Molecular biology

Question 1

Nucleic acids

Answer 1

DNA and RNA: chemicals used to make genes

Question 2

molecular biology

Answer 2

The relationship between genes and proteins; explains living processes in terms of the chemical substances involved.

Question 3

Urea and synthesis

Answer 3

Urea is produced by a living organism but can also be artificially synthesised because all its components were discovered, making it possible to recreate it in the lab. (Use: crop fertilisation) This falsified the Theory of Vitalism, which believed that organisms produce different matter than non-living matter.

Question 4

“R” group

Answer 4

makes amino acids either acidic or alkaline

Question 5

Carbon compounds and their bonds

Answer 5

Carbon atoms can form 4 covalent bonds allowing a diversity of compounds to exist; meaning two adjacent atoms share a pair of electrons, with one electron contributed by each atom.

• Covalent bonds are the strongest type of bond between atom so stable molecules based on carbon can be produced.
• Carbon can bond to multiple elements (e.g. ethanol - alcohol found in beer and wine).
• The four bonds can be all single covalent bonds or there can be two single and one double bond (e.g. in the carboxyl group of ethanoic acid - the acid in vinegar)

Question 6

Living organisms use four main classes of carbon compound:

Answer 6

Carbohydrates — characterised by their composition: carbon, hydrogen and oxygen, with hydrogen and oxygen in the ration of two hydrogen atoms to one oxygen, hence the name.

Lipids — broad class of molecules that are insoluble in water, including steroids, waxes, fatty acids and triglycerides.

Proteins — composed of one or more chains of amino acids. All of the amino acids in these chains contain the elements carbon, hydrogen, oxygen and nitrogen, but two of the twenty amino acids also contain sulphur.

Nucleic acids — chains of subunits called nucleotides, which contain carbon, hydrogen, oxygen, nitrogen and phosphorus. There are two types of nucleic acid: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)

Question 7

Anabolism

Answer 7

The synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation using ATP.

Examples: •Protein synthesis using ribosomes, •DNA synthesis during replication, •Photosynthesis, including production of glucose from carbon dioxide and water, •Synthesis of complex carbohydrates including starch, cellulose and glycogen.

Question 8

Catabolism

Answer 8

The breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers, releasing ATP.

Examples: •digestions of food in the mouth, stomach and small intestine, •Cell respiration in which glucose or lipids are oxidised to carbon dioxide and water, •digestion of complex carbon compounds in dead organic matter by decomposers.

Question 9

Water molecules

Answer 9

• formed by covalent bonds between an oxygen atom and two hydrogen atoms
• The bond between hydrogen and oxygen involves unequal sharing of electrons — it is a polar covalent bond. (this is because the nucleus of the oxygen atom is more attractive to electrons than the nuclei of the hydrogen atoms)
• Because of unequal electrons sharing, the hydrogen atoms have a partial positive charge and oxygen has a partial negative charge - dipole.
• Positively charged particles (positive ions) and negatively charged particles (negative ions) attract each other and form an ionic bond.
• Hence, water molecules attract each other, which is vital to living things, since it has this special properties. (the force is weak, but in the large quantities…)

Question 10

what bonds are inside a water molecule

vs

what are the intermolecular bonds between the water molecules

Answer 10

water molecule: covalent bonds

intermolecular: hydrogen bonds / ionic bond

Question 11

What explains the cohesive, adhesive, thermal and solvent properties of water?

Answer 11

• hydrogen bonding and bipolarity*
• Cohesive properties: refers to the binding together of two molecules of the same type, for instance two water molecules. (water transport in plants)
• Adhesive properties: hydrogen bonds can from between water and other polar molecules, causing water to stick to them. (water sticking to leaves)
• Solvent properties: The polar nature of the water molecules means that it forms shells around charged and polar molecules, preventing them from clumping together and keeping them in solution. (medium for metabolism)
• Thermal properties:
• High specific heat capacity: Hydrogen bonds restrict the motion of water molecules and increases in the temperature of water require hydrogen bonds to be broken. Energy is needed to do this. As a result the amount of energy needed to raise the temperature of water relatively large. To cool down, water must lose relatively large amounts of energy. Water’s temperature remains relatively stable in comparison to air or land, so it is a thermally stable habitat for aquatic organisms.
• High latent heat of vaporisation: When a molecule evaporates it separates from other molecules in a liquid and becomes a vapour molecule. That heat need to do this is called the latent heat of vaporisation. Evaporation therefore has a cooling effect. Considerable amounts of heat are needed to evaporate water, because hydrogen bonds have to be broken – sweating.
• High boiling point: The boiling point of a substance is the highest temperature that it can reach in a liquid state. For the same reasons that water has a high latent heat of vaporisation, its boiling point is high. 0° to 100° is the temperature range where most habitats are found on earth.

