Topic 1 - Biological molecules

Question 1

What is a covalent bond?

Answer 1

When atoms share a pair of electrons in their outer shells. As a result, the outer shell of both atoms is filled and a more stable compound, called a molecule is formed.

Question 2

What is an ionic bond?

Answer 2

When ions with opposite charges attract one another. This electrostatic attraction is known as an ionic bond. For example, the positively charged sodium ion and negatively charged chloride ion form an ionic bond to make sodium chloride. Ionic bonds are weaker than covalent bonds.

Question 3

Describe hydrogen bonding.

Answer 3

When the electrons within a molecule are not evenly distributed but tend to spend more time at one position. This region is more negatively charged than the rest of the molecule. A molecule with an uneven distribution of charge is polarised. The negative region of one polarised molecule and the positively charged region of another attract each other. A weak electrostatic bond is formed between the two. Although each bond is individually weak, they can collectively form important forces that alter the physical properties of molecules. This is especially true for water

Question 4

What is a monomer?

Answer 4

The smallest single unit of a chain. They can be joined together to form dimers and polymers.

Question 5

Explain the reaction that joins monomers together.

Answer 5

Polymerisation occurs through many condensation reactions, which join individual monomers into chains to form a polymer. A molecule of water is formed in a condensation reaction.

Question 6

Explain the reaction that breaks apart monomers.

Answer 6

Reactions that break apart dimers are called hydrolysis reactions. they require a molecule of water to occur.

Question 7

What is meant by the term metabolism?

Answer 7

All the chemical processes that take place in living organisms are collectively called metabolism. It acts to breakdown biological molecules into simpler forms for easier absorption.

Question 8

What is a mole?

Answer 8

The mole is the standard index (SI) unit for measuring the amount of a substance. One mole contains the same number of particles as there are in 12 grams of carbon-12 atoms (Avogadro’s Constant).

Question 9

What is a Molar solution?

Answer 9

A molar solution (M) is a solution that contains one mole of solute in each litre of solution. A mole is the molecular mass (molecular weight) expressed as grams (= one gram molecular mass) E.g. the molecular mass of NaCl is 58.5. Therefore, a Molar solution of NaCl is made up of 58.5 grams of NaCl in 1 litre of solution.

Question 10

What is a monosaccharide? Give some examples.

Answer 10

The single subunit of carbohydrates. Have the general formula (CH2O)n where n = 3-7. An example is glucose (C6H12O6)

Question 11

What is a reducing sugar? Describe how you would test for it.

Answer 11

All monosaccharides and some Disaccharides are reducing sugars. A reducing sugar is a sugar that can donate electrons (i.e. reduce) another chemical. To test for the presence of a reducing sugar, you can use a chemical reagent such as Benedict’s solution which changes colour when it is reduced. E.g. in the Benedict’s test is blue when not reduced (its an alkaline solution of copper sulphate), but when there is a reducing sugar present, it becomes an insoluble red precipitate (of copper oxide) (after heating).

Question 12

Describe some common disaccharides and what monomers they are formed from.

Answer 12

Maltose is formed from 2 a-glucose molecules.
Sucrose is made from glucose and fructose.
Lactose is made from glucose and galactose.

Question 13

What bond is formed in the condensation reaction between 2 monosaccharides?

Answer 13

A glycosidic bond

Question 14

Draw out the structure of alpha glucose

Answer 14

Question 15

Draw out the structure of beta-glucose

Answer 15

Question 16

Draw the condensation and hydrolysis reaction between two alpha glucose molecules.

Answer 16

Question 17

How do you test for non-reducing sugars?

Answer 17

Some disaccharides e.g. maltose are reducing sugars but other such as sucrose are non-reducing sugars. In order to detect a non-reducing sugar, it must first be hydrolysed into its monosaccharide components. So before doing a Benedict’s test, you must add dilute hydrochloric acid to the test sample and leave in a water bath. Then add some sodium hydrogen carbonate to neutralise the acid. The conduct Benedict’s test as normal.

Question 18

What is a polysaccharide? Name some examples.

Answer 18

A polymer formed by the condensation of monosaccharides and disaccharides. Examples include Cellulose, starch and glycogen.

Question 19

What is the structure and function of starch? How do you test for it?

