Biochem

IB Biochemistry option B 2016-2024

Anabolism

reaction of synthesis (monomer → polymer) Requires energy

Metabolic pathways

a series of chemical reactions in a cell

Catabolism

Reaction of breakdown (polymer → monomer) Releases energy

Where do most metabolic reations takes place?

highly controlled aqueous environments (since 90% of a cell’s cytoplasm is water)

Factors affecting function and ability to react successfully in metabolic processes

• Shape

• Structure

• Chirality (HL)

Factors that must be maintained to ensure optimal cell function in metabolic process

• PH

• Temperature

• Concentration of components within the cell’s cytoplasm

Photosynthesis

The synthesis of energy-rich molecules from carbon dioxide and water using light energy. (endothermic)

Respiration

A complex set of metabolic process providing energy for cells. (exothermic)

Aerobic vs Anaerobic

Aerobic: with oxygen

Anaerobic: in the absence of oxygen

write the equilibrium equation for photosynthesis and cellular respiration

Condensation reaction

• produces water from H+ and OH-

• Heat and acidic environment is often required

• Anabolic

Hydrolysis

• water breaking → H2O splits to H+ and OH-

• Heat + Acid catalyst/enzymes required

• Enzymes ensure it doesn’t reverse

• Catabolic

Proteins

biopolymers of 2-amino acids, joined by amide links / peptide bonds

Polypeptide chains

• more than 3 amino acids joined by peptide bonds

• formation occurs in condensation reactions, reversed in hydrolysis

Isoelectric point

the pH at which a molecule carries no net electrical charge. It is the pH at which a molecule is electrically neutral.

What determines Isoelectric point

R groups. Acidic R groups favour acidic isoelectric point, vice versa.

Zwitterion

A molecule with both positive and negative charges, making it electrically neutral. It forms when an amino acid is at its isoelectric point.

Primary protein structure

• sequence of a chain of amino acids

• bond: contains peptide bonds

• example: polypeptide chains

Secondary protein structure

• amino acid folds into a repeating pattern due to H-bonds

• bond: Hydrogen bonds between COOH and NH2

• example: alpha helix and beta pleated sheets

Tertiary protein structure

• Three dimensional folding pattern of a protein due to side chain interactions

• Bonds: between R-Groups

  • Hydrogen bonds: helps stabilise protein molecule

  • Disulfide bonds: strong covalent formed by oxidation of -SH groups in cystein side-chains

  • LDF: when two molecules are close to eachother they can appear

  • Ionic bonds: Weak electrostatic interactions

• Example: myoblin or enzymes

Quarternary protein structures

• Proteins consisting of multiple polypeptide chains

• Bond: between R-Groups

• Example: Haemoglobin

What determines the role of a protein

3D shape determines its role in structural components (e.g. inside cells, tissues, organs, etc) or in metabolic processes

Globular proteins

• spherical in shape

• soluble in water due to polar R groups being on the outside, whilst non-polar R groups are on the inside

• act as chemical messengers (hormones), catalysts (enzymes), and tranpsport molecules.

• high temperatures denature the protein by weaking it’s IMF

Fibrous proteins / scleroproteins

• Long linear bundles of polypeptide chains, held together by covalent bonds, SS bridge, or H-Bond.

• insoluble in water due to exposed R groups being a mix of polar / non polar

• Form the basis of structural elements (cells, tissues, etc.) in organisms

• not as sensitive to high temperatures, as covalent bonds > IMF

Enzymes

• “biological catalysts”

• IB: most enzymes are proteins that act as catalysts by binding specifically to a substrate at the active site

• usually aqueous as they are homogenous catalysts (same state as other reactants)

Lock and key model

• An enzyme has a cleft in its surface, called the active site. The substrate molecule has a complimentary shape

• An enzyme-substrate complex is temporarily formed. The R groups of the amino acids in the active site interact with the substrate.

• The substrate is broken apart and the two product molecules leave the active site without damaging the enzyme molecule.

Induced fit model

• An enzyme has a cleft in its surface, called the active site. The substrate molecule does not have a complimentary shape

• The enzyme changes shape slightly as substrate binds

• enzyme-substrate complex is temporarily formed. The R groups of the amino acids in the active site interact with the substrate.

• The substrate is broken apart and the two product molecules leave the active site without damaging the enzyme molecule.

