Molecular biology (topics 2, 7, 8)

core: topic 2; AHL: topic 7, topic 8.1

molecular biology

field of study focusing on investigating biological activity on molecular level

organic compounds

compounds containing carbon found in living things (except for carbides, carbonates, carbon oxides, cyanides)

what properties allow carbon to form many diverse compounds?

* the ability to form 4 covalent bonds
* the bonds are stable

main function of carbohydrates

* source of energy
* recognition molecule in cells

main functions of lipids

* main component of the cell membrane
* long-term energy storage
* signalling molecule

main function of nucleic acids

* genetic material
* instructions for the synthesis of proteins

main function of proteins

* involved in catalysis
* structural molecules

vitalism

organic molecules could __only__ be synthesised by living systems

how was vitalism disproved?

* in 1828
* heating an inorganic salt produced urea
* artificial synthesis of urea proves that organic compounds can be produced artificially

metabolism

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

functions of metabollic reactions

* provide a source of energy for cellular processes
* enable the production and assimilation of new materials within the cell for its use

anabolism

reactions resulting in the building up of larger molecules from simpler ones

catabolism

the reactions resulting in breaking up larger molecules into smaller ones

monosaccharides are joined via…

glycosidic bonds

amino acids are joined via

peptide bonds

glycerol and fatty acids are joined via

ester linkages

nucleotides are joined via

phosphodiester bonds

examples of trace elements

Ca, P, Fe, Na, S

function of calcium

neurotransmitter release from synapses, muscle contractions

functions of iron

hemoglobin - needed for oxygen transport

function of sodium

sodium potassium pump, generation of nerve impulses in neurons

functions of phosphorus

make up cell membranes and nucleic acids

function of sulphur

found in some amino acids, allow disulphide bridges in proteins to form

what is the benefit of water’s dipolarity?

forming polar associations with other compounds, being the essential medium of life and the universal solvent

properties of water

thermal, cohesive/adhesive, solvent properties

thermal properties

* due to strong intermolecular hydrogen bonds that require a lot of energy before they can be broken
* high heat capacity. high heat of evaporation

application of the thermal properties of water: sweat

* input of energy required to change water from liquid to gas
* energy is provided by the surface of the skin when it’s hot
* as skin gives out its heat to evaporate water, it becomes cooler
* high heat capacity = good coolant

cohesion

the ability of like molcules to stick together

adhesion

the ability of dissimilar molecules to stick together (e.g. water sticks to the surface)

surface tension

* possible thanks to cohesion and adhesion
* hydrogen bonding is so strong that it allows the surface of water to resist low external force
* thanks to this, small organisms such as insects can move on the surface of water

capillary action

* attraction to charged polar surfaces allows water to flow in the directtion opposing gravitational forces
* necessary to transport water up the stem in plants via the transpiration stream

solvent properties

* universal solvent
* dissolves polar substances, ions
* the attraction of water can weaken the intermolecular forces, which causes the atoms of certain compounds to fall apart

the name of the reaction joining two sugar monomers (monosaccharides)

condensation

monosaccharides

* one sugar unit
* typically taste sweet
* immediate energy source for cells
* glucose, fructose, galactose

disaccharides

* two sugar units
* can be soluble in water, used in transport
* sucrose, maltose, lactose

polysaccharides

* many sugar units
* energy storage, cell recognition, structural support
* cellulose, glycogen, starch

cellulose

* structural function - cell wall in plants
* made of beta-glucose
* indigestible for most animals, except for ruminants

what is the difference between alpha-glucose and beta-glucose?

