EH1008 Biomolecules

Lecture 2: Inorganic and organic chemistry

limian.zheng@ucc.ie

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Inorganic & Organic Chemistry• Inorganic Chemistry: generally, substances that do not contain

carbon

• Inorganic molecules:lack C and H chains

Exceptions: CO, CO2, and HCO3-

Often formed by ionic bonds, but not always

e.g. H2O, O2, CO2, salts, acids, bases, calcium phosphate

• Organic Chemistry: study of carbon-containing substances. Those that are biologically active are called biochemicals.

• Organic molecules

based on C and H chains

structurally complex

typically formed by covalent bonds

e.g. sugars, amino acids, vitamins, etc.2

Water• Cells need a continuous supply of nutrients, removal of waste products.

• Living cells contain mostly water and GENERALLY interact with an aqueous environment:

• blood plasma (extracellular f luid ): 92% water• 50% of female body weight and 60% of male

•Water is the vital SOLVENT:- a (liquid) substance in which SOLUTES are dissolved.

•inorganic salts (eg NaCl, KCl, nitrates, phosphates)•small organic molecules (eg sugars, amino acids)•dissolved gases (eg oxygen, carbon dioxide)

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Weak hydrogen bondsform between the +ve chargedH atoms of one H2O molecule and the –ve chargedO atoms of another H2O molecule.

The attraction of one H2O molecule to another -Cohesion

Hydrogen bonds organise H2O in to a lattice

Adhesion: the same attractive force attracts other moleculesAdhesion+ Cohesion hold cells together & movement fluid through body

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Physical and Chemical Properties of Water

Advantages of water:

1. Temperature

Liquid @ body temperature (37°C)

H-bonding resists rapid temp change

high boiling point

low freezing point very stable: stabilizes body temp

2.Protection• Lubricant, tears protect surface of eyes• Cushion cerebrospinal fluid protects brain

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3. Chemical reactivity:

•Indirect - Many reactions take place in water

•Direct – H2O participates in chemical reactions

Polarity allows it to serve as reactant in many reactions:

(i) Hydrolysis: decomposition using waterATP +H2O � ADP + Pi + energy

(ii) Dehydration synthesis: synthesis using waterADP + Pi � ATP + H2O

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4. Good solvent

•Water is considered as the universal solvent

•Polar and ionic substances dissociate easily in water to form solutions

•Solution: mixture of liquids, gasses, or solids that are uniformly distributed and chemically combined

Solvent: that which dissolves the soluteSolute: that which dissolves in the solvent

•Eg sweat is a salt solution: water is the solvent, salt (ionic substance) is the solute

•Water also dissolves certain organic substances e.g sugar and alcohols that do not dissociate into ions in solution but do have polar properties.

•Notewater does NOT dissolve or dissolve in compounds that are completely nonpolar eg. fats and oils

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Hydrophilic & Hydrophobic molecules•Compounds that dissolve in H2O are hydrophilic, those that

do not are hydrophobic

•Strict hydrophobic compounds do not mix well in H2O eg. lipids

•Some molecules have a hydrophobic and a hydrophilic end –amphipathic polar and non-polar end

•Amphipathic substances make good emulsifiers they can attract hydrophilic and hydrophobic molecules to them, eg sodium oleate/soap

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Properties of H2OWater also serves as a good mixing medium

Mixture : substances physically but NOT chemically combined

Solution: mixture of liquids, gases, or solids that are uniformly distributed and ARE chemically combined

Suspension: is a mixture of materials that separate unless stirred. Eg Sand and water, Blood - Plasma and red blood cells

Colloid: a mixture with properties between those of a solution and fine

suspension.

The dispersed (solute like) substance is distributed throughout a dispersing (solvent like) substance.

Proteins are dispersed particles Proteins +H2O = Colloids

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Solution Concentrations

• Concentration: measure of number of particles of solute per volume of solution

• Osmosis:movement of solvent along a concentration gradient across a semipermeable membrane. The cell membrane is semi-permeable.

• Osmole (Osm): moles of solute contribute to the osmotic pressure of a solution.

• Osmolality (Osm/kg): the amount (osmole/Osm) of particles dissolved in 1Kg of water

• Concentrations of particles in the human body: milliosmoles (mOsM)• 300 mOsMis average in the human body

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• Circulatory systemcarries water and solutes to capillaries, where exchange with cells occurs. Solutes must cross capillary wall, interstitial space and cell membrane to reach cell. How?

• Diffusion: movement of molecules due to random, spontaneous thermal motion. Net movement occurs along a gradient (chemical ± electrical).• Cell Membrane Diffusion: video

• Chemical potential: concentration gradient; charged particles

• Electrical potential: electrical gradient / potential.

• Electrochemical potential:energy driving movement due to combined effects of chemical and electrical gradients

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Acids and Bases; Salts and Buffers• Acid: molecules that DONATE protons in solution

• Base: molecules that ACCEPT protons in solution

• Water also tends to ionise acts

• as acid: OH- (hydroxyl anion)

• as base: forms H3O+ (hydronium ion – main form of protons in water)

• Salt: cation (but not H+) and anion (but not OH-)

• Formed by the interaction of an acid and a base:

HCl + NaOH� NaCl +H2O

• Buffer : Aqueous solution consisting of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid.

