Unit 1 - Molecules

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Organic Molecules

Are of great significance in the structure and the functioning of living organisms.

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Metabolism

describe all reactions taking place within cells.

can be anabolic (compunds are being built up->synthesised) or catabolic (->compounds are broken down.)

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Anabolic

compunds are being built up->synthesised

require energy

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Catabolic

->compounds are broken down.

release of energy

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Water

1. medium in which all chemical reactions occur in living organisms. 2. important chemical constituent in all cells. , 3. dipolar nature (->form hydrogens bonds->solvent&transport medium), 4. habitat for organisms.

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Structure of Water Molecule

2 hydrogen atomes (H) and one oxygen atom (O)->joined by CONVALENT bonds.

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How many shells can a atom have and how many electrons can each shell hold?

4 shells -> 1st shell holds 2 electr. , 2nd shell holds 8 electrons, 3rd shell holds up to 18 electrons, and 4th shell can hold up to 32 electrons.

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Covalent bonds

when the electrons are shared between 2 or more molecules and form a bond. ->electrons are not always shared equally

->as for instance oxygen nucleus attract the electrons more than the hydrogen nuclei do. -> so the exygen atoms have a slight (-) charge while the hydrogen atoms have a slight (+) charge->uneven charge distribution->polar/dipolar

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polar molecule

if a molecule is being polar it means that there is an uneven charge distribution.

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Carbohydrates are found in one of three forms

1. Monosaccharides, 2. Disaccharides (both sugars), 3. Polysaccharides

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Monosaccharides

is a carbohydrate which consists of a single sugar unit such as glucose->(CH2O)n where n is a number between 3 and 9->classified according to the number of carbon atoms

polar->disolve easily

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The monosaccharides you will have to know fall into these categories:

C = 3 = triose, C = 4 = tetrose, C = 5 = pentose, C = 6 = hexose

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Trioses:

(e.g. glyceraldehydes), intermediates in respiration and photosynthesis.

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Pentoses:

(e.g. ribose, ribulose), used in the synthesis of nucleic acids (RNA and DNA), co-enzymes (NAD, NADP, FAD) and ATP.

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Hexoses:

e.g. glucose, fructose), used as a source of energy in respiration and as building blocks for larger molecules.

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alpha or beta-configurations

Depending on the orientation of the OH group on carbon 1, the monosaccharide can have either alpha or beta-configurations

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Disaccharides and glycosidic bonds

These are formed when two monosaccharides are condensed together. One monosaccharide loses an H atom from carbon atom number 1 and the other loses an OH group from carbon 4 to form the bond.

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condensation reaction

The reaction, which is called a condensation reaction, involves the loss of water (H2O) and the formation of a 1,4-glycosidic bond.

Depending on the monosaccharides used, this can be an alpha-1,4-glycosidic bond or a beta-1,4-glycosidic bond

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hydrolysis

The reverse of the condensation reaction, the formation of two monosaccharides from one disaccharide, is called a hydrolysis reaction and requires one water molecule to supply the H and OH to the sugars formed.

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Examples of Disaccharides

Sucrose: glucose + fructose Lactose: glucose + galactose Maltose: glucose + glucose

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Sucrose

Constitutent monomers: glucose + fructose

is used in many plants for transporting food reserves, often from the leaves to other parts of the plant.

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Lactose

Constituent monomers: glucose + galactose

One role in living organisms: Carbohydrate source (the sugar found) in the milk of mammals

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Maltose

Constitutent monomers: glucose + glucose Role in living organisms: Energy/food source in germinating seeds.

is the first product of starch digestion and is further broken down to glucose before absorption in the human gut.

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Biochemical tests in Monosaccharide (Disaccharides):

All monosacch & some disacch incl maltose/lactose r reducing sugars which can be tested for->adding Benedict's reagent to sugar->heating in water bath->if red. sugar is present->solut turns green->yellow->&finally produces a brick red precipitate

Non-reducing sugars can also be tested for using Benedict's reagent.First require addition of acid&heating to hydrolyse (break apart)sugar. Acid must then be neutralised using alkali (sodium hydroxide) before carrying out the test as described above.