Answer 19

Starch is found in many parts of a plant (It is not made in animal cells) in the form of small grains (as storage). It forms an important component of food and is a major energy source. It is made up of chains of a-glucose linked by glycosidic bonds. The chains may be branched or unbranched. The unbranched chain is wound tightly into a tight coil that makes the molecule very compact. You can easily test for starch using iodine. Orange iodine goes blue/black in the presence of starch

Question 20

What properties of starch make it a good storage molecule?

Answer 20

It is insoluble and therefore doesn’t affect water potential, so water is not drawn into the cells by osmosis.
It is large so does not diffuse out of cells.
It is compact, so a lot can be stored in a small space.
When hydrolysed, it form a-glucose which can be both easily transported and used in respiration for energy.
The branched forms have many ends which can be acted on by enzymes simultaneously meaning that glucose monomers are released rapidly.

Question 21

What is the structure and function of glycogen?

Answer 21

Glycogen is very similar to starch, but is made by animal cells. It is more highly branched that starch so has more ends and can be acted on simultaneously by enzymes to release large amounts of a-glucose. This is important to animals which have a higher metabolic rate and therefore respiratory rate that plants because they are more active.

Question 22

What is the structure and function of cellulose?

Answer 22

Cellulose is found in plant cells and is made from monomers of beta glucose. Therefore, rather than forming a coil (like with alpha-glucose made starch), cellulose is made up of straight, unbranched chains that run parallel to each other, with hydrogen bonds forming crosslinks between branches. The cellulose molecules grouped together to form microfibrils which add structural integrity to plant cell walls. This prevents the cell from bursting/shrivelling due to water movement in and out of the cell.

Question 23

What are lipids? What are their main properties? What are the main groups of lipids called?

Answer 23

Lipids are a group of substances which have a wide variety of functions in cells. They contain carbon, hydrogen and oxygen (the proportion of oxygen to carbon and hydrogen is smaller than in carbohydrates). Lipids are insoluble in water but soluble in organic solvents such as alcohol. The main groups of lipids are triglycerides and phospholipids.

Question 24

Name some general roles of lipids.

Answer 24

They are a source of energy.
They provide waterproofing due to their insolubility
They are insulating
They protect the organism (E.g. layers of fatty tissue around vital organs)

Question 25

What is the structure of triglycerides?

Answer 25

Triglycerides have 3 fatty acid chains combined with glycerol. Each fatty acid forms an ester bond which glycerol in a condensation reaction. Hydrolysis of a triglyceride therefore produces glycerol and three fatty acids. Triglycerides have different properties depending on which fatty acid chains they contain (there are over 70 different ones)

Question 26

What does saturated and unsaturated mean in the context of fatty acids? What effect does this have on their properties?

Answer 26

Fatty acids have a carboxyl group, with a hydrocarbon chain attached. If the hydrocarbon chain contains non double bonds between carbon atoms, then the fatty acid is said to be saturated. If it contains one double bond it is mono-unsaturated, and if it contains multiple it is poly-unsaturated. The double bonds in the chain cause it to bend, and therefore the triglyceride with that fatty acid chain cannot pack together as tightly, making them more liquid at room temperature (an oil rather than solid fat)

Question 27

Explain how the properties and functions of triglycerides relates to their structure.

Answer 27

Triglycerides have a high ratio of energy-storing carbon-hydrogen bonds of carbon atoms and are therefore an excellent source of energy.
Triglycerides have a low mass to energy ratio, making them good storage molecules because lots of energy can be stored in a small volume.
Being large, non-polar molecules, triglycerides are insoluble in water. As a result, their storage does not affect osmosis in cells or the water potential of them.

Question 28

What is the structure of phospholipids?

Answer 28

Instead of 3 fatty acid molecules, phospholipids have 2 fatty acid molecules and one phosphate group. Fatty acid chains repel water (are hydrophobic) and the phosphate molecule attracts water (is hydrophilic). Therefore phospholipids are said to be amphiphilic and therefore polar. They also always position themselves with their hydrophobic end away from water - this gives them very interesting properties.

Question 29

Explain how the properties and functions of phospholipids relates to their structure.

Answer 29

Because of their hydrophilic head and hydrophobic tail, in an aqueous environment (when water is present) phospholipids self-organise into a a bilayer within cell surface membranes causing the cell to have a hydrophobic barrier between the inside and outside of the cell.
The hydrophilic phosphate heads of the phospholipids help to hold at the surface of the cell-surface membrane.
The phospholipids structure allows them to form glycolipids by combining with carbohydrates within the cell-surface membrane. These glycolipids are important in cell recognition.