What factors affect enzymatic activity

• Concentration

• Temperature

• pH

• Heavy metal ions

How does concentration of enzymes/substrates affect enzymatic activity

How does temperature affect enzymatic activity

• Enzymes are globular proteins, therefore heat can denature them by interupting IMF

• Denatured (changed shape) enzyme cannot perform its function, since the active site has changed shape

• Enzymes has a maximum rate of activity at a certain optimal temperature, which is why our bodies control temperature

How does pH affect enzymatic activity

• changes to pH of aqueous environment can cause amino acid residues to gain or lose protons, therefore changing their shape and interactions

• Enzymatic activity has an optimal pH level

Heavy metal ions and enzymes

• some heavey metal ions can bind to an enzyme, causing a decrease in enzymatic activity

• common ions like lead (II) and mercury (II) can bind to enzymes and cause negative health effects

• bond is covalent, the binding is strong and permanent

How are proteins broken down into component amino acids for protein analysis

Hydrolysis reaction using conc. HCl

Describe steps of paper chromatography

1. Small sample of amino acid mixture spotted on the origin

2. Filter paper is supended in solvent with the origin above the solvent level

3. As solvent rises, amino acids will distribute themselves between 2 phases:

   • stationary phase - absorbs more strongly to stationary phase means its lower down

   • mobile phase - more soluble in mobile phase means it will go higher up

4. Once removed, sprayed with ninhydrin (organic dye / locating reagent)

5. Analysis can be conducted

What is the retention factor and what does it do

Number between 0 and 1, given by equation above. Helps identify the amino acid, by comparing to known values

What is gel electrophoresis and describe steps

a method of seperation and analysis of biomacromolecules and their fragments based on their size and shapes

1. amino acid mixture is placed in the sample wells of the gel (usualy polyacrylamide)

2. A potential difference (voltage) is applied

3. amino acids with a positive charge in the buffer are attracted to the cathode, vice versa (smaller goes further also)

4. once seperated, sprayed with ninhydrin (organic dye)

5. identified by measuring distance travelled then comparing to known samples

What’s a lipid and what are the types and functions

• Organic molecules with long hydrocarbon chains that are soluble in non-polar solvents.

  • Triglycerides - energy storage / thermal insulation

  • Phospholipids - components of cell membranes / electrical insulation in nerves

  • Steroids - hormones

  • involved in the transportations of fat soluble vitamins (A, D, E, and K)

why are fats better at energy storage gram for gram

Fats are more reduced than carbohydrates, therefore yield more energy when oxidised

Solubility and energy storage of carbohydrates and fats

Carbohydrates

• Soluble in water - polar OH groups form H-bonds

• therefore more rapidly transported in body, so it’s used for short term energy storage

Fats

• Insoluble in water - as they have non-polar hydrocarbon chains

• therefore slowly transported in the body, so it’s used for long term energy storage

Fatty acids

“building blocks of fat”

Carboxylic acids with a long hydrocarbon chain. Can be saturated, monounsaturated, or polyunsaturated.

Saturated fatty acids + melting point

• called “fats”

• 109.5 degree bond angle (tetrahedral)

• single C-C bonds

  • therefore no kinks due to double bond

  • therefore allows molecules to pack closely together

  • therefore stronger LDF

  • higher M.P

unsaturated fatty acids + Melting point

• called “oils”

• mono: singular C=C bond

• poly: multiple C=C bond

• 120 degree bond angle (trigonal planar)

  • double bond causes kinks in the chain

  • molecules can’t pack closely

  • weaker LDF

  • lower M.P

Triglycerides

Produced in a condensation reaction between a molecule of glycerol and 3 fatty acids.

Phospholipids

Derivatives of triglycerides, with non polar tails (fatty acids) and a polar head (phosphate group) on a glycerol backbone

Phospholipid bilayer

A phospholipid bilayer is a double layer of phospholipid molecules that forms the basis of cell membranes. It consists of hydrophilic heads facing outward and hydrophobic tails facing inward, creating a barrier for the cell.

