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Biology 1

Lecture 08-04-19

Topic 1: Chemical constituents of cells (Part 1) Wa t e r Introduction  

Cools Body 83% of blood o Components of blood: Plasma, Red Blood Cell, White Blood Cell, Platelet

Structure  

‘V’ Shape Angle of 104.5° o Dipoles - electrons tend to repulse; causing a ‘V’ shapre  Polar molecule – has charges {slide 7} δ- = Partially negative δ+ = Partially positive In the water molecule, the oxygen atom contains 2 pairs of unshared electrons (aka. ‘Lone Pairs’).  Electrons not equally shared;  Thus – causes oxygen to pull e- towards the nucleus  Causing – partial electronegativity  The electrons are now closer to oxygen, so the oxygen end is partially negative (δ-), and the hydrogen end is partially positive (δ+).  Thus; covalent bond is polar due to asymmetrical distribution of e-. Bonds within water molecule = Covalent bond Bonds between water molecule = Hydrogen bond  The positive end of one water molecule is attracted to the negative end of another water molecule.  Oxygen can attract two nearby hydrogen atoms from other water molecules Hydrogen bond is the slightly weaker bond.  Easily break and reform  The H bond between the water molecules are very fragile (This allows water molecules to maintain liquid state in ordinary temperature)  With H bond water molecule can bind w/ 4 other water molecules

Summary     

104.5° - Why? Electronegativity Bonds between/within water molecule(s) H bond Advantages of Hydrogen bond

Dipole Moment (Extra) Dipole moment is the measure of net molecular polarity. Dipole moments tell us about the charge separation in a molecule. The larger the difference in electronegativities of bonded atoms, the larger the dipole moment. Polar molecules and Dipole-Dipole Interaction

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A polar molecule is a molecule where one end has a positive electrical charge and the other end has a negative charge due to the arrangement or geometry of its atoms. Because polar molecules have a positive and negative charge ends, the positive charge end of a molecule will attract to the negative end of adjacent molecule with the same or different kind of molecule. The attraction beween two polar molecules is called dipole-dipole interaction. The attraction between two dipoles create a very strong intermolecular force, which have great influence in the evaporation of liquid and condensation of gas.

Advantages of Hydrogen Bonds (Extra) 1. Hydrogen bonds are very weak, so how is it possible that they are so important in the properties of water? Hydrogen bonds in water provide many characteristic benefits to water: cohesion (holding water molecules together), high specific heat (absorbing heat when breaking, releasing heat when forming; minimizing temperature change), high heat of vaporization (several hydrogen bonds must be broken in order to evaporate water), lower density of ice (molecules in ice are spaced farther apart), and solubility (polar molecules are attracted to ions and polar compounds, making them soluble in water). 2. Why do we feel cooler immediately after we go swimming than we do after we have fully dried off? We feel cooler immediately after we go swimming than we do after we have dried off because it takes a lot of heat to evaporate water; however, once we dry off we remove much of the water from our skin, and the water is evaporated much more quickly. 3. If water were non-polar, would our temperature heat up less quickly or more quickly if we went outside on a hot day? Why? More quickly. Because hydrogen bonds within water slow down the movement of molecules and allow for water to have a very high specific heat. Each water molecule can form two hydrogen bonds involving their hydrogen atoms plus two further hydrogen bonds utilizing the hydrogen atoms attached to neighboring water molecules. These four hydrogen bonds optimally arrange themselves tetrahedrally around each water molecule as found in ordinary ice (see right). In liquid water, thermal energy bends and stretches and sometimes breaks these hydrogen bonds. However, the 'average' structure of a water molecule is similar to this tetrahedral arrangement and endows water with its high cohesiveness. The diagram shows such a typical 'average' cluster of five water molecules. In the ices this tetrahedral clustering is extensive, producing crystalline forms. In liquid water, the tetrahedral clustering is only locally found and reduces with increasing temperature. However, hydrogen-bonded chains still connect liquid water molecules separated by large distances.

Properties 1. Universal Solvent  Due to Polar molecules – Adv: When H2O molecule breaks, positively charged and negatively charged ions are released. Ex. When NaCl dissociates  ‘Opposite charges attract, Same charges repel’

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Lecture 08-04-19 

2.

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Solubilize polar molecules and ionic molecules due to electrostatic interaction between water molecules.  Partial charges on water molecules are attracted to polar molecules. High specific heat capacity  Definition: Amount of heat (energy) needed to raise water temperature of 1 kg of water by 1 °C  The fragility of the H bond promotes high specific heat capacity.  More energy is used to break H bonds  Water has good ‘adaptability’ which other solvents don’t have.  Adv: {Slide 14} i. Water acts as a good habitat for aquatic organisms ii. Temperature buffer against sudden change in cells (essential for enzymes) Water molecules can cool the environment – eventually all the enzymes be conserved by having this S.H.C  Water molecules break/reform to adapt to the specific environmental feature High heat of vaporization  Definition [Vaporization]: Amount of heat (energy) needed to convert water from liquid into vapour  Definition [Fusion]: Amount of heat (energy) to be removed from water to turn it into ice  Evaporation – cools down body. Water has ‘Cooling property’ Low density at solid state  Ice is less dense than water – due to the different arrangement at different states. i. Liquid: 1. Very close/tight arrangement ii. Solid: 1. Hexagonal/Pentagonal Shape 2. Lattice/Crystalline – creates more space – lowers density. (Density=Mass/Volume)  In liquid water, Hydrogen bonds constantly break and reform, enabling a denser spacing than in ice  In ice, maximum number of hydrogen bonds form, causing molecules to be spread apart High surface tension  Hydrogen bonding between water molecules = Cohesive forces. A ‘pulling’ creates a force (aka) ‘tension’ on the surface  Strong force=Tension  Cohesion: The tendency of water molecules sticking together  Adhesion: The tendency of water molecules sticking to other types of molecules/substances {Slide 18}  High surface tension = Able to support smaller weight organisms

