BIOL10008: Life and Macromolecules

Concepts 1 and 2

Define the characteristics of living organisms.

• made up of a set of common elements

• Comprised of cells

• Contain genetic info (allows coding of proteins)

• Grow and change

• Respond to environment

• Use molecules + make new molecules

• Extract + use energy

• Exist in populations, can evolve

What evidence does DNA provide to explain evolution?

All organisms have the same genetic code (DNA or RNA) as they have all arisen from earlier primitive forms over the past 4 billion years through processes of evolution

Explain different hypotheses for life formation on Earth.

1. Chemical evolution - conditions on primitive Earth led to the formation of simple molecules, which led to the formation of life forms

   Evidence - Miller–Urey experiment showed that it was possible for amino acids to be formed from gases that were hypothesized to have been in Earth’s early atmosphere

2. Extra terrestrial origin

   Evidence - meteorite from space carried molecules that are characteristic of life on Earth

Discuss how Stromatolites provide evidence for the beginning of life on Earth.

Stromatolites - geologic formations which consist of layers of limestone, calcium carbonate

Allowed for the fossilization of bacteria such as cyanobacteria because they can be trapped in between the layers

The bacteria found can be dated back to the beginning of life

Properties of Water

• Water molecules are able to interact with each other via hydrogen bonding, providing a high heat capacity

• Polar molecule - oxygen more electronegative and thus carries a partially negative charge compared to the hydrogen atoms which carry a partially positive charge

• Relatively high melting + boiling point

• High heat of vaporization

• Undergo cohesion (between h2o) and adhesion (attraction to other molecules)

• less dense as a solid than as a liquid

• Surface tension - water molecules at the surface are hydrogen bonded to other water molecules below them

Describe how the properties of water are important for life

• High heat capacity - takes a lot of energy to raise the temperature of a certain amount of water by a degree, so temperature can be regulated easily (stay constant)

• High heat of vaporisation - heat is absorbed by water to break hydrogen bonds, allowing evaporation which has a cooling effect

• Cohesive and adhesive properties - allow fluid transport

• Solid form less dense than liquid - prevents ponds from freezing from the bottom up, allowing life to thrive under the insulating layer of ice

What is Dipole Dipole attraction

• Exists between oppositely charged poles of two different molecules

• Between polar molecules (have one or more polar bond)

Describe a Hydrogen Bond

When hydrogen bonds to either F, O, or N, it becomes partially positively charged due to the difference in electronegativity. The H proton becomes exposed, and consequently is attracted to a lone pair of electrons on a different atom of any element.

What are London dispersion forces?

• Type of Van De Waals force

• Present in any molecule, only force present between non-polar molecules

• occur due to fluctuations in electron distribution that lead to momentary polarisation in one molecule, which induces polarization in another molecule and subsequent attraction between them

• Bigger molecule = more electrons --> more frequent and stronger dispersion forces

What are the functions of carbohydrates in organisms?

General formula (CH₂O)_n

• source of stored energy

• used to transport stored energy

• serve as carbon skeletons that can be rearranged to form new molecules

• form extracellular assemblies such as cell walls that provide structure

How are carbohydrates categorised?

1. Monosaccharides (mono, “one,” + saccharide, “sugar”), such as glucose, are simple sugars. They are the monomers from which the larger carbohydrates are constructed.

2. Disaccharides (di, “two”) consist of two monosaccharides linked together. Through condensation reaction where water is lost and a glycosidic link (ether bond) is formed Ex: sucrose

3. Oligosaccharides (oligo, “several”) are made up of several (3–20) monosaccharides.

4. Polysaccharides (poly, “many”), such as starch, glycogen, and cellulose, are polymers made up of hundreds or thousands of monosaccharides.

What is the role and structure of starch?

• energy storage compound of plants

• polymer of glucose

• contain α-1,4 glycosidic bonds which produce branching at carbon 6

• Branching limits the number of hydrogen bonds that can form in starch molecules, making starch less compact than cellulose, only to single molecule

• readily hydrolysed into glucose monomers

What is the role and structure of glycogen?

