Topic 2: Molecular Biology

Question 1

How is urea produced?

Answer 1

Urea is the chief nitrogenous end product of the metabolic breakdown of proteins in all mammals and some fishes. It is not only present in the urine of mammals but also in their blood, bile, milk, and perspiration. Urea is most commonly produced by reacting carbon dioxide with ammonia at 200ºC. After reacting, urea is evaporated and processed by prilling or granulating to produce a solid end product.

Question 2

What are the characteristics, structure and examples of carbohydrates?

Answer 2

• Composed of C, H, O
• Composed of monosoccarhrides
• Link through a condensation reaction
• Linkage itself is called a glycosidic bond

Question 3

What are the characteristics, structure and examples of lipids?

Answer 3

Triglycerides are a form of lipid, made up of one molecule of glycerol with three fatty acids attached to it. These fatty acids have long hydrocarbon ‘tails’. Fatty acids occur in two forms: Saturated fatty acids and unsaturated fatty acids (unsaturated fatty acids can be monosaturated or polyunsaturated)

Lipids are macromolecules, like carbohydrates, and contain carbon, hydrogen, and oxygen atoms. Unlike carbohydrates, lipids contain a low proportion of oxygen. More of the oxygen required for their respiration has to come from the air. This allows lipids to be energy-dense, maximizing the energy content per gram versus carbohydrates. Lipids are insoluble. Fat is stored in the adipose cells but shrinks when the fat is respired to generate metabolic energy.

Lipids also have physical protection of soft organs e.g. visceral fat around the heart, thermal insulation from subcutaneous fat e.g. whale blubber, buoyancy aid, waterproofing secretions, electrical insulation, and photosynthetic pigments.

Storage
Osmolarity
Digestion
ATP yield
Solubility

Question 4

What are the characteristics, structure and examples of proteins?

Answer 4

Proteins are polymers (and macromolecules) made of monomers called amino acids. The sequence, type, and number of the amino acids within a protein determines its shape and therefore its function. Proteins are extremely important in cells because they form all of the following:
- Enzymes
- Cell membrane
- Hormones
- Immunoproteins
- Transport proteins
- Structural proteins
- Contractile proteins

A protein may consist of a single polypeptide or more than one polypeptide linked together. Some proteins exist as a single polypeptide chain (of amino acids). Other proteins are made up of two or more polypeptide chains joined together. Single polypeptide chain proteins include lysozyme, an enzyme present in mucus secretions and tears, that kills bacteria as part of our primary defences against pathogens. Proteins with 2 polypeptide chains include insulin and integrins.

Proteins with 3 polypeptide chains include collagen and ones with 4 include haemoglobin. Proteins have a 3-D structure and shape. Haemoglobin is a globular protein that forms a globe-shaped protein. Collagen is a fibrous protein that forms a rope-like protein for tensile strength.

Structure
Hormonal
Immunity
Transport
Sensation
Movement
Enzymatic

Question 5

What are the characteristics, structure and examples of nucleic acids?

Answer 5

Nucleic acids DNA and RNA are polymers of nucleotides. Each nucleotide is formed from a pentose sugar

Question 6

Differentiate between saturated, unsaturated, and polyunsaturated lipids.

Answer 6

Saturated fatty acids lack double bonds between the individual carbon atoms, while in unsaturated fatty acids, there is at least one double bond in the fatty acid chain. Polyunsaturated fats are simply fat molecules that have more than one unsaturated carbon bond in the molecule, this is also called a double bond.

Question 7

Identify/draw how condensation and hydrolysis reactions occur.

Answer 7

Hydrolysis reactions are used to break large molecules, such as proteins, polysaccharides, fats, and nucleic acids, into smaller molecules. The reverse reaction is called condensation, and condensation reactions are used to make these large molecules from smaller ones.

Question 8

Differentiate between anabolism and catabolism.

