+ CHAPTER 1 REVISION. + The Cell- a chemical factory Each cell is highly organised assembly of...

+

CHAPTER 1 REVISION

+The Cell- a chemical factory

Each cell is highly organised assembly of atoms and molecules, which interact with thousands of simultaneous chemical reactions.

Therefore a knowledge of chemistry is needed to understand how the cell works.

+What do all cells need to do?

Take in small nutrient molecules and make very large bio-macromolecules

Remove waste products Produce energy to drive chemical reactions Produce useful by-products for export from cell to cell Receive and respond to signals Grow, reproduce and pass on genetic information to the

next generation

+Coherent Conceptual Framework

MoleculesInteraction

sbetween

molecules

Determines the shape of

moleculesProducebinding sitesthat can havehigh

specificity

The big idea in Unit 3

+ Matter has mass and takes up space Consists of atoms Element X has A mass number (no. of protons and neutrons)

and Z atomic number (number of protons). It is the number of protons that defines the element.

Aχz

+If they have a different number of

neutrons but the same number of protons they are called isotopes which can be unstable.

Outer shell electrons = valence electrons = create compounds.

Lose electrons = +vely charged = +ve ions = cations

Gain electrons = -vely charged = ive ions =anions

+Structure of an Atom

+Chemical Bonding

The properties of electrons in an atom’s outer shell determine its chemical behaviour.

When different chemical combine via chemical bonding they form a compound.

+Bonds

Ionic bondingOpposites attract – when atoms of

metals combine with non metals they transfer there outer electrons.

Atoms of metals + atoms of -> ionic compound(cations) non metals (solid lattice)

(anions)

+

Covalent bondingCombination of two non metals atoms.

This results in a molecular compound.

Eg h2o

+

Polar – unequal charge distribution .

Non-polar – equal charge distribution.

+The role of molecules found in living cells – Macromolecules.Complex carbohydratesProteinsLipidsNucleic acidsWater (the most abundant molecule found

in cells 70%-90% and the medium in which most cellular processes occur)

+Water Water consists of 1 oxygen atom with 2

hydrogen atoms Each hydrogen atom is linked to oxygen atom

by a strong covalent bond Oxygen end has a slightly negative charge Hydrogen end a slightly positive charge Unequal sharing of the bonding electron pairs Water is dipolar (two charges, one at each end) Water molecules inturn are weakly held

together by weak hydrogen bonds

+Water

Dissolving ionic compounds

A grain of salt contains many NaCl molecules. When salt is placed in water, salt molecules dissociate because of the attraction of Na and Cl to different parts of the water molecules.

A ring of water molecules surrounds each sodium and chloride atom and they remain in solution.

+Properties of waterProperty of Water Explanation

1. Cohesion Liquid water is cohesive, molecules stick together due to the hydrogen bonds that hold the molecules together.

2. High specific heat Heat must be absorbed to break the hydrogen bonds, before the water molecules can move faster and the temperature rises.

3. Solid is less dense than liquid

Water molecules forms a lattice structure that is less dense than water

4. Heat of vaporisation

A large amount of heat is needed to break the hydrogen bonds for liquid water to be converted into water vapour.

5. Solvent Water molecules are attracted to solutes that carry a charge (polar molecules) and cause dissolving.

+Hydrophylic ('Water Loving’) and Hydrophobic ('Water Hating') Molecules Hydrophylic Molecules Substances that dissolve readily

in water are termed hydrophilic. They are composed of ions or polar molecules that attract water molecules through electrical charge effects.

Water molecules surround each ion or polar molecule on the surface of a solid substance and carry it into solution.

Ionic substances such as sodium chloride dissolve because water molecules are attracted to the positive (Na+) or negative (Cl-) charge of each ion.

Polar substances such as urea dissolve because their molecules form hydrogen bonds with the surrounding water molecules.

+Cohesion and Surface Tension The strong hydrogen bonds give water a high cohesiveness and, consequently, surface tension. This is evident when small quantities of water are put onto a non-soluble surface and the water stays together as drops. Eg. Water on oil.

Oil, for example, is a non-polar molecule. Because there is no net electrical charge across an oil molecule, it is not attracted to water molecules and therefore does not dissolve in water.

This feature is important when water is carried through xylem up stems in plants; the strong intermolecular attractions hold the water column together, and prevent tension caused by transpiration pull.