Steroids

A structure consisting of 4 fused hydrocarbon rings- 3 hexagons and 1 pentagon (steroidal backbone)

Uses and abuses of steroids

Uses:

• Female steroid hormones in oral contraceptive or HRT

• assist with rehab in building depleted muscles

Abuses:

• Anabolic steroids used by athletes to get unfair advantage

Health effects of anabolic steroid abuse

On men:

• infertility

• breast development

• shrinking of testicles

• male-pattern baldness

• become indian

On women:

• decrease in breast size

• decrease in body fat

• deepening of the voice

• excessive body hair

General:

• Heart attacks and liver cancer

Cholesterol

• has steroid backbone (3 cyclohexane, 1 cyclopentane)

• transported around by lipoproteins -LDL + HDL

• Cholesterol is a waxy substance found in your blood. Your body needs cholesterol to build healthy cells, but high levels of cholesterol can increase your risk of heart disease. With high cholesterol, you can develop fatty deposits in your blood vessels.

LDL (Low density lipoprotein)

• Transports cholesterol to the arteries where it leads to the thickening of the walls of the arteries (atherosclerosis)

• Main source: saturated fats; lauric acid, myristic acid and palmitic acid

Atherosclerosis

narrowing of artereries because lipids clog them

HDL (High density lipoprotein)

• removes cholesterol from the walls of arteries

How to calculate iodine number

don’t do it the bullshit way. M(fat) is molar mass of fat

What does the iodine number tell us

Helps determine the unsaturation of a fat

What hydrolises fats and oils

lipase

types of hydrolysis of lipids

• Acid hydrolysis

  • Hydrolysed in a hot aqueous solution of strong acid

  • triglyceride + water →(H^+ and heat)→ glycerol + 3 fatty acids

• Alkaline hydrolysis

  • Produces salts of fatty acids (soaponification)

  • triglyceride + base → glycerol + soap

• Phospholipids hydrolysis

  • occurs in the human body

  • phospholipid + water → glycerol + 2 fatty acids + phosphate group

Rancid

Disagreeable smell, texture, or appearance; Nick wang

Hydrolytic Rancidity:

Triglyceride + water → glycerol + 3 fatty acids

• occurs quicker in heat and moisture, catalysed by the enzyme lipase

• smell is due to release of fatty acids, can be reduced by refrigeration

• sites of reactivity: ester linkages in triglycerides

Oxidative rancidity (auto-oxidation)

• oxygen added across a C=C bond

• catalyzed by light or enzymes and metal ions

• occurs in highly unsaturated fatty acids

• can be controlled with anti-oxidants

• sites of reactivity: C=C unsaturated bonds

Monosaccharides empirical formula

CH2O

Haworth projections

3D Diagrams

Monosaccharides

• Simplest carbohydrate - cannot be hydrolysed to a smaller carbohydrate

• one carbonyl group (-C=O) and two or more Hydroxyl groups (-OH)

• in aqueous solutions, straight chain sugars form ring structures with an ether linkage (the O)

Disaccharides

• Carbohydrate formed from two monosaccharides bonded by glycosidic links in condensation reactions

• soluble molecules that can be hydrolysed into monosaccharides by acid hydrolysis or enzyme catalysed reactions

Disaccharides general formula

Cx(H2O)y

Polysaccharides

• long chain of monosaccharides bonded by glycosidic links

• used for energy storage:

  • starch: plants

  • glycogen: human

  • cellulose: structural material in plants and a dietary fibre for a balanced diet

Vitamins

• organic micro-nutrients (substances needed in the body in amounts of <0.005% of body mass)

• Not synthesised in body (except vitamin D), so must be obtained in diet

• solubility can predict structure

Fat soluble vitamins

• Vitamin A and D

  • non-polar hydrogen ring

  • one OH group, however non-polar part dominates

  • D: synthesised by sunlight on skin

  • A: important for low light vision (eat carrots)

Water soluble vitamins

• Vitamin C

  • many polar OH groups from H-bond with H2O

  • high solubility in water means it’s not retained in the body for long

  • C=C bonds & OH groups are readily oxidised (by air or light)

  • fridge slows down oxidation

  • water soluble vitamins are sensitive to heat

Vitamin deficiencies causes

• lack of distribution of global resources

• depletion of nutrients in soil

• lack of education about balanced diets

• over-processing of foods

Vitamin deficiencies solutions

• fortifying staple foods with vitamins

• taking nutritional supplements

• genetically modifying foods to increase vitamin content

• educating people about balanced diets

Xenobiotics

Chemical substances found within an organism that are not naturally produced by or expected to be present within that organism

xeno - strange; alien

biotics - consists of living organisms

Antibiotics + sewage treatment

• antibiotics are xenobiotics in animals

• certain bacteria can become resistant to antibiotics

• sewage treatment plants can promote the spread of antibiotic resistance between bacteria

• water discharge into lakes and rivers from sewage treatment plants can contain significant concentrations of the genes that make bacteria antibiotic resistant

Polychlorinated biphenyl’s (PCB’s) and Dioxins and the environment

• Toxic chemicals that persist in the environment

• accumulate in body due to chemical stability

• long-term exposure causes adverse health effects; possibly carcinogenic (cancer causing)

Biomagnification

The increase in concentration of a xenobiotic in a food chain

Example of DDT biomagnification

phytoplankton < zoo plankton < small fish < large fish < fish eating birds (in PPM of DDT).