the location of one of the OH groups (they are isomers)

starch

* energy storage in plants
* composed of alpha-glucose
* amylose: linear, helical, only 1-4 linkages, less soluble, preferred as energy storage since it takes up less space
* amylopectin: branched, additional 1-6 linkages, more soluble

glycogen

* energy storage polysaccharide formed in the liver of animals
* composed of alpha-glucose with both 1-4 and 1-6 linkages, so it is branched
* branching every 10 subunits

condensation reaction

* takes away one water molecule
* requires two monomers to form a dimer
* energy is required
* enzymes are required to speed up the process
* consists of bond-making

hydrolysis

* breaks down a large molecule into a smaller ones
* releases energy
* requires enzymes
* one molecule of water is added, as bonds are broken

saturated fatty acids

have NO double bonds - have the maximum number of hydrogen atoms attached

unsaturated fatty acids

have double bonds, can be monounsaturated or polyunsaturated

cis vs trans isomers of fatty acids

* cis isomers have hydrogens attached on the same side of the double bond
* trans isomers have hydrogens on opposite sides of the double bond

what are triglycerides?

* largest class of lipids
* function as long-term energy storage molecules
* made up of glycerol and three fatty acids joined by an ester linkage during condensation (3 molecules of water are formed)
* animals store triglycerides as fats (solids) and plants as oils (liquids)

lipid health risks

* trans and unsaturated increase blood cholesterol
* found in sweets, candies, pizza, beef, etc.
* raise LDL levels, which carry the cholesterol from the liver to the rest of the body
* hardening and narrowing of arteries by deposition
* this will restrict blood flow
* if coronary arteries are clogged, coronary heart disease may occur
* obesity

(SODAS) comparison of lipids and carbohydrates

* Storage (long-term) is carried out more by lipids
* Osmolality - lipids have a lower effect on the osmotic pressure of a cell
* Digestion and utilisation is easier in the case of carbohydrates
* ATP yield is greater for lipids, as they store more energy per gram (twice as much)
* Solubility is greater for carbohydrates, so they are easier to transport in the bloodstream

formula for BMI

BMI=\[mass in kg\]/\[height in m squared\]

who is BMI not suitable for?

* pregnant women
* athletes
* BMI should not be used as a diagnostic tool, but rather one of many tests

function of lipids (SHIPS)

* Storage of energy for long-term use
* Hormonal roles (steroids such as estrogen)
* Insulation - both thermal and electrical
* Protection of internal organs
* Structural components of cells, e.g. phospholipids or cholesterol

generalised structure of an amino acid

* NH2 amine group
* COOH carboxyl group
* H atom
* interchangeable R group
* all bound to a central carbon atom

why do all amino acids have the interchangeable R groups?

* they have distinct chemical properties
* it causes the protein to fold up in a specific pattern, giving it distinct function

peptide bond formula

O=C-N-H

primary structure of proteins

the sequence of amino acids that determines the folding of proteins

secondary structure of proteins

* folded, stable structure resulting from the presence of hydrogen bonds
* alpha-helix - coil/spiral structure
* beta-pleated sheet - directionally-oriented staggered strand

tertiary structure of proteins

* three-dimensional
* influenced by interactions such as: ionic interactions, hydrogen bonding, disulphide bridges, polar associations
* functional

quaternary structure of proteins

* more than one polypeptide chain linked to each other
* may also have a prosthetic group that can be inorganic
* haemoglobin - haeme groups

denaturation of proteins

it is a change in the structure of proteins which usually results in the permament loss of functions and biological properties

denaturation by heat

* may disrupt hydrogen bonds that fold the protein
* loss of folding = loss of functionality
* in humans, the optimum temperature is around 37 degrees Celsius

denaturation by pH fluctuations

* change in pH alters the structure, which means that its solubility or overall shape will change
* optimum pH differs for each protein

conversion from genes to polypeptides

transcription - making mRNA based on DNA in the nucleus

translation - mRNA transcript used to link amino acids together at the ribosomes

one gene codes for how many polypeptides?

typically one

what is the purpose of alternative splicing of genes

producing multiple polypeptide variants

what is the purpose of genetic mutations

producing multiple polypeptide variants

proteome

the totality of proteins expressed within a cell, tissue or organism at a certain time; usually significantly larger than the number of genes

functions of proteins (SHITS ME)

