: Large variety of organic compounds.

Carbon atom Model

Linear (straight chain) with

double bonds


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Branched chain, and ring form

Carbohydrates

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Carbohydrates are made up of carbon, hydrogen and oxygen. The ratio of Hydrogen to

Oxygen is 2:1

Importance of carbohydrates:

Provide usable energy in plant and animal cells. Store energy in cells.

There are three types of carbohydrates depending on complexity:

1- Monosaccharides.2- Disaccharides.3- Polysaccharides.

1- Monosaccharides the simple sugars.They are the building units (monomers) of carbohydrates.

General formula of Monosaccharides: (CH2O) n Where: ncan be any number.(usually

between 3 and 8)

The ratio of Carbon to Hydrogen to Oxygen is 1:2:1


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Examples:

- Triose sugars: (n= 3) have 3 carbon atoms and the general formula: C3H6O3Importance:intermediate compounds produced in the mitochondria incellular respiration.

Pentose sugars: (n= 5) have five carbon atoms and the general formula: C5H10O5Importance:Ribose and Deoxyribose sugars are important in the nucleic acids DNA and

RNA which make up the genetic material.

Hexose sugars: ( n= 6) have six carbon atoms and the general formula: C6H12O6 .Importance: Glucose: Usable energy in cells

Galactose: sugar found in milk

Fructose: found in fruits.

General Formula: is the number of atoms of each element in the molecule.

Displayed Formula (structural formula): I s the arrangement of atoms in the molecule.

Isomers: aremolecules that have the same general formula but different displayed

formula.


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2- Disaccharides the double sugars.Disaccharides are made up of two monosaccharide molecules joined together.

Disaccharide Unit 1 Unit 2 Bond

Sucrose (table sugar, cane sugar, beet sugar, or saccharose) glucose fructose (12)

Lactose (main carbohydrate in milk) galactose glucose (1- 4)

Maltose: (found in germinating seeds such as barley) glucose glucose (1- 4)
http://en.wikipedia.org/wiki/Sucrosehttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Fructosehttp://en.wikipedia.org/wiki/Lactosehttp://en.wikipedia.org/wiki/Galactosehttp://en.wikipedia.org/wiki/Maltosehttp://en.wikipedia.org/wiki/Maltosehttp://en.wikipedia.org/wiki/Galactosehttp://en.wikipedia.org/wiki/Lactosehttp://en.wikipedia.org/wiki/Fructosehttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Sucrose


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Condensation reaction: Is the reaction in which two monosaccharide molecules are joined

and a molecule of water (H2O) is removed.

Glycosidic bond: Is the covalent bond that links the two monosaccharide molecules in a

disaccharide as a result of a condensation reaction.

General formula of disaccharides: (C6H10O5) n.

Many monosaccharides and disaccharides taste sweet.

-glucose -glucose


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Maltose

3- Polysaccharides:Polysaccharides are made up of many monosaccharide units joined by glycosidic bonds

as a result of many condensation reactions:

Oligosaccharides are molecules with 3 10 monosaccharides.

Polysacchrides are molecules with 11 or more monosaccharides.

Properties of polysaccharides:

As polysaccharides can form very compactmolecules, they are ideal for storingcarbohydrates in cells.

The glycosidic bonds in polysaccharides can be broken downby hydrolysis to releasemonosaccharides, the simple sugars needed for cellular respiration.

Polysaccharides are chemically and physically inactive, so storing them in cells does notinterfere with other functions of the cell.

Polysaccharides are not very soluble in water, so have very little or no osmotic effectina cell.

Types of polysaccharides:


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I- Starch: an important energy store in plants.II- Glycogen: is the only carbohydrate energy store found in animals.

Starch:

The sugars produced by photosynthesis are converted into starch, which is insoluble,

compact, can be broken downrapidly to release glucose. (Plant storage organs like

potatoes are rich in starch)

Structure and adaptation of starch:

Starch has a combination of straight chainamylose and branched chainamylopectin

molecules.

Amylose:

Long chains of repeated - glucose subunits linked by 1-4 glycosidic bonds that resultfrom condensation reactions, and that form between Carbon 1 on one glucose molecule,

and Carbon 4 on the other.

As the chain lengthens, the molecule coils (spirals), which makes it more compact. Length: 200-5000 glucose molecules. Glucose molecules can only be released by enzymes working from each end of the amylose

molecule: leading to a slower release over a longer period.

Amylopectin:

Branching chains of repeated - glucose subunits linked by: 1-4 glycosidic bonds: between Carbon 1 on one glucose molecule, and Carbon 4 on the

other along the same chain.


