IB Chem Option B: Biochemistry (SL)

Metabolism

the sum of chemical reactions occurring in a living organism

Metabolic pathways

reactions are controlled in sequences and cycles, the product of each stem is the reactant in the next

Metabolites

compounds taking part in metabolism

Enzymes

biological catalysts

Coupled metabolic reactions

the energy from one reaction is used to drive another

Anabolism

• building/synthesis of molecules from smaller organic molecules

• products are larger/more complex/of a higher energy

• generally require an input of energy (ie. endothermic)

Precursors

reactants of anabolism

Catabolism

• metabolic reactions of breakdown/degradation

• releases energy, produces energy-poor end products

• usually energy (ATP) produced from catabolic reactions is used to drive anabolic reactions — energy coupling

Futile cycles

• when stable complex structures cannot be formed because they are broken down as they are formed

• occurs when catabolic and anabolic reactions are not controlled by separate metabolic pathways

Trace elements required by living things

S, P, Ca, Fe — required in small amounts

Macromolecules

• large complex biomolecules composed of monomers

• relative molecular masses of several thousand

Condensation polymers

polymers whose synthesis involves a loss of H₂O per covalent bond

Polymerases

enzymes which catalyse condensation reactions

Hydrolysis reactions

• H₂O molecule added for each covalent bond removed

• catalysed by enzymes, may be favoured by heat or acidic/alkaline conditions

Examples of structure=function in biomolecules

• collagen and cellulose — tough and insoluble

• enzymes — shape of active site

• nucleotide —store/transmit genetic information by sequences of nitrogenous bases

Outline photosynthesis

• acts as a “carbon sink”

• captures solar energy using chlorophyll and uses it to synthesize energy-rich biomolecules

• Light energy drives a series of redox reactions in which water is split into hydrogen and oxygen

• hydrogen ultimately reduces CO₂ to simple sugars

• essentially, photosynthesis transforms energy poor reactants to energy-rich glucose with the release of O₂

Outline cellular respiration

• acts as a carbon source

• glycolysis releases a small proportion of glucose’s energy (anaerobic respiration stops here)

• in aerobic conditions, it involves cytochromes, which are successively reduced then re-oxidized

• oxygen is a terminal electron acceptor — when it is reduced to H₂O

Fibrous proteins

• structural components

• elongated molecules with dominant secondary structure

• water insoluble

Globular proteins

• tools that operate at the molecular level — as enzymes, carriers, receptors

• compact spherical molecules with

  dominant tertiary structure

• water soluble

2-amino acid condensed structural formula

NH₃-CHR-COOH

Amine-variable R group-carboxyl group

R-groups on amino acids

• variable - around 20

• Amino acids can be classified according to the chemical nature of their R group,

  usually based on their different polarities

Amino acids physical properties

• crystalline compounds with high melting points, usually above 200 °C, and they have much greater solubility in water than in non-polar solvents

• move in an electric field

• These properties are all typical of ionic compounds; suggesting that amino acids contain charged groups.

• The charges are a result of acid-base behaviour

• In aqueous solution and in crystalline form, amino acids commonly exist with both positive and negative charges within the molecule, known as zwitterions.

• They are sometimes referred to as internal salts, as the charges result from an internal acid-base reaction

  • with the transfer of a proton (H+) from the acid – COOH group to the basic –NH2 group in the same amino acid.

Amino acids acid/base properties

• contain both an acidic group and a basic group, they are amphoteric or amphiprotic

• In aqueous solution they will accept and donate H+ according to changes in the pH of the medium

• in the zwitterion it is the conjugates of the acid and the base that are

  responsible for this property.

• Amino acids can act as a Brønsted-Lowry acid

• at high pH (low [H+]), this reaction is favoured as the –NH3+ group loses its H+ and

  forms an anion

• Amino acids can act as a Brønsted-Lowry base

• at low pH (high [H+]), this reaction is favoured as the –COO– group gains H+ and

  forms a cation.

Isoelectronic point of amino acids

• The charge carried by an amino acid depends on the pH of the medium

• The isoelectric point is the intermediate pH at which it is electrically neutral.