* Structure - collagen (component of connective tissue in animals), spider silk (fiber used to make webs)
* Hormones - insulin (lowers blood sugar), glucagon (raises blood sugar)
* Immunity - immunoglobulins (antibodies produced by plasma cells that target specific antigens)
* Transport - haemoglobin (transporting oxygen, found in red blood cells)
* Sensation - rhodopsin (a pigment in the photoreceptor cells of the retina that is responsible for the detection of light)
* Movement - actin (thin filaments involved in the contraction of muscle fibres), myosin (thick filament involved in the contraction of muscle fibres)
* Enzymes - rubisco (enzyme involved in the light-independent stage of photosynthesis)

fibrous vs globular proteins (SPADES)

* Shape: long and narrow/spherical
* Purpose: structural/function
* Acid sequence: repetitive amino acid sequence/irregular
* Durability: less affected by pH or temp changes/more influenced
* Examples: keratin, fibrin, actin, myosin, elastin/rubisco, haemoglobin, immunoglobulins
* Solubility: insoluble/soluble

enzymes

globular proteins that act as biological catalysts and speed up chemical reactions by lowering the activation energy; they remain unchanged or unconsumed at the end of the reactions, which is why they can be reused

active site

the region of the enzyme to which the substrate binds

enzymes are…

substrate specific - they complement each other in terms of shape and chemical properties

how does enzyme catalysis work?

* typically in aqueous solutions
* substrate binds to enzyme and forms enzyme-substrate complex
* enzyme catalyses the conversion, forming enzyme-product complex
* dissociation of enzyme and product
* enzyme can catalyse further reactions as it is left intact

how can the rate of catalysis be increased?

* increased temperature to increase the kinetic energy of molecules
* increasing the concentration of substrates and enzymes

what is the purpose of enzyme immobilisation?

* fixed to a static surface in order to improve the efficiency of the catalysed reaction
* Enzyme concentrations are conserved as the enzyme is not dissolved – hence it can be retained for reuse
* Separation of the product is more easily achieved as the enzyme remains attached to the static surface

production of lactose-free milk

* The lactase is purified from yeast or bacteria and then bound to an inert substance (such as alginate beads)
* Milk is then repeatedly passed over this immobilised enzyme, becoming lactose-free

advantages of lactose-free milk

* As a source of dairy for lactose-intolerant individuals
* As a means of increasing sweetness in the absence of artificial sweeteners (monosaccharides are sweeter tasting)
* As a way of reducing the crystallisation of ice-creams (monosaccharides are more soluble, less likely to crystalise)
* As a means of reducing production time for cheeses and yogurts (bacteria ferment monosaccharides more readily)

the lock and key model

* According to the lock and key model, the enzyme’s active site complements the substrate precisely
* The substrate fits a particular active site like a key fits into a particular lock
* This theory of enzyme-substrate interaction explains how enzymes exhibit *specificity* for a particular substrate

induced fit model for enzymes

* the active site will undergo a __conformational change__ when exposed to a substrate to improve binding
* It explains how enzymes may exhibit *broad specificity* (e.g. lipase can bind to a variety of lipids)
* It explains how catalysis may occur (the conformational change stresses bonds in the substrate, increasing reactivity)

metabolic pathways

* typically organised into chains or cycles of enzyme-catalysed reactions


* allow for a greater level of regulation, as the chemical change is controlled by numerous intermediates

activation energy

the minimum amount of energy required for a reaction to occur

competitive inhibition

* substance binds to the enzyme’s active site
* the substance is chemically and structurally similar to the substrate
* substrate cannot bind to the enzyme due to the blocked active site
* increasing substrate concentration can solve the problem

non-competitive inhibition

* inhibitor binds to an allosteric site - not active site
* conformational changes in the active site are the result, hence the active site and the substrate no longer share specificity and the substrate cannot bind
* cannot be reduced by increasing the substrate concentration