• energy storage compound for animals

• Polymer of glucose

• Like starch, glycogen contains α-1,4 glycosidic bonds which produce branching at carbon 6

• hydrogen bonding occurs between a single molecule

• high amount of branching in glycogen makes its solid deposits more compact than starch

• readily hydrolysed into glucose monomers

What is the role and structure of celluose?

• component of plant cell walls

• polymer of glucose

• contain β-1,4 glycosidic bonds (-OH group facing up) that are chemically very stable -  requires a different enzyme to hydrolyse compared to alpha glycosidic bonds

• can form hydrogen bonds between adjacent molecules, resulting in bundles or fibres

What is the structure of a nucleotide?

Composed of:
- Five-carbon pentose sugar (deoxyribose or ribose sugar)
- Phosphate group (attached to 5' carbon)
- Nitrogenous base (attached to 1' carbon)

How are nucleotides linked together? How are DNA strands held together?

Hydroxyl from phosphate at 5' of one nucleotide reacts with hydroxyl on 3' carbon of another to form a phosphodiester bond

These bonds form the sugar-phosphate backbone of a nucleic acid (DNA or RNA)

Strands of DNA held by hydrogen bonds between complementary nitrogenous bases

How are amino acids linked?

 -OH from carboxyl group of one amino acid and hydrogen from amine group of a different amino acid undergo a condensation reaction where a peptide bond (-CONH) is formed

Gives rise to 'polarity' of proteins (due to N-H and carbonyl group (C=O)

This forms a polypeptide chain as more amino acids are linked

N terminus - amine group end

C terminus - carboxyl group end

Describe primary structure of protein and the bonds that stabilise it.

• amino acids joined to form polypeptide chain

• peptide bonds

Describe secondary structure of protein and the bonds that stabilise it.

• Polypeptide chains may form α helices or β pleated sheets.

• hydrogen bonds

Describe tertiary structure of protein and the bonds that stabilise it.

• Polypeptides fold and form shapes (3D structure), sometimes contain random coils

• Hydrogen bonds, disulphide bridges and hydrophobic interactions

• Shape determined primarily by sequence of amino acids

Describe quaternary structure of protein and the bonds that stabilise it.

• Two or more polypeptides assemble to form larger protein

• Hydrogen bonds; disulphide bridges; hydrophobic interactions; ionic bonds

Explain how each of the following could potentially cause denaturation of a protein:

• pH change

• temperature increase

• addition of high concentration of a polar molecule

• addition of a high concentration of a non-polar molecule

A pH change can cause ionization of exposed carboxyl and amino groups in the R groups of amino acids. This leads to differences in polarity which can alter the tertiary structure of the protein.

Temp increase can cause rapid molecular movements and thus can break hydrogen bonds and hydrophobic interactions

Polar molecules can disrupt hydrogen bonding

Non polar molecules may also disrupt hydrophobic interactions and alter structure.

How are disulphide bridges formed?

Two cystine molecules in a polypeptide chain form a disulphide bridge (-S-S-) by oxidation, covalent bond formed and H atoms removed

List the physical and chemical properties of lipids.

• Triglyceride composed of glycerol and 3 fatty acids

• hydrocarbons that are insoluble in water due to their many non-polar covalent bonds

• Dissolve readily in organic solvents (e.g., hexane, benzene)

• Compose mainly of C, H, O - smaller proportion of oxygen than carbs

• May contain other elements (phosphorus, nitrogen)

How are triglycerides made?

• three condensation reactions

• carboxyl group of a fatty acid bonds with a hydroxyl group of glycerol, resulting an ester linkage and the release of water

What is the main structural difference between saturated and unsaturated fatty acids?

Saturated

• All bonds between C atoms are single

• fatty acid molecules are relatively straight, and they pack together tightly

• Generally make fats, solids, e.g., palmitic acid

Unsaturated

• contain one or more double bonds (are inflexible)

• Has kinks caused by double bonds which prevent close packing

• Tend to be oils at room temp

What is the structure of a phospholipid?

• Hydrophilic head, hydrophobic tail

• Amphipathic compound - part hydrophobic, part hydrophilic

• Form closed vessels in aqueous environments