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1-6 glycosidic bonds: between Carbon 1 on one glucose molecule, and Carbon 6 on theother forming the branching chains (at the branching points).

The branching chains have lots of terminal (end) glucose molecules that can be brokenoff rapidly when energy is needed.

Glycogen

Glycogen is like starch made up of many glucose units, a compact molecule, is sometimes

referred to as animal starch.

N.B. The amylopectin releases glucose for cellular respiration rapidly

whenneeded, and the amylose releases it more slowly over a longer

period, which makes starchy carbohydrate-rich food good when doing

sport, keeping you going longer.


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However, the glycogen molecule has many side branches, can be broken down very

rapidly making it an ideal energy store for every active tissue such as muscle and liver

tissue, which need a readily available energy supply at all times.

Glycogen

Hydrolysis reaction:

A glycosidic bond can also be broken down to release separate monomer units.

This is the opposite of the reaction shown above. Instead of water being

given off, a water molecule is needed to break each glycosidic bond. This is

called hydrolysis because water is needed to split up the bigger molecule.


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Lipids__________

Lipids are made of Carbon, hydrogen and oxygen. The proportion of oxygen in lipids is

much less than in carbohydrates

Importance of lipids:

An important source of energy in the diet of animals. The most effective energy stores. Why? The ratio between Carbon and Oxygen is much

higher than 2:1, having more C-H bonds than carbohydrates and proteins. As C-H bonds

are high energy bonds, this causes lipids to contain more energy per gram than

carbohydrates and proteins.

Many plants and animals convert spare food into oils or fat for later use. e.g. the seeds ofplants contain oils to provide energy for the seedling when it starts to grow.

Lipids (phospholipids and cholesterol) play an important role in the cell membranes. Lipids play a protective role around organs such as the heart and the kidneys. Oils waterproof the fur and feathers of mammals and birds.


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Waxes waterproof the outer surfaces of insects and plants. A fatty sheath insulates the nerves, to speed up the electrical impulses. Fats insulate animals against heat loss: blubber in whales. Lipids have very low density so the body fat of water mammals helps them to float easily.

Types of lipids: Lipids include cholesterol, oils such as olive oil and fats such as butter. Oils are

liquid at room temperature, but fats are solids at room temperature.

Fats and oils:

Fats and oils are made up of two types of organic chemicals: Glycerol and Fatty acids.

Glycerol has the chemical formula: C3H8O3

Fatty acids are long hydrocarbon chains a pleated backbone of carbon atoms with hydrogen

atoms attached, - and a carboxyl group (-COOH) at one end.

Fatty acids differ in:

The length of the carbon chain. ( in living organisms it is between 15 and 17 carbon atoms. Their saturation with hydrogen atoms: saturated and unsaturated fatty acids:


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Saturated fatty acids: have no double bonds and each carbon atom is linked to the nextby a single covalent bond.

Unsaturated fatty acids: the carbon chains have one or more double bonds in them. Monounsaturated fatty acids: have one double bond; polyunsaturated fatty acids

have more than one double bond. E.g. linoleic acid, an essential polyunsaturated fatty acid

in our diet that we cannot make from other chemicals.

Formation of fat molecules

A fat or oil molecule consists of one glycerol molecule combined with one, two or threefatty acid molecules to form a mono-, di- or triglyceride.

An ester bond is formed between the carboxylic group (-COOH) of the fatty acid and oneof the hydroxyl groups (-OH) of the glycerol, resulting in the formation of a watermolecule.

This type of condensation reaction is called esterification.


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Saturated fats:

Have no double bonds. Are solid at room temperature. Come from animal sources. (Example: butter, cream and meat, except palm oil and

coconut oil)

Can lead to fatty plaques in the arteries, heart disease and death.Unsaturated fats:

Contain double bonds. Are liquid at room temperature. Come from vegetable sources. (Example: sunflower oil, corn oil) Double bonds in the carbon chains of fatty acids have a positive effect, helping the

body to cope better with saturated fats. (Polyunsaturated fats have an evenstronger positive effect on blood cholesterol level and the heart.

Phospholipids:

A phospholipid molecule consists of one glycerol molecule and one phosphate group (-ve),

forming the head, and two fatty acids forming the two tails.


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The head of each phospholipid molecule is polar (hydrophilic), while the two tails are non polar

(hydrophobic) or insoluble in water.

Phospholipids and water:

When these phospholipids come in contact with water, the hydrophilic (water -loving)phosphate heads are attracted to water, while the hydrophobic (water- hating) fatty acid

tails are repelled away from water.

If the phospholipids molecules are tightly packed in water, they form- Either a monolayer: with the hydrophilic heads in the water, and the hydrophobic

tails in the air.