end-product inhibition or feedback inhibition

* controlling metabolic pathways and the yield of products
* In end-product inhibition, the final product in a series of reactions inhibits an enzyme from an earlier step in the sequence
* The product binds to an allosteric site and temporarily inactivates the enzyme (via non-competitive inhibition)
* As the enzyme can no longer function, the reaction sequence is halted and the rate of product formation is decreased

examples of feedback inhibition

* threonine → isoleucine
* Isoleucine is an **essential amino acid**, meaning it is not synthesised by the body in humans (and hence must be ingested)
* **Food sources rich in isoleucine** include eggs, seaweed, fish, cheese, chicken and lamb
* In plants and bacteria, isoleucine may be synthesised from threonine in a five-step reaction pathway
* In the first step of this process, threonine is converted into an intermediate compound by an enzyme (threonine deaminase)
* Isoleucine can bind to an allosteric site on this enzyme and function as a non-competitive inhibitor

components of a nucleotide

* pentose sugar - deoxyribose or ribose
* phosphate group
* nitrogenous bases: G, T, U, C, A

adenine and thymine are connected by

two hydrogen bonds

cytosine and guanine are connected by

three hydrogen bonds

purines

double-ringed nitrogenous bases, adenine and guanine

pyrimidines

single-ringed nitrogenous bases, cytosine, uracil, thymine

nucleotides are connected by what type of bond?

phosphodiester

what does it mean that the two DNA strands are antiparallel?

they have to run in opposite directions in order to allow the base pairs to form

why is DNA organised in a double helix?

the atoms arrange in the most energetically stable configuration as the chains lengthen

what discoveries helped Watson and Crick develop their model of DNA structure?

* DNA is composed of nucleotides made up of a sugar, phosphate and base – *Phoebus Levene, 1919*
* DNA is composed of an equal number of purines (A + G) and pyrimidines (C + T) – *Erwin Chargaff, 1950*
* DNA is organised into a helical structure – ***Rosalind Franklin****, 1953*  *(data shared without permission)*

what were the early DNA models proposed by W&C?

* The first model generated was a triple helix
* Early models had bases on the outside and sugar-phosphate residues in the centre
* Nitrogenous bases were not initially configured correctly and hence did not demonstrate complementarity

what did W & C’s final DNA model represent?

* DNA strands are antiparallel and form a double helix
* DNA strands pair via complementary base pairing (A = T ; C Ξ G)
* Outer edges of bases remain exposed (allows access to replicative and transcriptional proteins)

Rosalind Franklin’s contribution to the development of the DNA structure

The final construction of a correct DNA molecule owed heavily to the X-ray crystallography data generated by Franklin

* This data confirmed the arrangement of the DNA strands into a helical structure
* The data was shared without Franklin’s knowledge or permission and contributed profoundly to the final design
* Hence, Franklin is now recognised as a key contributor to the elucidation of DNA structure

why can DNA replication be called a semi-conservative process?

the replicated DNA contains one newly formed strand and one that is conserved from the templete DNA molecule

Meselson-Stahl experiment

* 1958
* Meselson and Stahl were able to experimentally test the validity of these three models using radioactive isotopes of nitrogen
* DNA molecules were prepared using the heavier 15N and then induced to replicate in the presence of the lighter 14N
* DNA samples were then separated via centrifugation to determine the composition of DNA in the replicated molecules
* The results after two divisions supported the semi-conservative model of DNA replication
* After one division, DNA molecules were found to contain a mix of 15N and 14N, disproving the conservative model
* After two divisions, some molecules of DNA were found to consist solely of 14N, disproving the dispersive model

three hypotheses proposed prior to the Meselson-Stahl experiment about the mechanism of DNA replication

* *Conservative Model* – An entirely new molecule is synthesised from a DNA template (which remains unaltered)
* *Semi-Conservative Model* – Each new molecule consists of one newly synthesised strand and one template strand
* *Dispersive Model* – New molecules are made of segments of new and old DNA

PCR

polymerase chain reaction, artificial method of replicating DNA under laboratory conditions