Molecular Biology: 2.1 Molecules to Metabolism

Question 1

What is molecular biology about?

Answer 1

Molecular biology is a field of study that focuses on investigating biological activity at a molecular level

This includes elucidating the structure and function of chemical substances and determining their interactions as parts of living processes

Question 2

Why is carbon considered the basis of life? Further explain by stating its properties

Answer 2

Carbon forms the basis of organic life due to its ability to form large and complex molecules via covalent bonding

Carbon atoms can form four covalent bonds, with bonds between carbon atoms being particularly stable (catenation)

These properties allows carbon to form a wide variety of organic compounds that are chemically stable

Question 3

Outline carbohydrates as a group belonging to the main class of carbon compounds

Answer 3

Most abundant organic compound found in nature, composed primarily of C,H and O atoms in a common ratio – (CH2O)n
Principally function as a source of energy (and as a short-term energy storage option)
Also important as a recognition molecule (e.g. glycoproteins) and as a structural component (part of DNA / RNA)

Question 4

Outline lipids as a group belonging to the main class of carbon compounds

Answer 4

Non-polar, hydrophobic molecules which may come in a variety of forms (simple, complex or derived)
Lipids serve as a major component of cell membranes (phospholipids and cholesterol)
They may be utilised as a long-term energy storage molecule (fats and oils)
Also may function as a signalling molecule (steroids)

Question 5

Outline nucleic acids as a group belonging to the main class of carbon compounds

Answer 5

Nucleic acids are chains of subunits called nucleotides, which contain carbon, hydrogen, oxygen, nitrogen and phosphorus.
They are the Genetic material of all cells and determines the inherited features of an organism
DNA functions as a master code for protein assembly, while RNA plays an active role in the manufacturing of proteins

Question 6

Outline proteins as a group belonging to the main class of carbon compounds

Answer 6

Proteins are composed of one or more chains of amino acids. All of the amino acids in these chains are composed of C, H, O and N atoms (some may include Sulphur)
Major regulatory molecules involved in catalysis (all enzymes are proteins)
May also function as structural molecules or play a role in cellular signalling (transduction pathways)

Question 7

What are monomers?

Answer 7

Complex macromolecules may commonly be comprised of smaller, recurring subunits called monomers

Question 8

What group of carbon compounds are not comprised of monomers (are an exception)

Answer 8

Lipids do not contain recurring monomers, however certain types may be composed of distinct subunits (e.g. triglycerides)

Question 9

Outline the monomers of carbohydrates

Answer 9

Carbohydrates are composed of monomers called monosaccharides (‘single sugar unit’)

Monosaccharides are the building blocks of disaccharides (two sugar units) and polysaccharides (many sugar units)
Most monosaccharides form ring structures and can exist in different 3D configurations (stereoisomers)

Question 10

Outline the subunits in lipids

Answer 10

Lipids exist as many different classes that vary in structure and hence do not contain a common recurring monomer

However several types of lipids (triglycerides, phospholipids, waxes) contain fatty acid chains as part of their overall structure

Fatty acids are long chains of hydrocarbons that may or may not contain double bonds (unsaturated vs saturated)

Question 11

Outline the monomers of proteins

Answer 11

Proteins are composed of monomers called amino acids, which join together to form polypeptide chains

Each amino acid consists of a central carbon connected to an amine group (NH2) and an opposing carboxyl group (COOH)
A variable group (denoted ‘R’) gives different amino acids different properties (e.g. may be polar or non-polar, etc.)

Question 12

Outline the monomers of nucleic acids

Answer 12

Nucleic acids are composed of monomers called nucleotides, which join together to form polynucleotide chains

Each nucleotide consists of 3 components – a pentose sugar, a phosphate group and a nitrogenous base

The type of sugar and composition of bases differs between DNA and RNA

Question 13

What makes complex carbohydrates macromolecules different from each other?

Answer 13

The structure of complex carbohydrates may vary depending on the composition of monomeric subunits

Polysaccharides may differ according to the type of monosaccharide they possess and the way the subunits bond together

Glucose monomers can be combined to form a variety of different polymers – including glycogen, cellulose and starch

Question 14

Lipids can be roughly organised into one of three main classes (define them and give examples)

Answer 14

Simple (neutral) lipids – Esters of fatty acids and alcohol (e.g. triglycerides and waxes)
Compound lipids – Esters of fatty acids, alcohol and additional groups (e.g. phospholipids and glycolipids)
Derived lipids – Substances derived from simple or compound lipids (e.g. steroids and carotenoids)

Question 15

How are polymers of proteins formed?