• With no net charge at this pH, amino acids will not move in an electric field.

• the molecules will have minimum mutual repulsion and so be the least soluble at this pH.

Amide link/Peptide bond

a molecule of water is eliminated and a new bond is formed between the acid group of one amino acid and the amino group of the other.

general equation for the synthesis of a polypeptide from its amino acids

structure and therefore the function of a protein is determined by…

the sequence of amino acids in the polypeptide — the placements of amino acids /w diff R groups in the chain affects its structure and reactivity

Protein primary structure

• number and sequence of amino acids in its polypeptide chain held together by peptide bonds

• forms the covalent backbone of the molecule— once the primary structure has been determined, all the other levels of protein structure follow

Secondary protein structure

• refers to the folding of the polypeptide chain as a result of hydrogen bonding between peptide bonds along its length

• Hydrogen bonds can form between the

  –C=O group of one peptide bond and the

  –N–H group of another

  peptide bond further along the chain which will cause the chain to fold.

α-helix

• regular coiled configuration of the polypeptide chain—hydrogen bonds forming between two peptide bonds four amino acid units apart

• This twists the chain into a tightly coiled helix— 3.6 amino acids per turn

• flexible and elastic as the intra-chain hydrogen bonds easily break and re-form as the molecule is stretched

β-pleated sheet

• structure composed of ‘side by side’ polypeptides which are in extended form

• not tightly coiled as in the α-helix

• arranged in pleated sheets that are cross-linked by inter-chain hydrogen bonds

• is flexible but inelastic

tertiary structure

• further twisting, folding, and coiling of the polypeptide chain as a result of interactions between the R groups, known as side chains.

• structure that results is a very specific compact three-dimensional structure, known as the protein’s conformation.

• most stable arrangement of the protein

• the interactions between the side chains are all intra-molecular forces, as they occur within the one polypeptide chain.

Indicate which bonds form at each letter

a) hydrophobic interactions between non-polar side chains

b) hydrogen bond between polar side chains

c) ionic bond between charged side chains

d) disulfide bridge between Cys residues

Denaturing

• When a protein loses its specific tertiary structure as a result of disruptions

  • eg. heat, presence of metal ions, pH changes

Quaternary structure

• proteins that consist of more than one polypeptide chain

• This association involves similar forces and bonds to those found in the tertiary structure – hydrophobic interactions, hydrogen bonds, ionic bonds, and disuldide bridges.

Collagen quaternary structure

• a triple helix of three polypeptide chains, with inter-chain hydrogen bonds between them.

• This helps to give it a stable rope-like structure that is resistant to stretching.

Haemoglobin structure

• made up of four polypeptide

  chains that fit together tightly in the protein

  assembly

• each carry an iron-containing haeme group

relative energy of lipids compared to carbs

• lipids contain more energy per gram given they are more reduced molecules

  • their ration of H to O is greater

• as a result, they yield more energy when oxidized

• a gram of lipid releases almost twice as much energy as a gram of carbohydrate

Lipids as energy storage

• although lipids have more energy per gram than carbohydrates, lipids are non-polar (water insoluble) whereas carbohydrates are polar (water soluble)

• so more reactions are involved in their breakdown —their energy is released more slowly

• The fat stores in animals, known as adipose tissue or blubber, serve as reservoirs of energy, swelling and shrinking as fat is deposited and withdrawn.

• Plants also sometimes store lipids for energy, for example as oils in seeds.

Purposes of stored fat

• energy storage

• Stored fat helps to protect some body organs, such as the kidneys, and a layer of fat

  under the skin acts as a thermal insulator.