Question 30

Explain how you would test for lipids.

Answer 30

The emulsion test: Add ethanol to the sample and shake to dissolve. Then add water and shake. If there is lipids present, solution will become cloudy white due to lipid droplets (micelles) forming. The concentration of the lipid present can be investigated by looking at how much light passes through the cloudy solution (more lipid = more cloudy and therefore less light) and testing with a colourimetre.

Question 31

What are amino acids? What is their structure?

Answer 31

The functional subunits (monomers) that make up proteins. There are 21 different amino acids found in all organisms (but about 100 identified artificially). Every amino acid has a central carbon atom to which are attached 4 different chemical groups:

1. an amino group (-NH2)
2. a carboxyl group (-COOH)
3. a hydrogen atom (-H)
4. a function R group (each amino acid has a different R group which gives them their properties)

Question 32

What is the primary structure of a protein?

Answer 32

The polymer (polypeptide) formed by condensation reactions between amino acids. The order of amino acids in this chain (which is coded by DNA) determines what shape the protein will take once folded and therefore its function.

Question 33

What is the secondary structure of a protein?

Answer 33

Depending on the amino acids in the chain, the polypeptide can either coil in an alpha helix, or it take the form of a beta-pleated sheet.

Question 34

What is the tertiary structure of a protein?

Answer 34

The alpha helices or beta-pleated sheets are twisted and folded to create a more complex shape. These shapes are held in position by bonds between amino acids such as disulphide bridges, ionic bonds, and hydrogen bonds. The 3D shape of the protein is very important in determining how it functions. E.g. whether proteins are globular or fibrous.

Question 35

What is the quaternary structure of a protein?

Answer 35

Large proteins often form complex molecules with other polypeptides which are linked in various ways. E.g. haemoglobin in red blood cells is made up of 4 individual polypeptide chains and an iron molecule.

Question 36

How do you test for proteins?

Answer 36

The most reliable test for proteins in the Biuret test which detects peptide bonds. You add sodium hydroxide to the sample and heat. Add a few drops of very dilute copper sulfate and gently mix. The solution will be blue if no peptide bonds are present. But if the solution goes purple, peptide bonds (and hence proteins) are present.

Question 37

What are enzymes?

Answer 37

Enzymes are globular proteins that act as catalysts . Catalysts alter the rate of a chemical reaction (lower the activation energy) without undergoing permanent changes themselves.They can be reused repeatedly and are therefore effective in small amounts. Enzymes do not make reactions happen, but the speed up reactions that already naturally occur, but would otherwise take too long to be biologically sustainable.

Question 38

What tends to be the structure of an enzyme?

Answer 38

Enzymes have a 3D structure that usually contains a region with a very specific shape known as the active site. This site is usually specifically shaped to match the substrate that the enzyme will act on.

Question 39

Explain the ‘lock and key’ model of enzyme action.

Answer 39

One early model of enzyme action proposed that one enzyme works for a specific substrate, like one key works for one lock. But one limitation of this model is that the active site would then be expected to be a fixed shape, but scientists observed that other molecules, slightly differently shaped to the substrate could bind to the enzymes at the active site, and also at other sites on the enzyme. This altered the activity of the enzyme, and therefore must be changing the shape of the active site.

Question 40

Explain the ‘ induced fit’ model of enzyme action.

Answer 40

This model proposes that the active site forms as the enzyme and substrate interact. I.e. the enzyme is flexible and can mould itself to the shape of the substrate, providing it matches well. As it changes shape, the enzyme puts a strain on the substrate molecule. This strain distorts a particular bond or bonds int he substrate and consequently lowers the activation energy needed to break the bond. This model is likely more accurate that the lock and key model.

Question 41

Describe and explain some factors that affect the rate of enzyme-controlled reactions.

Answer 41

Temperature- rate of reaction increases up to the optimum, then above this, the enzyme’s active site may start to denature, causing a decrease in the rate of reaction.

pH- A pH higher or lower than the optimum for the enzyme will decrease the rate of reaction, and may also cause denaturing.