• DDT is readily soluble in fat and does not break down, so it accumulates in fatty tissue

• birds of prey suffered a decline in numbers due to the toxic effects of DDT, it has now been banned in many countries

Biodegradability

Biodegradable (compostable) plastics can be consumed or broken down by bacteria or other living organisms

The role of starch in biodegradability

• PLA is a biodegradable plastic derived from corn starch

• the break down of starch-based plastics produces CO2 and H2O (aerobic conditions)

• Bioplastics can be broken down in hydrolysis reactions due to ester linkages or glycosidic links (requires heat and moisture)

• when some biodegradable plastics decompose, they produce methane gas (anaerobic conditions)

note: while they produce CO2 they are carbon neutral due to the CO2 they save in production

Host guest complex + bonds

Host guess complexes are composed of two or more molecules or ions that are held together through non-covalent bonding

• Non covalent bonds:

  • H-Bonds

  • LDF

  • Dipole Dipole

  • Ionic

  • Hydrophobic interactions

host guest chemistry

Host guest chemistry involves the creation of synthetic host molecules that mimc some of the actions performed by enzymes in cels, by selectively binding to specific guest species

Applications of host guest chemistry

• removal of xenobiotics in the environment

• e.g. host-guest chemistry can remove Cs-137, which is radioactive from the environment

Vmax

Maximum rate of reaction where all active sites are bound to substrate (enzyme is saturated)

Km definition and meaning

The substrate concentration which is equal to half its maximum value

• High Km: high concentration of substrate must be present to saturate the enzyme

• Low Km: only a small amount of substrate is needed to saturate the enzyme

Competitive inhibitor

• binds at the active site of the enzyme

• chemical structure is similar to the substrate

• once binded they do not form products, hence blocking the active site

• increasing substrate concentration reduces extent of inhibition

• Km increases and vmax stays the same

non-competitive inhibitors (2 points + graph)

• binds at an allosteric site (away from active site)

• changes protein’s conformation which alters shape of active site

• km stays same and vmax decreases

pH of buffer solution

initial concentration of the salt and initial concentration of weak acid

Assumptions of pH of buffer solution

• weak acid partialy dissociates, therefore initial concentration of acid = equilibirium concentration

• salt completely dissociates in solution, therefore initial concentration of salt = equilibirum concentration of the anion

Beer-Lambert Law

used t0 determine the concentration of a protein in solution from a calibration curve

calibration curve

Using a range of solutions with known concentrations and measuring the absorbance with a spectrophotometer

in calibration curves absorbance is proportional to:

concentration (assuming fixed wavelength)

UV-Vis spectroscopy

Used in protein assays to measure the concentration of a protein in a sample

How does a spectrophotometer work

monochromatic light is incident on a protein sample with intensity i naught and hits the detector with intensity i

Absorption spectrum

least absorbed wavelength is emitted

Nucleotide

Phosphate group, pentose sugar and nitrogenous base (adenine)

Types of bonds between constituent parts of nucleotide or between nucleotides

phosphodiester bond in condensation reaction

DNA

• Stores genetic information

• Double helix

• Sugar phosphate backbones on outside, nitrogenous bases on inside holding the two strands together via Hydrogen-bonding

• Deoxyribose is the pentose sugar

RNA

• expresses the stored information (unzips DNA by breaking H-bonds)

• single-stranded polynucleotide

• sugar phosphate backbone

• ribose is pentose sugar

Base pairing

• A/T (2 H-bonds) or G/C (3 H-bonds) in DNA

• DNA A / mRNA U

• DNA T / mRNA A

Transcription

The process in which the information required to synthesise proteins is passed from DNA to mRNA. A segment of DNA is copied into mRNA by the enzyme RNA polymerase.

Translation

newly formed mRNA leaves the nucleus for the ribosome, producing a polypeptide chain

Codon

Triplet of nucelotides, represents one amino acid