• Lipids also act as electrical

  insulators —myelin sheath in nerve cells gives electrical insulation and speeds up nervous transmission

Atherosclerosis

• restricted blood flow due to the deposition of lipids on arterial walls given their low solubility

• associated with high blood pressure and can lead to heart disease

Obesity causes and consequences

• because of the body’s ability to convert excess fats into adipose tissue, a diet too rich in lipids can lead to the excess accumulation of body fat

• is linked to diabetes and a variety of cancers

Describe the transport of cholesterol in the blood

• transported bound in different lipoproteins: high-density lipoproteins (HDLs); low-density lipoproteins (LDLs)

• high levels of LDL cholesterol are associated with increased deposition in the walls of

  the arteries

• high levels of HDL cholesterol seem to protect against heart attack —tends to carry cholesterol away from the arteries, so slowing

  its build-up.

Sources of LDL cholesterol

saturated fats and trans fats

polyunsaturated fats sources and role in the diet

• fish, nuts, corn oil, etc

• considered beneficial in lowering levels of LDL cholesterol

essential fatty acids

• those which cannot be manufactured by the body so must be digested

• eg. omega-3-poly-unsaturated fatty acid

omega-3-poly-unsaturated fatty acid sources and benefits

• found in fish oils and flax seeds

• be linked with reduced risk of cardiovascular disease as well as with optimum neurological development.

lipids in the form of ________ are found in hormones

steroids

Female steroid hormone examples

• Used in contraceptive pill formulations

• Used in HRT (hormone replacement therapy) sometimes prescribed during menopause

Male steroid hormones name and uses

• androgens — testosterone is the most important

• aka anabolic steroids as they are involved in promoting muscle tissue growth

• Synthetic forms of them are used medically to help gain weight after debilitating diseases

• used as performance-enhancing drugs by athletes —can increase strength and endurance.

Structure of triglycerides

• composed of a glycerol molecule covalently bonded to three fatty acids — called an ester linkage

• Involves a condensation reaction called an esterification reaction, yields three H₂O when the COOH and OH group bond

• In most natural oils and fats the three fatty acids that form one triglyceride molecule

  are not all the same. They can be designated R1, R2, and R3

  • differ by length of tail and degree of saturation

Glycerol structure (IUPAC name)

three carbons, each with a hydroxyl group: propane-1,2,3-triol

Saturated fatty acids structure (VSEPR, IMFs) and examples

• C_nH_2n+1COOH

• The carbon chain is made

  from C-C single bonds

• tetrahedral bond angles (109.5°) so molecules to pack relatively closely together.

  • so strong LDFs and relatively high BPs, their triglycerides are solid at SATPT

• Known as fats - eg butter/lard

Unsaturated fatty acids structure and examples

• containing one or more C-C double bonds and 120° bond angles,

• have kinks in the chains—molecules can’t pack closely

• form unsaturated triglycerides which have weaker intermolecular forces and lower melting points

  • liquid at SATP

• They are known as oils and are found mostly in plants and fish.

• eg. corn oil and cod liver oil.

Trends in BP in fatty acids

Generally, the melting points increase with increasing molar mass (length of the hydrocarbon chains) and with increasing degree of saturation.

Iodine number definition and explanation

• Unsaturated fatty acids undergo addition reactions by breaking the C=C bond and adding incoming groups to the Cs

• This occurs with I₂

  • one mole of iodine will react with each mole of double bonds

    in the fat

• iodine number, defined as the number of grams of iodine which reacts with 100 grams of fat — measures degree of unsaturation

Hydrogenation of fatty acids

• increases saturation of fatty acids

• partial hydrogenation yields trans fats — C’s are on either side of the double bond

Hydrolytic rancidity

• fat breaks down by hydrolysis reactions, using the water in food.

• The site of reactivity is the ester linkages in the triglycerides.

• Conditions: occurs more readily in heat (eg. deep-fat frying) — catalyzed by lipase —favoured in the presence of certain bacteria

  • hence can be reduced by refrigeration

• the rancid smell and flavour is due to the release of free fatty acids, such as butanoic and octanoic acids which are released from rancid milk

Oxidative rancidity

• unsaturated fats react with oxygen from the air — auto-oxidation

• The site of reactivity is the C=C bond

• The products responsible for the rancidity are volatile aldehydes and ketones.

• accelerated by light and enzymes or metal ions

• proceeds via a free-radical mechanism and so yields a mixture of products.