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hydrolyse

break apart

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Polysaccharide:

1. Starch, 2. Glycogen, 3. Cellulose

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Starch

Main storage polysaccharide in plants.->Made of 2 polymers - amylose and amylopectin->Insoluble therefore good for storage

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Amylose:

a polymer of glucoses joined by alpha-1,4-glycosidic bonds. Forms a helix with 6 glucose molecules per turn and about 300 per helix.

Helix is compact.

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Amylopectin:

a polymer of glucoses joined by alpha-1,4-glycosidic bonds but with branches of alpha-1,6-glycosidic bonds. This causes the molecule to be branched rather than helical.

The branches mean that the compound can easily hydrolysed to release the glucose monomers.

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Glycogen

Main storage polysaccharide in animals and fungi, Structure: Similar to amylopectin but with many more branches which are also shorter.

Relationship of structure to function:The number and length of the branches means that it is extremely compact and very fast hydrolysis.

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Cellulose

Main structural constituent of plant cell walls, Structure: Adjacent chains of long, unbranched polymers of glucose joined by b-1,4-glycosidic bonds hydrogen bond with each other to form microfibrils

Relationship of structure to function:The microfibrils are strong and so are structurally important in plant cell walls.

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Functions of carbohydrates

1. Substrate for respiration (glucose is essential for cardiac tissues)., 2. Intermediate in respiration (e.g. glyceraldehydes). 3. Energy stores (e.g. starch, glycogen), 4. Structural (e.g. cellulose, chitin in arthropod exoskeletons and fungal walls).

5. Transport (e.g. sucrose is transported in the phloem of a plant), 6. Recognition of molecules outside a cell (e.g. attached to proteins or lipids on cell surface membrane).

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Bichemical test for polysachharides

Iodine solution or potassium iodide solution can be used to test for the presence of starch. A positive result changes the solution from an orange-brown to a blue-black colour. - refer to gcse and title biochemical test forcarboydrate.

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Lipids

are made up of the elements carbon, hydrogen and oxygen but in different proportions to carbohydrates. The most common type is the triglyceride->can exist as fats, oils and waxes. Fats and oils are very similar in structure (triglycerides).

At room temperature, fats are solids and oils are liquids. Fats are of animal origin, while oils tend to be found in plants->Waxes have a different structure (esters of fatty acids with long chain alcohols) and can be found in both animals and plants.

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Trygliceride

These are made up of 3 fatty acid chains (which may be identical or they may have different structures. )attached to a glycerol molecule

->This is called a condensation reaction because 3 water molecules are formed from 3 OH groups from the fatty acids chains and 3 H atoms from the glycerol.

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Fatty acids chains

chains of carbon atoms, the terminal one having an OOH group attached making a carboxylic group (COOH). The length of the chain is usually between 14 and 22 carbons long (most commonly 16-18).

->the carbon atoms may have single bonds between them making the lipid saturated. These are usually solid at room temperature and are called fats.->If one or more bonds between the carbon atoms are double bonds, the lipid is unsaturated. These are usually

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carboxylic group

(COOH).

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glycerol molecule

which has 3 OH groups attached to its 3 carbons.

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ester linkage

The bond between the fatty acid chain and the glycerol is called an

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Functions of lipids

1. Storage, 2.High-energy store, 3. Production of metabolic water, 4. Thermal insulation, 5. Electrical insulation, 6. Waterproofing, 7.Hormone production, 8.Buoyancy

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non-polar

non-polar and so are insoluble in water, i.e. lipids

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Why do lipids have a high energy store?

they have a high proportion of H atoms relative to O atoms and so yield more energy than the same mass of carbohydrate.

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How do lipids Produce metabolic water?

some water is produced as a final result of respiration.

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Why do lipids act as a thermal insulation?

fat conducts heat very slowly so having a layer under the skin keeps metabolic heat in.

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What hormones do lipids help to produce?

steroid hormones. Oestrogen requires lipids for its formation, as do other substances such as plant growth hormones.

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Explain Buoyancy

as lipids float on water, they can have a role in maintaining buoyancy in organisms

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Phospholipids

A phosphate-base group replaces one fatty acid chain. It makes this part of the molecule (the head) soluble in water whilst the fatty acid chains remain insoluble in water.