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 Ex. Small Organisms (ants/water striders), Transpiration in Xylem 6. Low viscosity of water  H bond can be easily broken enabling molecules to slide over each other  Ex. i. Efficient transport in plants ii. Lowers viscosity in blood allows blood and plasma to flow easily {Slide 20} Learning Check 1. High Surface tension – Small organisms float on the surface of the water 2. Strong cohesive forces – Transport of substances in plants (also adhesion) 3. High specific heat capacity – Change of temperature

Acids, bases and buffers {Slide 21} Acids:  Donates H+ ion when in water  Litmus paper blue to red  Sour  Ex. HCl (HCl –> H+ + Cl-) Bases  Receives H+ ion  Litmus paper red to blue  Slippery  Ex. Ammonia

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pH: A measure of the concentration of H+ ion 

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Affects solubility of various substances Enzymes

Buffers 

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Definition: A solution that resists change in pH Reacts with any added acid or base to control pH Detects small changes in pH {Slide 27} Works by donating Hydrogen ions when the pH increases and accepting hydrogen ions when the pH decreases Buffer = A mixture of o A weak acid + its conjugate base o A weak base + its conjugate acid Why – {Slide 8}

pH of blood = 7.34 – 7.45  Haemoglobin acts as a buffer in our system

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Biological Molecules  Carbohydrates, Proteins, Lipids, Nucleic acids Monomer = smallest unit (ex. Glucose) Polymer = large structural units of a molecule connected by a covalent bond (ex. Carbohydrates, Lipids) 1. Condensation a. Formation of Polymers b. Removal of 1 water molecule 2. Hydrolysis a. Addition of water b. Break down polymers

Proteins  

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C, H, O, N (may: Sulphur, Phosphate) Monomer: Amino acids (20 types) o Essential: Amino acids which body cannot produce, obtained through diet o Non-essential: Amino acids that the body can produce Structure of Amino Acids: o Carbon w/ 4 chemical groups (Covalent bond) o Amino group & Carboxyl group o A.a is an amphoteric (can react with both acid & base) and Zwitterion (Neutral molecule with both positive and negative charge) o Side chain defines the amino acid o Each Amino acid has a different side chain

Structure and bonding of Amino Acids  2 Amino acids are linked by a peptide bond Condensation:  Between α-carboxyl & α-amino group

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OH is removed from the carboxyl group of one of the a.a  H is removed from the amino group of another a.a Condensation of 2 Amino Acids=Dipeptide

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Protein Structure 4 levels of protein structure 1. Primary Structure  Linear sequence polypeptide chain  Stabilized by peptide bonds (covalent bonds) 2. Secondary Structure  Stabilised by H bond  Due to the attraction between O of C=O & H of NH of two amino acids  Linear sequence fold:  Pleated shape – β pleated  Helix shape – α Helix  The linear sequence twists 3. Tertiary Structure  Folding of secondary structure into its precise 3D structure  Due to attraction between R groups  The side chains link with each other Stabilized by: i. Hydrogen bonds a. Hydrophilic (attracts water) / polar groups

ii. iii.

iv.

b. Broken by high temperature/pH change Hydrophobic interaction a. Non-polar R groups/ hydrophobic (repels water) Ionic bonds a. Between R groups of amine & carboxyl b. Broken by pH changes Disulphide bonds/bridge a. Between cysteine molecules b. Broken by reducing agents

4. Quaternary Structure  Association of 2/more polypeptide chains due to attraction between 2 R-groups  Ex. Haemoglobin (Haemoglobin is made from 2 alpha chains [141 a.a] and 2 beta chains [146 a.a])

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Biology 1

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Types of Protein 1. Fibrous Protein i. Long, parallel chains ii. Cross link between molecules forms strong fibres iii. Insoluble in water iv. Stable v. Role: Mechanical & Structural support vi. Ex. Keratin, Collagen

2. Globular Protein i. Polypeptide chains folded into compact, spherical shape ii. Hydrophobic facing inwards, hydrophilic facing outwards iii. Soluble in water iv. Unstable structure v. Easily denature – no string fibres vi. Role: Metabolic reactions vii. Ex. Enzymes, Insulin, Hormones, Antibody Conjugates protein – Some globular protein that attaches to non-protein component (prosthetic group) [Non-globular] Ex. Haemoglobin

Functions of Protein        

Hair & Nail (Keratin) Blood (Haemoglobin) Brain and nerves (Ion channel proteins control brain signalling allowing small molecules into and out of nerve cells) Enzymes (In saliva, stomach, small intestines – help digest food) Cellular construction workers (Huge clusters of proteins form molecular machines that do the cells’ heavy work, such as copying genes during sell division and making new proteins) Muscles (Muscles proteins called actin and myosin enable all muscular movement) Cellular Messengers (Receptor proteins stud the outside of your cells and transmit signals to partner proteins in the inside of the cells) Antibodies

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