• characteristic of fats and oils that have a high proportion of C=C bonds

• Can be controlled by addition of antioxidants

Relative stability of saturated and unsaturated fats

As they cannot undergo auto-oxidation, saturated fats are more stable than unsaturated fats

Label the phospholipid —lecithin

A - Choline

B - Phosphate

C - Glycerol

D - 2 Fatty Acids

Phospholipid varieties differ by

• the group attached to the phosphate

• fatty acid chain

Phospholipid bilayer

• Spontaneously form a bilayer due to the phosphate head being hydrophilic and the fatty acid tails being hydrophobic

• maximizes the interactions between the polar groups and water, while creating a non-polar, hydrophobic interior.

Saponification reactions

• reverse of esterification reactions

• used in soap production

• Alkaline hydrolysis produces the salt of the fatty acid

Conditions for hydrolysis of triglycerides and phospholipids

• can occur in acidic or alkaline conditions, or catalyzed by enzymes known as lipases

• This occurs during the digestion of lipids in the gut, where the activity of the enzymes is controlled largely by local changes in pH.

Steroids structure

• lipids with a structure consisting of four fused rings, known as a steroidal backbone

Cholesterol functions

• used as a precursor in the synthesis of many biomolecules including other steroids such as sex hormones, bile acids, and Vitamin D.

• component of cell membranes as it helps to provide fluidity and permeability to the structure

  • The hydroxyl group interacts with the polar head groups of phospholipids in the membrane, while the non-polar rings and hydrocarbon chain interact with the hydrophobic tails of the phospholipid bilayer

Carbohydrates general formula + explanation

C_x(H₂O)_y

• oxygen and hydrogen are always in the same ratio as water

• carbohydrate = hydrated carbon

Carbohydrate monomers

monosaccharides

Carbohydrate polymers

polysaccharides

Monosaccharide functions

• soluble in water — taken up by cells rapidly

• used as the main substrate for respiration, releasing energy for all cell processes.

• act as precursors in a large number of metabolic reactions, leading to the synthesis of other molecules such as fats, nucleic acids, and amino acids.

Polysaccharide functions

• are insoluble, used as the storage form for carbohydrates

• Animals use glycogen as storage in the liver and muscles

• plants store starch in cells

• energy reserves can be broken down into

  monosaccharides, which are then oxidized in respiration to release energy for the cell’s

  activities

• cellulose is used structurally in plants

Monosaccharides empirical formula

CH₂O

Monosaccharides functional groups

2+ hydroxyl groups (water soluble)

carbonyl group (aldehyde or ketone)

Monosaccharides ring vs straight chain structures

In aqueous solution these sugars undergo an internal reaction resulting in the more familiar ring structures

Haworth projection formulas

• representations of the ring forms of sugars

• The edge of the ring nearest the reader is represented by bold lines, and the letter C for the carbons in the ring are usually omitted from the structure.

glycosidic linkage

• bonds between monosaccharides

• involves a condensation reaction: two OH- groups on different sugars bond to form one molecule of H₂O

Disaccharides properties

• soluble molecule

• can be hydrolysed into two monosaccharides by acid hydrolysis or by enzyme-catalysed reaction.

• Combining different monosaccharides will produce different disaccharides.

polysaccharides differ by…

isomer of glucose used and amount of cross-linking in the chain

Micronutrients

• needed in extremely small amounts, generally less than 0.005% of body mass

• are usually measured in mg or μg per day.

• These substances are needed to enable the body to produce enzymes, hormones, and other biomolecules.

Absence of micronutrients can →

deficiency diseases

Vitamins

organic compounds, needed in small amounts for normal growth and metabolism, which (with the exception of vitamin D) are not synthesized in the body.

They are usually broken down by the reactions in which they are involved, so must be taken in from suitable food sources in the diet. They are often classifed according to their relative solubility in water or in lipid.

Classification of vitamins

They are often classified according to their relative solubility in water or in lipids.

Water-soluble vitamins

• have polar bonds and the ability to form hydrogen bonds with water.