Answer 15

Amino acids join together by peptide bonds which form between the amine and carboxyl groups of adjacent amino acids

The fusion of two amino acids creates a dipeptide, with further additions resulting in the formation of a polypeptide chain

The subsequent folding of the chain depends on the order of amino acids in a sequence (based on chemical properties)

Question 16

Outline how nucleic acids (polymers) are formed from subunits (explain how the structure of DNA arises)

Answer 16

Nucleotides form bonds between the pentose sugar and phosphate group to form long polynucleotide chains

In DNA, two complementary chains will pair up via hydrogen bonding between nitrogenous bases to form double strands
This double stranded molecule may then twist to form a double helical arrangement

Question 17

What is metabolism?

Answer 17

Metabolism describes the totality of chemical processes that occur within a living organism in order to maintain life

It is the web of all enzyme-catalysed reactions that occur within a cell or organism

Question 18

Metabolic reactions serve two key functions:

Answer 18

They provide a source of energy for cellular processes (growth, reproduction, etc.)
They enable the synthesis and assimilation of new materials for use within the cell

Question 19

What controls chemical reactions in a cell? (hence metabolism)

Answer 19

Cells use enzymes in order to increase the likelihood that a collision will lead to a useful chemical reaction. All biological processes (which happens via chemical reactions) are tightly regulated by enzymes.

Enzymes are composed of protein molecules, and act as catalysts that speed up the rate of biochemical reaction by lowering the activation energy of cellular reactions by mediating the orientation of reacting molecules in a way that leads to a collision resulting in a reaction while utilising less energy to do so.

Question 20

When two molecules collide, there are a large number of factors that determine whether a reaction occurs or not. Some of these factors include the:

Answer 20

identity of the colliding molecules
orientation of the colliding molecules (where they hit each other)
the speed of the molecules when they collide

Question 21

What is anabolism?

Answer 21

Anabolic reactions describe the set of metabolic reactions that build up complex molecules from simpler ones

Question 22

How does anabolism occur?

Answer 22

The synthesis of organic molecules via anabolism typically occurs via condensation reactions and it requires the use of energy (as bonds are being made) and they are typically reduction reactions

Condensation reactions occur when monomers are covalently joined and water is produced as a by-product

Use enzymes called synthase

Question 23

Examples of anabolic reactions

Answer 23

Monosaccharides are joined via glycosidic linkages to form disaccharides and polysaccharides
Amino acids are joined via peptide bonds to make polypeptide chains
Glycerol and fatty acids are joined via an ester linkage to create triglycerides
Nucleotides are joined by phosphodiester bonds to form polynucleotide chains

DNA synthesis during replication
Protein synthesis using ribosomes
Photosynthesis, including production of glucose from carbon dioxide and water.

Question 24

What is catabolism?

Answer 24

Catabolic reactions describe the set of metabolic reactions that break complex molecules down into simpler molecules

Question 25

How does catabolism occur?

Answer 25

The breakdown of organic molecules via catabolism typically occurs via hydrolysis reactions

Hydrolysis reactions require the consumption of water molecules to break the bonds within the polymer

It releases energy (as bonds are breaking) in the process and are classified as oxidation reactions

Use enzymes called hydrolase

Question 26

Examples of catabolic reactions

Answer 26

Digestion of food in the mouth, stomach and small intestine.
Cell respiration in which glucose or lipids are oxidized to carbon dioxide and water.
Digestion of complex carbon compounds in dead organic matter by decomposers.

Question 27

What is vitalism?

Answer 27

Vitalism was a doctrine that dictated that organic molecules could only be synthesised by living systems

It was believed that living things possessed a certain “vital force” which is different from the purely chemical and physical forces to make organic molecules
Hence organic compounds were thought to possess a non-physical element lacking from inorganic molecules

Question 28

How was vitalism falsified?

Answer 28

Vitalism as a theory has since been disproven with the discovery that organic molecules can be artificially synthesised

In 1828, Frederick Woehler synthesized urea artifcially using silver isocyanate and ammonium chloride
Urea is a metabolic waste product produced by deamination process in the liver (removal of nitrogen from excess amino acids in the body) and is eliminated by the kidneys in mammals
The artificial synthesis of urea demonstrates that organic molecules are not fundamentally different to inorganic molecules