- Or clusters called micelles: all the hydrophilic heads point outwards, and all thehydrophobic tails are hidden inside.

Phospholipids in the cell membrane:


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Phospholipids constitute the major lipid in the cell membrane. Since the cell membrane

is surrounded by water inside the cell: cytoplasm, and water outside the cell:

extracellular fluid, the phospholipid molecules form a bilayer with the hydrophilic

heads pointing into the water (outside the membrane) and the hydrophobic tails are

protected in the middle.


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Proteins

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Proteins contain carbon, hydrogen and oxygen, in addition to Nitrogen. Some proteins

contain sulfur, and some contain phosphorus.

Proteins are macromolecules made of repeated small monomer units called amino acids.

Importance of proteins:

Proteins constitute 18% of your body forming your hair, your skin, and your nails. Enzymes which control intracellular chemical reactions are proteins. Many hormones that control the working of other organs are also proteins. Actin and myosin are muscle proteins responsible for muscular contraction. Antibodies are proteins that protect the body against infectious diseases. Hemoglobin is a protein that transports oxygen and to a lesser extent carbon

dioxide in the blood.

The chemicals involved in blood clotting are proteins.


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Amino acids:

There are 20 different naturally occurring amino acids that can combine indifferent number and sequence to form a vast range of different proteins.

All amino acids have the same basic structure:-A central carbon atom, to which are attached 4 groups:

1- An amino group: (-NH2)2- A carboxyl group: (-COOH)3- A hydrogen: H4- The R group, which is the group that varies between amino acids.

Some R groups are polar, others are non polar, some contain sulfur

groups etc.

It affects the way amino acids bond with each other in a protein.

Two Amino acids join together by a condensation reaction between the amino group ofone amino acid ( which loses a hydrogen atom) and the carboxyl group of the next amino

acid (which loses a hydroxyl group) releasing a water molecule and forming a dipeptide.

The bond formed is called a peptide link. More amino acids join to form a polypeptide chain, which can be folded or coiled or

associated with other chains- through the formation of other bonds- to form a protein.

Other bonds in proteins:1-Hydrogen bonds:

-Form between the slightly negative oxygen of the carboxyl groups, and theslightly positive hydrogen of the amine groups.

-Can be easily broken down and reformed if pH and temperature conditionschange. (weak bonds)

-Responsible for folding and coiling of the polypeptide chains.


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2- Ionic bonds:-Form between some of the strongly positive and strongly negative amino acid

side chains (R groups)buried deep in the protein.

Strong bonds.

3-Sulfur bridges:-Form between side chains of two sulfur containing side chains such as

methionine or cysteine molecules.

-An oxidation reaction takes place between these 2 sulfur containing groupsforming a strong covalent bond or disulfide link.

-Hold the folded polypeptide chains in place.

Levels of protein structure:

Primary structure:

-It is the number and sequence of amino acids that make up the polypeptidechain.

-Bonds involved: peptide bonds. (covalent)-Determined by the sequence of bases on the DNA molecule that codes for

each protein.

Secondary structure:

-It is the coiling of the polypeptide chain into an helix, or the folding of thechains into pleated sheets.

-Bonds involved: Hydrogen bonds between the ve O of CO groups, and the+ve H of NH groups along the polypeptide chains.

-Determined by the primary structure. (Sequence of a.a.)


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Tertiary structure:

-The helices and pleated sheets are folded further into 3D globularshapes.

-Bonds involved include: H-bonds, ionic bonds and sulfur bridges.

Quaternary structure:

-When a protein consists of more than one polypeptide chain, bonds formbetween R groups of different chains to hold them together.

-Bonds involved include: H-bonds, ionic bonds and sulfur bridges.

Denaturation of proteins:

When weak bonds involved in the formation of a protein are exposed to changes in temperature

and pH, the bonds break resulting in the loss of the 3D-shape of the protein.

Fibrous proteins:

-Long parallel chains with occasional cross-linkages no tertiary structure.-Insoluble in water.-Tough suitable for structural functions.-Found in connective tissue, tendons, collagen, structure of muscles, silk of

spiders webs, silkworm cocoons, in keratin that makes up hair, nails,

feathers and horns.

Globular proteins:

-Have complex tertiary and sometimes quaternary structures.-Folded into spherical globular shapes.


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-Soluble in water because of the presence of ionic carboxyl and amine ends.(being big they form colloids)

-Play important roles in the cell membrane, immune system (antibodies),enzymes and hormones.

Conjugated Proteins

Roles of Enzymes

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2- Organic Molecules in Living Things