Answer 8

ANABOLISM
- Anabolic reactions are involved with the building of large molecules from smaller ones
- Requires an input of energy (endergonic)
- Builds large molecules from small ones
- Used to store energy in chemical form
- Involves condensation reactions
- Used for growth, repair, and energy storage
- Both are made up of enzyme - catalyzed reactions
- Both are coupled to ATP, the principal energy carrier in cells

CATABOLISM
- Released energy (exergonic)
- Breaks down large molecules into smaller ones
- Used to release chemical energy as heat and for movement, active transport etc.
- Involves hydrolysis reactions
- Performs several activities, e.g energy supply, digestion, excretion
- Both are made up of enzyme - catalyzed reactions
- Both are coupled to ATP, the principal energy carrier in cells

Question 9

Properties of water molecules and their bonds (cohesion, adhesion, solvent).

Answer 9

Water is composed of atoms of hydrogen and oxygen. One atom of oxygen combines with 2 atoms of hydrogen by sharing electrons (covalent bonding). Water is a polar molecule since one ed is negatively charged and the other is positively charged.
- Excellent solvent: many polar substances can dissolve in water (because it’s a polar molecule)
- High specific heat capacity (due to many hydrogen bonds being present in water it takes a lot of thermal energy to break them and a lot of energy to build them back up; it is also optimal for enzyme activity)
- High latent heat of vaporization
- Water is less dense when a solid
- Water has high surface tension and cohesion
- Acts as a reagent

PROPERTY:
Solvent
High specific heat capacity
High latent heat of vaporisation

ROLE IN ORGANISMS:
- Allows chemical reactions to occur and transport medium
- Allows for water to be a suitable habitat and provides optimal temperature maintained within cells and bodies
- Coolant

REASON:
- Polarity of water
- Presence of many hydrogen bonds
- Presence of many hydrogen bonds

Question 10

How can water be used to cool our bodies?

Answer 10

Water’s high latent heat of vaporization makes it an excellent coolant. Animals have evolved sweating (perspiration) as a way of disposing of excess heat generated through physical activity. The hypothalamus detects changes to blood temperature and when temperatures rise, it stimulates the secretion of sweat. Small droplets of water are secreted from sweat glands onto the skin’s surface. Vasodilation of arterioles just beneath the skin carries more blood close to the surface. Sweat (mainly water, also contains salts and other solutes) evaporates, carrying the excess heat away into the surrounding air and reducing the temperature of the organism. Water’s high latent heat of vaporization allows only small volumes of water to be needed to carry away a lot of heat.

Question 11

Identify the structure and formula of all 4 monosaccharides (glucose, galactose, fructose, ribose)

Question 12

Identify how monosaccharides form polysaccharides

Answer 12

Monosaccharides are converted into disaccharides in the cell by condensation reactions. Further condensation reactions result in the formation of polysaccharides. These are giant molecules that, importantly, are too big to escape from the cell.

Question 13

What monomers make up maltose, lactose, and sucrose?

Answer 13

Name of Disaccharide:
Maltose
Sucrose
Lactose

Names of monosaccharide components:
a -glucose, a-glucose
a-glucose, fructose
a-glucose, galactose

Question 14

Compare and contrast cis and trans fatty acids.

Answer 14

The cis fatty acid has both hydrogen atoms located on the same side. On the contrary, the trans fatty acid has two hydrogen atoms on opposite sides. CIS MAKES A C AND TRANS ARE JUST THE OPPOSITE.

Question 15

What bonds are made in cellulose, starch, and glycogen? (1,4 or 1,6 glycosidic bonds)

Answer 15

Starch, cellulose, and glycogen are polysaccharides. Polysaccharides are macromolecules that are polymers formed by many monosaccharides joined together by glycosidic bonds. The bonds form from condensation reactions, resulting in polysaccharide chains. These chains may be: branched or unbranched, folded (making molecules compacts which is ideal for storage e.g. starch and glycogen)

Starch and glycogen are storage polysaccharides because they are compact and insoluble. Cellulose is a structure polysaccharide because it is strong
and durable, insoluble, slightly elastic, and is an ideal material for plant cell walls (good for animals that eat plants too).

Amylose is one of the two polysaccharides. It is an unbranched helix-shaped chain with 1,4 glycosidic bonds between a-glucose molecules, and the helix shape enables it to be more compact and thus it is more resistant to digestion.

Amylopectin has 1,4 glycosidic bonds between a-glucose molecules as well as 1,6 glycosidic bonds creating branched molecules. The branches result in many terminal glucose molecules that can be easily hydrolyzed, for use during cellular respiration or added for storage.