Question 12

What happens when one or two non-polar molecules are surrounded by water molecules?

Answer 12

Hydrophobic interactions:

Hydrogen bonds form between the water molecules, but not between the non-polar molecule and the water molecules. If two non-polar molecules are surrounded by water molecules and random movements bring them together, they behave as though they are attracted to each other. There is a slight attraction between non-polar molecules, but more significantly, if they are in contact with each other, more hydrogen bonds can form between water molecules. This is not because the are water-fearing: it is simply because water molecules are much more attracted to each other than to the non-polar molecules. As a result, non-polar molecules tend to join together in water to form larger and larger groups. The forces that cause non-polar molecules to join together into groups in water are known as hydrophobic interactions.

Question 13

significance of water to life

Answer 13

coolant - because thermal properties

transport medium - because adhesion, solvent and thermal properties

habitat - because cohesion and thermal properties

many more

Question 14

Monosaccharides

Disaccharides

Polysaccharides

How are disaccharides and polysaccharides formed?

Answer 14

• Monosaccharides are single sugar units.
• Disaccharides consist of two monosaccharides linked together. For example, maltose is made by linking two glove molecules together. Sucrose is made by linking a glucose and a fructose.
• Polysaccharides consist of many monosaccharides linked together. Starch, glycogen and cellulose are polysaccharides. They are all made by linking together glucose molecules.
• Formation of disaccharides/polysaccharides:*

Monosaccharide monomers are linked together by condensation reactions.

• Linking together monosaccharides to form disaccharides and polysaccharides is an anabolic process and energy is needed, which is in form of ATP.

Question 15

Condensation and Hydrolysis

Answer 15

This involves the loss of an -OH from one molecule and an -H from another molecule, which together form H2O. When they break up, it’s called hydrolysis.

Hydrolysis = water added

Condensation = water removed

Example: when monosaccharides combine.

Question 16

Triglycerides (+ uses)

Answer 16

One of the principal groups of lipid and is made by combining three fatty acids with one glycerol.

Each of the fatty acids is linked to the glycerol by a condensation reaction, so three water molecules are produced. (this linkage is called an “ester bond”)

Uses:

• energy stores, where the energy can be released by aerobic cell respiration.
• Because they do not conduct heat well, they are also used as heat insulators

Question 17

name this molecule

Answer 17

ribose

Question 18

name this molecule

Answer 18

glucose

Question 19

Body Mass Index (BMI)

Answer 19

Used to assess whether a person’s body mass is at a healthy level, or is too high or too low. Can be measuring using a nomogram (connect two sides with straight line).

Question 20

structure of fatty acids

types of saturation of fatty acids

Answer 20

Fatty acids structure: a chain of carbon atoms (length variable), with hydrogen atoms linked to them by single covalent bonds. It is therefore a hydrocarbon chain. At the end of the chain is the acid part of the molecule. This is a carboxyl group, which can be represented as -COOH.

saturated - maximum number of hydrogen atoms are bonded to the carbon chain via single bonds

unsaturated - contain one or more double bonds, which hinders additional hydrogen atoms to bond

monounsaturated - only one double bond

polyunsaturated - two or more double bonds

Cis unsaturated - hydrogen atoms are bonded to carbon atoms on the same side of a double bond

Trans unsaturated - hydrogen atoms are bonded to carbon atoms on opposite sides of a double bond

Question 21

Formation of polypeptides

Answer 21

Amino acids are linked together by condensation. These chains of amino acids linking together happens on ribosomes by a process called translation.

Polypeptides are the main component of proteins and in many proteins they are the only component.

The condensation reaction involves the amine group (-NH2) of one amino acid and the carboxyl group (—COOH) of another. Water is eliminated and a peptide bond is formed between the two amino acids.

Question 22

dipeptides and polypeptides

Answer 22

A dipeptide is a molecule consisting of two amino acids linked by a peptide bond.

A polypeptide is a molecule consisting of many amino acids linked by peptide bonds.

Question 23

Amino acid diversity

Answer 23

There are 20 different amino acids in polypeptides synthesized on ribosomes (although hundreds could be produced).

• This suggests common ancestry.
• There are two additional amino acids used (outside the 20). However, it is likely that organisms that use them, have evolved afterwards, and therefore do not falsify the theory that 20 amino acids are baisc in all organisms.
• It is the R group that gives a polypeptide its character
• the carbon atom is also bonded to an R group, which is different in each amino acid

Question 24

Polypeptide Diversity

Answer 24

Amino acids can be linked together via peptide bonds in any sequence, giving a huge range of possible polypeptides.