• pH of the solution changes very little when a small amount of strong acid or base is added to it

O H OH

HH

OH

H OH

H+

+-

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pH Scale

• pH: “potential of Hydrogen”

-logarithmic expression of amount of H+ in solutions: -log10 [H+]

• Log scale= 10 fold change

• pH calculated as – log10 [H+] in moles/Liter (scale 0-14)

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The pH Scale

• Refers to the hydrogen ion concentration in a solution

– Neutral: pH of 7[H+] = [OH-]

– Acidic: higher [H+], pH < 7

– Alkaline or basic: higher [OH-], pH > 7

– Physiologic pH is 7.4

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Acids bases and buffers in the body

• The body contains many acids and bases which alter body function by releasing and binding protons

• Most organisms grow best around neutral pH

• The normal pH range for human blood is 7.35 to 7.45

Blood < 7.35 Acidosis depressed nervous system disorientatedBlood >7.45 Alkalosis overexcited nervous system convulsions

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Acids bases and buffers in the body

• Chemical behaviour of many molecules changes as the pH of the solution in which they are dissolved changes.

• Maintaining a normal range of H+ and OH- ions is necessary for most biological processes

• Enzymes work best within a narrow range of pH

Homeostatic mechanisms:i. Respiratory system

ii. Kidneys

iii. Buffers are used in living things to absorb H+ ions released during metabolism to keep the pH from changing.

Eg. bicarbonate, phosphates, amino acids and proteins.

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Oxygen and Carbon Dioxide

• Oxygen (O2): Inorganic molecule

• 21% atmosphere is O2• Essential for most living organisms

• required in the final step in the series of reactions used to extract energy from food.

• Carbon dioxide (CO2): produced during the catabolism of organic compounds eg glucose.

– Metabolic waste product.

– Exhaled during respiration

– Combines with water in plasma and forms H+ thus affecting acid/base balance

CO2 + H2O H2CO3 H+ + HCO3-

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Molecules & Macromolecules

• Molecular weight < 1000 = ‘small’ molecule

• Molecular weight > 1000 = ‘large’ or macromolecule

• One role of small molecules is to serve as material for construction of larger molecules

• Remember from Lecture 1, some macromolecules are polymers, formed from smaller molecules, or monomers

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Importance of Carbon

• Organic chemicals contain carbon

• Carbon atoms bound together by covalent bonds constitute the ‘backbone’ of many large molecules

• Carbon’s ability to form covalent bonds with other atoms allows the formation of the large, diverse complicated molecules necessary for life

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Diversity of Life

• A wide variety of molecules are available due to:

– Variation in length of the carbon chains

– Different combinations of atoms

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Molecules & Macromolecules:fall in to one of 4 main families

‘Small’ molecules

• Sugars

• Fatty acids

• Amino acids

• Nucleotides

Macromolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

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Lipids

• Composed mainly of: – Carbon– Hydrogen– Oxygen

• Some lipids contain small amounts of other elements, e.g.– Phosphorous– Nitrogen

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Lipids

• High ratio of carbon and hydrogen to oxygen and other elements

• Poorly soluble in water

• Dissolve in nonpolar organic solvents

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Types of Lipids

• Fats

• Phospholipids

• Eicosanoids

• Steroids

• Fat-soluble vitamins

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Role of Lipids in the Body

Role Example

Protection Fat surrounds and pads organs

Insulation Fat under skin prevents heat loss

Regulation Steroid hormones regulate many physiological processes:oestrogen/testosterone responsible for many female/male differences

Vitamins Fat-soluble vitamins provide a variety of functions: vitamin E promotes wound healing

Structure Phospholipids and cholesterol important components of cell membranes

Energy Lipids can be stored and broken down later for energy

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Fats

• Fats ingested from food

• Broken down in cells to release energy for those cells

• If more fat is ingested than is needed it can be stored in the body as fat for later use

• Triglycerides make up 95% of the fats in humans

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Triglycerides

• 2 building blocks:– Glycerol x 1

– Fatty acid x 3

Fatty Acids

saturated unsaturated27

Fatty Acids

• Saturated – only single covalent bonds between carbon atoms– Beef, milk, cheese, butter, eggs

• Monounsaturated – 1 double covalent bond– Olive oil

• Polyunsaturated –≥ 2 double covalent bonds– Fish oils

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Saturated vs. Unsaturated

• Saturated fats contribute to cardiovascular disease• Unsaturated fats do not (less rigid, so do not stick

to blood vessel walls)

• Trans fats are unsaturated fats, chemically altered to make them more saturated (longer shelf-life) by the addition of hydrogen

• Even greater factor than saturated fats in the risk for cardiovascular disease

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Triglycerides

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Phospholipids

• Similar to triglycerides, except that 1 fatty acid is replaced by a molecule containing phosphate and, usually, nitrogen � video

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Phospholipids• Polar (hydrophilic) at one end; nonpolar (hydrophobic) at other

• Function: important structural component of cell membranes

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Steroids

• Composed of carbon atoms bound together into 4 ringlike structures

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Steroids

• Cholesterol, bile salts, oestrogen, progesterone, testosterone

• Component of cell membranes; physiological regulators

• High levels of cholesterol in blood increase risk for cardiovascular disease, certain amount is vital for normal function

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Fat-soluble vitamins

Vitamin Function

A Forms retinol; necessary for seeing in the dark

D Promotes calcium uptake

E Promotes wound healing

K Necessary for synthesis of proteins responsible for blood clotting

Essential for many normal body functions, eg.

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