Question 16

Examples of health risks of trans fats and saturated fats.

Answer 16

Trans-fatty acids occur in small quantities in natural products such as dairy and red meat. Artificial trans-fats are made industrially by the hydrogenation of liquid vegetable oils. Trans fats are favored by food manufacturers for commercial reasons. Trans-fats alter the balance of various types of cholesterol, they increase low-density lipoprotein (LDL) levels in circulation (so-called ‘bad cholesterol’). The decrease high-density lipoprotein (HDL) levels in circulation (so-called ‘good cholesterol’) LDL is known to increase the risk of coronary heart disease, blood clotting, and strokes. Other conditions linked to trans-fats include:
- Allergy
- Breast cancer
- Colonic cancer
- Cardiovascular diseases
- Premature birth
- Nervous system disorders
- Diabetes
- Obesity
- Vision defect in infants

Question 17

Identify BMI on a nomogram.

Answer 17

Body Mass Index =

Height^2 (meters)

BMI below 18.5 is underweight
BMI 18.5-24.9 is normal
BMI 25-29.9 is overweight
BMI 30-39.9 is obese
BMI of 40 or more is morbidly obese

Question 18

Draw how peptide bonds join amino acids.

Answer 18

Amino acids are the monomers of polypeptides. In order to form a peptide bond a hydroxyl group (-OH) is lost from the carboxylic group (-COOH) of one amino acid and a hydrogen atom is lost from the amine group (-NH2) of another amino acid. The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid. This is a condensation reaction so water is released. Dipeptides are formed by the condensation of two amino acids. Polypeptides are formed by the condensation of many (3 or more) amino acids. A protein may have only one polypeptide chain or it may have multiple chains interacting with each other. During hydrolysis reactions, the addition of water breaks the peptide bonds resulting in polypeptides being broken down into amino acids.

Question 19

What are the characteristics of immunoglobins?

Answer 19

Immunoglobulins or antibodies are essential in protecting against bacteria, viruses, and fungi. When there is a deficiency of these. The five primary classes of immunoglobulins are IgG, IgM, IgA, IgD, and IgE.glycoproteins, recurrent infectious diseases occur.

Question 20

What are the 4 levels of protein structure?

Answer 20

The shape of a protein can be described by four levels of structure: primary, secondary, tertiary and quaternary.

The primary structure is the unique and linear sequence of amino acids in a protein. It is the sequence in which amino acids are added to a growing polypeptide during translation.
With 20 different amino acids, the number of primary sequences is almost infinite.
It is the primary structure that determines how (and where) the polypeptide will fold to give a protein its shape. Thus, primary structure determines the higher levels of protein structure.
Small changes in primary structure can result in large changes in protein shape and function.

Secondary structure describes regions where the polypeptide is folded into localized shapes. There are two types of secondary structure (alpha helix and Beta pleated sheet).
The alpha helix is a delicate coil formed by hydrogen bonding between a hydrogen atom on one amino acid and an oxygen atom on the fourth amino acid away.
The beta sheet results from hydrogen bonding between different polypeptide chains or between different sections of the same polypeptide.

Tertiary structure is the overall shape of the protein. Most proteins (e.g. lysozyme, hemoglobin and insulin) have a compact, globular tertiary structure.
Some proteins are fibrous. Fibrous proteins like collagen (tendons, cartilage) and keratin (hair, feathers, horns, hoofs, etc.) have the alpha helix formation over their entire length. Other fibrous proteins like fibroin (the structural protein of silk) are dominated by beta sheets.
Tertiary structure is influenced by ionic bonds between opposite charged R-groups, hydrogen bonds between R-groups bearing opposite partial charges, and hydrophobic interactions resulting from the tendency of nonpolar R-groups to stay close together in an aqueous solution.
Another important bond affecting tertiary structure occurs in proteins that contain the amino acid cysteine. Where two cysteine monomers are close together, the sulfur of one cysteine bonds to the sulfur of the other, forming strong covalent bonds known as disulfide bridges.