Enzyme concentration - The rate of reaction increases as the enzyme concentration increases, as there are more active sites for substrates to bind to. Increasing the enzyme concentration past as certain point has no effect on the rate, because the number of free active sites will outnumber the substrate available.

Substrate concentration- As concentration of substrate increases, rate of reaction increases as more enzyme-substrate complexes are formed. However, beyond a certain concentration, the rate of reaction no longer increases as enzyme concentration becomes the limiting factor.

Question 42

Explain how competitive inhibitors work.

Answer 42

Competitive inhibitors act to block the active site of the enzyme, usually because they are a similar shape to the substrate. This decreases the rate of reaction because less enzyme-substrate complexes can form.

Question 43

Explain how non-competitive inhibitors work.

Answer 43

Non-competitive inhibitors bind to a non-active site part of the enzyme (usually called the allosteric site). This binding causes a change in the shape of the active site of the enzyme, which reduces the rate of reaction due to less enzyme-substrate complexes forming.

Question 44

Describe the structure of DNA.

Answer 44

DNA (deoxyribose nucleic acid) is made up of two polynucleotide strands which wrap to form a double helix structure. The nucleotides are attached together by phosphodiester bonds, and the strands are bonded through hydrogen bonds between complementary nucleotide bases on opposite strands.

Question 45

Explain and draw the structure of a nucleotide.

Answer 45

Nucleotides consist of a ribose sugar (deoxy in DNA), a phosphate group, and a nitrogen base.

Question 46

Describe some similarities and differences between the structure of RNA and DNA.

Answer 46

DNA is double stranded and RNA is usually single strands

DNA strands are much longer than RNA strands

DNA contains the bases adenine, thymine, guanine and cytosine. RNA contains uracil instead of thymine.

Question 47

Which nucleotide bases are complementary pairs?

Answer 47

Cytosine and guanine

Adenine and thymine/uracil

Question 48

Explain the steps of DNA replication.

Answer 48

1. DNA helicase unravels the double helix and breaks the hydrogen bonds between the two strands.
2. Free nucleotides bind to their complementary bases on each of the single strands.
3. DNA polymerase moves down the strand and rejoins the phosphate-sugar backbone by catalysing the phosphodiester bonds between the free nucleotides.

Question 49

Why is DNA replication known as semi-conservative?

Answer 49

Each of the DNA strands is used a template, so the resulting DNA is formed from an old strand and a new strand.

Question 50

What is the structure of ATP?

Answer 50

ATP stands for adenosine triphosphate and is made up of an adenine base, and ribose sugar and three phosphate groups.

Question 51

Explain how ATP is formed, and broken down.

Answer 51

ATP is produced by ATP synthase in a condensation reaction, from an inorganic phosphate and ADP.

ATP is broken down in a hydrolysis reaction which produces ADP and an inorganic phosphate.

Question 52

Explain why ATP is a good source of energy.

Answer 52

Energy is released quickly when ATP is hydrolysed. This is because the bonds broken the phosphate molecules are unstable so have a low activation energy.

The energy released is not too much for the cell to deal with.

The production and breakdown of ATP is reversible, and the phosphate molecules produced from ATP hydrolysis can be used to produce other useful molecules in the cell.

ATP isn’t stored so can be easily reformed.

Question 53

What are the properties of water that are important for life.

Answer 53

Water is a metabolite which means it is used in condensation and hydrolysis reactions.

Water is a polar molecule due to the uneven distribution of charge. This means water molecules can ‘attach’ together through hydrogen bonds, which gives it cohesion. This allows water to be transported as a ‘tube’ and also gives it a high surface tension and water-air boundaries.

Water is a good solvent, so different materials can be transported dissolved in water.

Water has a high specific heat capacity, which means that it acts as a buffer to temperature fluctuations, which is important for homeostasis.

Water has a high latent heat of vaporisation, which means that a lot of energy is required for evaporation, so lots of energy can be lost with small amounts of sweating, providing a cooling effect.

Question 54

Name some inorganic ions, and describe their function in the body.

Answer 54

Hydrogen ions - determine the pH of substances, and are also used during chemiosmosis for the production of ATP.

Iron - a component of haemoglobin, and binds with oxygen to transport it around the body.

Sodium and potassium ions - Used in the reabsoprtion of glucose and amino acids, and also action potentials

Phosphate ions - a component of important molecules such as nucleic acids and ATP