Due to this arrangement, phospholipids form bilayers (the main component of cell and organelle membranes).

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Proteins

Different proteins can appear very different and perform diverse functions (e.g. the water-soluble antibodies involved in the immune system and the water-insoluble keratin of hair, hooves and feathers). However, each one is made up of amino acid subunits

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amino acids

There about 20 different amino acids that all have a similar chemical structure but behave in very different ways because they have different side groups. Hence, stringing them together in different combinations produces very different proteins.

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condensation

When 2 amino acids are joined together (condensation) the amino group from one and the acid group from another form a bond, producing one molecule of water. The bond formed is called a peptide bond.

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peptide bond

When 2 amino acids are joined together (condensation) the amino group from one and the acid group from another form a bond, producing one molecule of water. The bond formed is called a peptide bond.

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Hydrolysis

is the opposite of condensation and is the breaking of a peptide bond using a molecule of water.

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Fibrous proteins

these are made of long molecules arranged to form fibres (e.g. in keratin). Several helices may be wound around each other to form very strong fibres.

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Globular proteins

are made of chains folded into a compact structure. One of the most important classes are the enzymes. Although these folds are less regular than in a helix, they are highly specific and a particular protein will always be folded in the same way

If the structure is disrupted, the protein ceases to function properly and is said to be denatured.

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quaternary structure

If a protein is made up of several polypeptide chains, the way they are arranged is called the quaternary structure. Again, each protein formed has a precise and specific shape (e.g. haemoglobin)

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Functions of proteins

1.Most enzymes are proteins 2.Structural:eg. collagen&elastin in connective tissue, keratin in skin etc.3.Contractile proteins:actin&myosin in muscles allow contraction->movement 4.Hormones:many hormones->protein structure(e.g. insulin/glucagon/growth hor

5.Transport:ie. haemoglobin facilitates oxygentransp. in body, some albumin in blood transport fatty acids 6.Transp into/out of cells: carrier/channel proteins in cellmembranes regul movement across 7.Defence:immunoglobulins protect body;fibrinogen in the

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Enzymes

The majority of the reactions that occur in living organisms are enzyme-controlled. Enzymes are proteins and thus have a specific shape. They are therefore specific in the reactions that they catalyse - one enzyme will react with molecules of one substrat

The site of the reaction occurs in an area on the surface of the protein called the active site.

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active site.

The site of the reaction occurs in an area on the surface of the protein called the

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Enzyme Controlled Reactions

Reactions proceed bcs the products have less energy than the substrates.->However, most substrates require an input of energy to get the reaction going, (the reaction is not spontaneous).->The energy required to initiate the reaction is called activ. ene

When the substrate(s) react, they need to form a complex called the transition state before the reaction actually occurs. This transition state has a higher energy level than either the substrates or the product.

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activation energy

The energy required to initiate the reaction is called the

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Enzymes - Factors Affecting the Rate of Reaction

1. Temperature, 2. pH, 3. Enzyme Concentration, 4. Substrate Consentration

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Enzymes - Cofactors

Most enzymes require additional help from cofactors, of which there are 2 main types:

1. COENZYMES->are organic compounds, often containing vitamin molecule as part of structure 2.METAL IONS->most speed up formation of enzyme-substrate complex by altering the charge in the active site e.g. amylase req chlorideions, catalase req. iron

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Inhibitors

slow down the rate of a reaction. Sometimes this is a necessary way of making sure that the reaction does not proceed too fast, at other times, it is undesirable

there are Reversible Inhibitors and eversible Inhibitors:

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Reversible Inhibitors:

Competitive reversible inhibitors, Non-competitive reversible inhibitors

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Irreversible Inhibitors:

These molecules bind permanently with the enzyme molecule and so effectively reduce the enzyme concentration, thus limiting the rate of reaction,

ie. cyanide irreversibly inhibits the enzyme cytochrome oxidase found in the electron transport chain used in respiration. If this cannot be used, death will occur

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Chromatography

This technique separates out mixtures of chemicals by using their different solubilities in certain solvents.

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*Hydrophobic

means insoluble in water->does not disolve in water->non-polar

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*Why is the cell surface membrane of phospholipids described as a fluid mosaic?