Quaternary structure occurs in proteins that are made up of more than one polypeptide chain.
Combining different polypeptides leads to a greater range of biological activity. Collagen, for example, is made of three subunits intertwined into a triple helix, and hemoglobin is made of four heme groups, each a different polypeptide.
An influence on the quaternary structure of some proteins is the presence of a prosthetic group: a small molecule that is not a peptide but that tightly binds to the protein and plays a crucial role in its function. For example, the four heme groups on a hemoglobin protein are prosthetic and they function to carry oxygen.

Question 21

Difference between fibrous and globular proteins.

Answer 21

Globular proteins form a globe-shaped protein. Some of the haemoglobin’s outer parts are hydrophilic to be in contact with water whilst its inner parts are made up of amino acids with hydrophobic R groups.

Fibrous proteins form rope-like proteins for tensile strength. They have a repeating sequence of amino acids to create a helical structure. The chain of amino acids remains in an elongated conformation to give fibrous strength.

Question 22

Explain how temperature and/or pH can cause a protein to change/denature.

Answer 22

Denaturation is the irreversible change of protein structure caused by temperature and pH extremes. Heat and extreme pH are the most common causes of denaturation as they both break the weak bonds between R groups.

Question 23

What is an enzyme/action of enzymes?

Answer 23

Enzymes are biological catalysts because they speed up the rate of chemical reactions

Question 24

Explain how substrates and enzymes interact with one another.

Answer 24

Enzyme catalysis involves molecular motion and the collision of substrates with the active site. For an enzyme-catalysed reaction to take place, substrates collide at random with the enzyme’s active site. It must happen at the correct orientation and speed in order for the reaction to happen.

Question 25

Factors affecting rate of enzyme activity (identify graphs as well)

Answer 25

Temperature, pH, and substrate concentration affect the rate of activity of enzymes. Enzymes have a specific optimum temperature - the temperature at which they catalyze a reaction at the maximum rate. Lower temperatures either prevent reactions from proceeding or slow them down. Higher temperatures speed up reactions.

Extremes of pH can also alter hydrogen bonding within an enzyme’s structure and cause irreversible denaturation. Each enzyme has an optimum pH but not all enzymes have an optimum pH near neutral.

The more substrate molecules are present in a solution, this increases the frequency of collisions with the enzyme’s active site. Active sites are occupied or ‘blocked’ by substrates whilst the reaction is taking place.

Question 26

Explain how lactose free milk is made…advantage of immobilizing enzymes.

Answer 26

An immobilized enzyme is an enzyme that is attached to an insoluble material to prevent mixing with the product and through this method, the enzyme can be reused in subsequent reactions.

ADVANTAGES
- There is no enzyme in the product and therefore there is no need to further process or filter the end product.
- The immobilized enzyme can be reused multiple times (cost-effective)
- Greater tolerance for temperature and pH changes

DISADVANTAGES
- Expensive equipment
- More costly to buy for smaller industries
- Rate of reactions is sometimes lower

Lactose is a disaccharide that is hydrolyzed into glucose and galactose. Alginate beads bound with lactase. Lactase breaks down the lactose into glucose and galactose which can be easily absorbed by the lactose intolerant.

Question 27

Difference between hydrophobic and hydrophilic.

Answer 27

Hydrophilic = water-loving
Hydrophobic = water hating

Polar molecules and molecules with positive or negative charges can form hydrogen bonds with water (and dissolve) so are generally hydrophilic

Non-polar molecules with no positive or negative charge, cannot form hydrogen bonds with water so they are hydrophobic

Question 28

What is vitalism?

Answer 28

Vitalism is the theory that a living force was necessary for the synthesis of all organic molecules.

Question 29

How did the formation of urea help disprove the theory of vitalism?

Answer 29

Urea was thought to be synthesized only in living organisms. Urea had been thought to be found only in living organisms, however, the formation of urea from ammonium cyanate helped to disprove the theory of vitalism, which has been completely falsified by subsequent findings.

Question 30

Define monomer.

Answer 30

A molecule that can join with other identical monomers to form a larger structure called a polymer by a process called polymerisation.

Question 31

Define polymer.

Answer 31

Polymers are very big molecules called macromolecules made up of many smaller molecules called monomers layered together in a repeating pattern.

Question 32

Define macromolecules.

Answer 32

Macromolecules are very large molecules that contain 1000 or more atoms, therefore having a high molecular mass.

Question 33

What is metabolism?