• They are transported directly in the blood

• and excesses are filtered out by the kidneys and excreted.

• Vitamins B and C are water soluble.

Lipid-soluble vitamins

• mostly non-polar molecules with long hydrocarbon chains or rings.

• They are slower to be absorbed

• excesses tend to be stored in fat tissues where they can produce serious side-effects.

• Vitamins A, D, E, and K are fat soluble.

Vitamin A (Retinol) solubility and properties

• fat soluble

  • The hydrocarbon chain and ring are non-polar and influence the solubility more than the one – OH group

• involved in the visual cycle in the eye, and particularly important for vision in low light intensity

Vitamin C (Ascorbic Acid) solubility and properties

• water soluble

  • several – OH groups enable hydrogen bonds to form with water

• acts as cofactor in some enzymic reactions,

• important in tissue regeneration following injury

• and resistance to some diseases

• contains several functional groups (– OH and – C=C –) that are relatively easily oxidized —vitamin is easily destroyed by most methods of food processing and storage —best obtained from fresh fruits and vegetables.

Vitamin D (calciferol) Solubility and Properties

• fat soluble

  • predominantly a hydrocarbon molecule with four non-polar rings and only one – OH group

• chemically similar to cholesterol

• stimulates the uptake of calcium and phosphorous ions by cells from small intestine and important in the health of bones and teeth (those ions are involved in bone mineralization)

Sensitivity of vitamins to heat

• water-soluble vitamins, eg C, are most sensitive to heat

• but other vitamins also lose some activity after being heated.

causes of malnutrition arising from vitamin deficiency

• lack of distribution of global resources

• depletion of nutrients in the soil and water

• lack of education about, or understanding of, the importance of a balanced diet

• over-processing of food for transport and storage

• the use of chemical treatments such as herbicides in food production.

possible solutions to the varying challenges of malnutrition

• the fortification of different staple foods with micronutrients

• the availability of vitamin supplements in many forms

• the possible improvements to nutrient content of food through genetic modification

• increased labelling of foods with content information

• education regarding the nature of a balanced diet and promotion of the importance of personal responsibility in dietary choices.

Xenobiotics

• chemical compounds present in an organism that are foreign to them

• Also describes chemicals found in organisms in higher-than-normal concentrations and compounds that are not produced naturally

  but only by synthetic processes

• eg. drugs, some hormones, insecticides, heavy metals, plastics, food additives, pollutants

Describe the successful metabolization of non-polar xenobiotics

• non-polar xenobiotics diffuse passively into the cell

• may be modified by enzymes and then detoxified in the cell

• This describes how drugs are metabolized as well as pesticides in plants

  • may lead to resistance to the effect of the chemical in some cases

Bioaccumulation

• occurs when a xenobiotic cannot be modified in the organism so it builds up in the cell —its concentration increases in an organism

• eg. mercury poisoning is caused by the build-up of methylmercury in the brain

pharmaceutically active compounds effects in the environment

• eg. antibiotics, painkillers, and chemotherapy drugs

• may be discharged from industries

  or hospitals, or passed through the human body and released unmodified or partially metabolized in urine

• Sewage treatment plants may break the xenobiotic down through bacterial action, but often this process is incomplete

• the compounds are released and can be taken in by fish

• There is some concern about male fish becoming feminized (ie. unable to reproduce) due to female estrogen present in sewage water from individuals who take the synthetic contraceptive pill

Biomagnification

• the increase in concentration of a xenobiotic in a food web

• due to the lack of enzymes to break them down — harmful substances produced by biological processes are broken down and hence don’t build in concentration in the environment

• if a xenobiotic cannot be metabolized, it is passed along a food chain through feeding, affecting animals at the top of the food chain to the greatest extent

Describe the biomagnification of DDT

• It was used as an insecticide to control mosquito-spread diseases

• it is not able to be broken down by organisms and is fat soluble so it bioaccumulates in tissue and is passed along a food chain

• because its concentrations increased along trophic levels, birds of prey eg. ospreys experienced the greatest consequences: the thinning of their eggs led to a decrease in population