(Fluid because) phospholipids move (around membrane)

(Mosaic because) membrane contains proteins/glycoproteins (lying amongst phospholipids /eq)

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*Describe how the presence of a reducing sugar is detected using Benedicts reagent.

(Solution) heated->boiled (with Benedict's solution/reagent)=>green/yellow/orange/red/brown (precipitate)=>

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*If Benedict's reagent test was negative for reducing sugars, describe what steps you would need to carry out before you could show that non-reducing sugar was present.

Hear with acid or add sucrase->Neutralise or incubate (if using enzyme)->(Heat with) Benedict's ->repeat test/ eq

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*Describe how Benedict's reagent could be used to compare the concentrations of reducing sugar present in 2 solutions:

Same/staded, volumes of each (test) solution->Same/stated, volume Benedict's solution (to each)->Stated/same ->time/temperature (for heating)

boil in waterbath->Weight precipitate/colour comparison/reference to colorimeter comparison/time taken to reach standart of same colour/reference to rate of colour change

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Isotopes

Elements which have the same chemical properties as the normal element but have a different mass.

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Element

One of the 103 known chemical substances that cannot be divided into simpler substances by chemical means. A substance whose atoms all have the same atomic number.

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Molecule

Smallest identifiable unit into which a pure substance can be divided and retain its composition and chemical properties

Division into still smaller parts, eventually atoms, involves destroying the bonding that holds the molecule together.

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Atoms

Smallest unit into which matter can be divided and still retain the characteristic properties of an element.

Atoms always combine into molecules in fixed proportions.

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Inert

Unreactive. Refers to a substance which will not chemically react with anything under normal circumstances

ie. when the outer electron shells are full the atom is most stable , the least reactive. (If full it is inert?)

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What is the name of CH4?

Methane

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What is the name of CO2?

Carbon dioxide

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Monomers

A monomer is a molecule which acts as a single unit. It may combine with other monomers to form a polymer. The terms, monomer and polymer are used to describe the molecular structure of biological molecules

Examples of monomers (and their polymers) are styrene (polystyrene), ethylene (polyethylene), and amino acids (proteins).

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Carbohydrates

Made up of C, H, O->each molecule has 2xas many hydrogen atoms as oxygen

include: sugars, starches, glycogen and cellulose->stored in plants as starches and in animals as glycogen.

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Glucose

consists of a ring of atoms made up of 5x (C) and 1x (O), as sixth carbon atom is attached to the ring->hydrogen and oxygen atoms are attached to the carbons

there are alpha- and beta-glucose where the OH group is either on the bottom or the top of the C1 group

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How are carbon atoms numbered?

the (C) atom on the right hand side of the (O) atom is numbered 1 and there the numbering continues clockwise

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Water Potential

Water molecules move randomly. When water is encl. by a membrane, some of the moving water molecules hit the membrane, exerting pressure on it->WPis measured in units of pressure, usually kilopascals (kPa)->Pure water has a water potential of 0->greatest

A solution will have a lower concentration of water molecules so it will have a negative water potential->if we add solute to H2O->water molecules form a shell around each solute mol->decre. No of "free" water mol->decre. pressure->decreases water potent

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Concentration Gradient

The relation of two given areas, where the concentration of a particular substance differs between those areas.->from a high concentration to a low concentration.

changing the concentration gradient of one substance does not change the gradient and therefore the rate of diffusion of another.

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Diffusion

The movement of molecules along a concentration gradient, i.e. from areas of high concentration to a low concentration until their is an equilibrium.

Ions and most large molecules cannot diffuse through the phospholipid bilayer. They have to go through the protein pores.

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Particles

the molecules and ions in solids, liquids and gases ->are constantly moving.

the movement of particles depends on two things:->a) the physical state of the substance (gas, liquid, solid)->b) temperature:

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Facilitated Diffusion

hydrophilic molecules canot pass through the phospholipid bylayers->they are transportet across the membrane by carrier proteins.

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Reducing (Sugar)

Any process in which electrons are added to an atom or ion (as by removing oxygen or adding hydrogen); always occurs accompanied by oxidation of the reducing agent.

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