Answer 33

Metabolism is a catch-all term used to describe all the chemical reactions that take place within cells and organisms. Metabolism can be thought of as the chemical reactions of life.

Question 34

What are some key functions of hydrogen bonds?

Answer 34

• Dissolves solutes in water
• Cohesion and adhesion of water molecules
• These properties allow water to move up the trunks of really tall trees
• Base-pairing between the two strands of DNA
• Hydrogen bonds help to form part of the secondary and tertiary levels of structure in proteins
• Hydrogen bonds found between cellulose and collagen give molecules tensile strength.
• Weak, they are constantly breaking and reforming
• Excellent solvent: many polar substances can dissolve in water
• High specific heat capacity
• High latent heat of vaporization
• Water is less dense when a solid
• Water has high surface tension and cohesion
• Acts as a reagent

Question 35

Where do hydrogen bonds form between water molecules?

Answer 35

They occur between the oxygen of one water molecule to the hydrogen atom of another.

Question 36

Explain the role of water in our blood.

Answer 36

Water in blood plasma is essential in transferring heat around the body, helping to maintain a fairly constant temperature, especially at body extremities e.g. fingerprints. As blood passes through more metabolically active (‘warmer’) regions of the body, heat energy is absorbed but the temperature remains fairly constant. Water tissue fluid also plays an important regulatory role in maintaining a constant body temperature.

Question 37

Explain water being a coolant in plants.

Answer 37

Plants transpire. A large tree will stand directly in sunlight all day, so it will absorb a huge amount of heat on a hot day. A tree cannot seek shade because it requires light energy for photosynthesis. A tree is also immobile and provides shade for other organisms. A transpiration stream of water flows up the tree, from the roots to xylem to leaves throughout the day. Water evaporates inside the spongy mesophyll layer of leaves, so water vapor can diffuse out via the stomata.

Question 38

Compare DNA and RNA

Answer 38

PROPERTIES
pentose sugar
bases
number of strands

DNA
Deoxyribose
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
Double-stranded (double helix)

RNA
Ribose
Adenine (A)
Uracil (U)
Cytosine (C)
Guanine (G)
single-stranded

Question 39

Explain the Crick and Watson model.

Answer 39

In “A Structure of Deoxyribose Nucleic Acid,” Watson and Crick described DNA as a double helix that contained two long, helical strands wound together. In their model, each DNA strand contained individual units called bases, and the bases along one DNA strand matched the bases along the other DNA strand.

Question 40

What is transcription vs Translation?

Answer 40

The process by which DNA is copied to RNA is called transcription, and that by which RNA is used to produce proteins is called translation.

Question 41

Define Cellular Respiration.

Answer 41

Cell respiration is the controlled release of energy from organic compounds to produce ATP. Respiration is a series of chemical reactions that happens in every cell. Its purpose is to release energy in usable forms from the chemical energy stored in food e.g. glucose. Respiration is a catabolic process/ Glucose is the main respiratory fuel used in cells. Lipids and proteins can also be used.

Question 42

Define ATP.

Answer 42

ATP is a source of energy for cellular processes. The energy can be released immediately, exactly when it is required. All organisms require a constant supply of energy to maintain their cells and stay alive.

Question 43

Define Anaerobic Respiration.

Answer 43

Anaerobic respiration occurs without oxygen and releases less energy but more quickly than aerobic respiration. Anaerobic respiration in microorganisms is called fermentation.

Question 44

Define Aerobic Respiration.

Answer 44

Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose. The presence of oxygen allows glucose to be broken down fully into carbon dioxide and water. This yields far more energy than anaerobic respiration. CO2 is a waste product that has to be excreted (except for plants it is used for photosynthesis. Water is a by-product and contributes to the organism’s water needs. Most reactions of aerobic respiration, in eukaryotes, take place in the mitochondria.

Question 45

Define photosynthesis.

Answer 45

Photosynthesis is the process by which plants use sunlight, water, and carbon dioxide to create oxygen and energy in the form of sugar.

Question 46

Why does anaerobic respiration produce less ATP than aerobic respiration?

Answer 46

Aerobic respiration is much more efficient and produces ATP much more quickly, than anaerobic respiration. This is because oxygen is an excellent electron acceptor for the chemical reactions involved in generating ATP.