• For a polypeptide of n amino acids there 20n possible sequences.*
• Since “n” can be nearly everything, adding up all the possible sequences, the number is effectively infinite.

Question 25

Genes and Polypeptides

Answer 25

The amino acid sequence of each polypeptide is stored in a coded form in the base sequence of a gene.

Question 26

Protein Conformations

Answer 26

The amino acid sequence determines the three-dimensional conformation of a protein.

…

Question 27

Denaturation of Proteins

Answer 27

The three-dimensional conformation of proteins is stabilised by bonds or interaction between R groups of amino acids within the molecule. Most of these bonds and interactions are relatively weak and can be disrupted or broken. This results in a permanent change to the conformation of the protein.

• Heat can cause denaturation because it causes vibration within the molecule that can break intermolecular bonds or interactions. Proteins may vary in their heat tolerance. Some microorganisms that live in volcanic springs have proteins that are not denatured by temperatures of 80°C, which is why they are widely used in biotechnology. (e.g. Thermos aquaticus)
• Extremes of pH, both acidic and alkaline, can cause denaturation. This is because charges on R-groups are changed, breaking ionic bonds within the protein or causing new ionic bonds to form.

Question 28

Some of the many vital functions of proteins in organisms

Answer 28

• Catalysis — there are thousands of different enzymes to catalyze specific chemical reactions within the cell or outside it.
• Muscle Contraction — actin and myosin together cause the muscle contractions used in locomotion and transport around the body.
• Cytoskeletons — tubulin is the subunit of microtubules that give animal cells their shape and pull on chromosomes during mitosis.
• Blood clotting — plasma proteins acts as clotting factors that cause blood to turn from a liquid to a gel in wounds.
• Transport of nutrients and gases — proteins in blood help transport oxygen, carbon dioxide, iron and lipids.
• Cell adhesion — membrane proteins cause adjacent animal cells to stick to each other within tissues.
• Membrane transport — membrane proteins are used for facilitated diffusion and active transport, and also for electron transport during cell respiration and photosynthesis.
• Hormones — some such as insulin, FSH and LH are proteins, but hormones are chemically very diverse.
• Receptors — binding sites in membranes and cytoplasm for hormones, neurotransmitters, tastes and smells, and also receptors for light in the eye and in plants.
• Packing of DNA — histones are associated with DNA in eukaryotes and help chromosomes to condense during mitosis.
• Immunity — this the most diverse group of proteins, as cells can make huge numbers of different antibodies.

Question 29

Rubisco

Answer 29

The enzyme that calayses the photosynthesis reaction that fixes carbon dioxdie from the atmsophere.

Question 30

Insulin

Answer 30

The hormone that is carried dissovled in the blood and binds specifically and reversibly to insulin receptors in the mebranes of body cells, causing the cells to be absorb glucose and lower the blood glucose concentraiton.

Question 31

Immunoglobulins

Answer 31

Antibodies that bond to antigens on pathogens; produced in a huge range, each with their immune specificity.

Question 32

Rhodopsin

Answer 32

The pigment that makes the rod cells of the retina light-sensitive. It has a non-amino acid part called retinal that absorbs a photon of light and when this happens the rod cells send a nerve impulse to the brain.

Question 33

Collagen

Answer 33

A structural protein that has three polypeptides wound toegther to form a rope-like conformation and is ued in skin to prevent tearing, in bones to prevent fractures and in tendons and ligaments to give tensile strength.

Question 34

biotechnical uses for proteins

Answer 34

• enzymes for removing stains
• monoclonal antibodies for pregnancy tests
• insulin for treating diabetics

Increasingly, genetically modified organisms are being used as microscopic protein factories.

Question 35

a proteome (+ how to find out)

Answer 35

A proteome is all of the proteins produced by a cell, a tissue or an organism.

Whereas the genome of an organism is fixed, the proteome is variable because different cells in an organism make different proteins.

Within a species there are strong similarities in the proteome of all individuals, but also differences. The proteome of each individual is unique, partly because of differences of activity but also because of small differences in the amino acid sequences of proteins.

To find out how many different proteins are being produced, mixtures of proteins are extracted from a sample and then separated by gel electrophoresis. To identify whether or not a particular protein is present, antibodies that have been linked to a fluorescent maker can be used. If the cell fluoresces, the protein is present.

Question 36

enzymes

Answer 36

Enzymes are globular proteins that work as (biological) catalysts — they speed up chemical reactions without being altered themselves. Catalyst lower the energy required to trigger the chemical reaction/change.

substrate —enzyme—> product

The area where the substrate binds to the enzyme is called active site. The shape and chemical properties of the active site and substrate match each other. This property is called enzyme-substrate specificity. It is a significant difference between enzymes and non-biological catalysts.

Question 37

Enzyme procedure

Answer 37

Enzyme catalysis involves random molecular motion and the collision of substrates with the active site.

1. The substrate binds to the active site of the enzyme. Some enzymes have two substrates that bind to different parts of the active site.
2. While the substrates are bound to the active site they change into different chemical substances, which are the products of reaction.
3. The products separate from the active site, leaving it vacant (free) for substrates to bind again.

Question 38

Enzyme activity affecting factors

Answer 38

pH

Most enzymes have an optimum pH, at which their activity is highest. If the pH is increased or decreased from the optimum, enzyme activity decreases and eventually denatures.

substrate concentration

If the concentration of substrates is increased, substrate-active site collisions will take place more frequently and the rate at which the enzyme catalyses its reaction increases. The rate will plateau eventually because the active site will be occupied at all time.

temperature

In liquids, the particles are in continual random motion. When a liquid is heated, the particles in it are given more kinetic energy. Both enzymes and substrate molecules therefore move around faster at higher temperatures and the chance of a substrate molecule colliding with the active site of the enzyme is increased. Enzyme activity therefore increases. Too hot and the bonds break from the vibration and denaturation occurs. Too cold and movement ceases.

Question 39

Immobilized enzymes

Answer 39

The enzymes used in industry are usually immobilized. This is attachment of enzymes to another material or into aggressions, so that the movement of the enzyme are restricted.

Methods:

• attaching the enzymes to a glass surface
• trapping them in an alginate gel
• bonding them together to form enzyme aggregates (collections) of up to 0.1mm diameter.

Enzyme immobilization has several advantages:

The enzyme can easily be separated from the products of the reaction, stopping the reaction at the ideal time and preventing contamination of the products.

Enzymes can be recycled, saving cost, especially as many enzymes are very expensive

Stability of enzymes is increased to changes in temperature and pH, reducing the rate at which they are degraded and have to be replaced.

Enzyme concentrations can be higher, speeding up reaction rates.

Question 40

Lactose-Free Milk

Answer 40

Lactose is the sugar that is naturally present in milk.

It can be converted into glucose and galactose by the enzyme lactase:

lactose —lactase—> glucose + galactose

Lactase is obtained from Kluveromyces lactis, a type of yeast that grows naturally in milk.

reasons for lactase:

• Some people are lactose-intolerant
• Galactose and glucose are sweeter than lactose, so less sugar needs to be added to sweet foods containing milk, such as milk shakes or fruit yoghurt.
• Lactose tends to crystallise during the production of ice cream, giving a gritty texture. Because glucose and galactose are more soluble than lactose they remain dissolved, giving a smoother texture.
• Bacteria ferment glucose and galactose more quickly than lactose, so the production of yogurt and cottage cheese is faster.

Question 41

Induced Fit Model

Answer 41

As the substrate approaches the enzymes, and hasn’t attached yet, the enzyme shape changes to create a perfect match.

So, one enzyme can let more than one substrate bind to their active site since, as a similar substrate comes close the enzyme, the enzyme changes it shape to fit the approaching exactly.

Question 42

Structure of nucleic acids & nucleotides

Answer 42

The nucleic acids DNA and RNA are polymers of nucleotides.

Two types of nucleic acid: DNA & RNA

Nucleic acids are molecules that are constructed anabolically by linking together nucleotides to form a polymer.

Nucleotides are the building blocks of DNA & RNA

Nucleotides consist of three parts:

• a phosphate group, which is the acidic, negatively-charged part of nucleic acids
• a pentose sugar (has five carbon atoms)
• a nitrogen base and has either one or two rings of atoms in its structure.

The base and the phosphate group are both linked by covalent bonds to the pentose sugar.

Question 43

Differences between DNA and RNA nucleotides

Answer 43

1. The type of pentose is ribose in RNA but deoxyribose in DNA.
2. The fourth base is thymine in DNA but uracil in RNA. Ademine, cytosine and guanine stay the same.
3. RNA usually has one strand of nucleotides and DNA usually two. (polymers = strands)

Question 44

What bond links the nucleotides in strands and where?

Answer 44

Covalent bonds between the pentose sugar of one nuecleotide and the phosphate of the next one.

Question 45

Full description of DNA structure

Answer 45

DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs.

Question 46

All bases of DNA (+ RNA equivalent) and complementary base pairing

Answer 46

​A with T

G with C

_____

• adenine and guanine are purines (big molecule (two blocks))
• thymine and cytosine are pyrimidines (small molecule (one block)

thymine –> uracil in RNA