+pH in Practice

In theory, pure water has a pH of 7. In practice, pure water is very difficult to produce. Water left exposed to air for any length of time will rapidly dissolve carbon dioxide, forming a solution of carbonic acid, with a limiting pH of ~5.7

Blood pH = 7.4

+Acid or Alkaline? Pure water has a PH 7.0 which is neutral Ph is a scale that measures hydrogen ions in a solution

and hence the acidity or alkalinity of a solution

+ORGANIC MOLECULESOrganic molecules contain carbon.

Molecules containing covalently bonded carbon backbones are called ORGANIC COMPOUNDS.

Each carbon atom can form strong, stable bonds with four other atoms at a time – these are usually oxygen, hydrogen, nitrogen, sulphur, and phosphorus atoms.

Covalently linked carbon atoms can form linear chains, branched chains, and cyclic and cage like structures.

+ Organic molecules are large molecules made of smaller sub-units or monomers that are repetitively linked together to form long strands called polymers.

Compounds formed in this way are called polymers.

+Monomers and Polymers

Each organic molecule group has small molecules (monomers) that are linked to form a larger organic molecule (macromolecule). Monomers can be joined together to form polymers that are the large macromolecules made of three to millions of monomer subunits.

+

Monomer Polymer

Fatty acid Fats, Lipids, membranes

Monosaccharide Polysaccharide

Amino acid Polypeptide (protein)

Nucleotide Nucleic acid (DNA, RNA)

+Carbohydrates

+Carbohydrates

Originally known as "hydrates of carbon" because they had the empirical formula CH2O.

Now defined as polyhydroxy aldehydes and ketones.

Example cellulose (plants), starch (potato), glycogen (excess carbs stored as glycogen- liver and skeletal muscles), and most sugars (glucose) .

+

3 major classes of carbs:Monosaccharide’sDisaccharidesPolysaccharides“saccharide” is derived from the Greek word ‘sakkharon’ meaning sugar

+Carbohydrates

+Glucose

Glucose is a product of PHOTOSYNTHESIS. During the formation of glucose in plants, energy of the sun is transformed into energy in the glucose molecule.

Plants convert excess glucose into starch for storage.

+Glycogen

The liver and skeletal muscles are major depots of glycogen.

Animals store excess glucose by polymerizing it to form glycogen.

Glycogen is broken back down into glucose when energy is needed (a process called glycogenolysis).

+Cellulose

Probably the single most abundant organic molecule in the biosphere.

Polysaccharide with glucose as its monomer.

Fibrous, tough and water insolubleFound in stalks, stems, trunks and all the woody parts

+Lipids

+Lipids• A fat molecule

consists of three long chain fatty acids attached to a glycerol molecule (triglyceride)

• The glycerol part is the lower end of the molecule.

• Lipids are classified by their solubility which is determined by their shape and bonding.

+Phospholipids

+Plasma Membrane

+Lipids

Diverse group of fatty substances found in all living organisms.

do not dissolve in water but are soluble in alcohol, ether, or other organic solvents.

Phospholipids (most imp of lipids) limit the passage of water and water-soluble compounds through the membrane, enabling the cell to keep its contents separate from the outside environment.

+The lipids of physiological importance for humans have four major functions: They serve as structural components of

biological membranes. They provide energy reserves,

predominantly in the form of triacylglycerols. Both lipids and lipid derivatives serve as

vitamins and hormones. Lipophilic bile acids aid in lipid

solubilization.

+Proteins

+PROTEINS Proteins are made up of: Carbon (C) Hydrogen (H) Oxygen (O) some contain Sulfur (S) Examples of proteins Antibodies: they recognise molecules of invading

organisms. Receptors: part of the cell membrane, they recognise other

proteins, or chemicals, and inform the cell... 'The Door Bell'. Enzymes: assemble or digest. Neurotransmittors and some hormones Channels and pores: holes in the cell membrane (with or

without a gate).

+Structure of Proteins contain both the amino (-NH2) and carboxyl (-COOH) groups

+Structure of proteins

The role (or function) of a protein depends on its shape, and chemical formula. Therefore, the structure of proteins will be explained first.

There are four types of protein structure: Primary: sequence of amino acids in the chain Secondary: the shape of the protein molecule caused by

hydrogen-bonding between -C=O and -N-H groups within the chain

Tertiary: the interaction between R-groups that causes folding and bending – this structure determines their function

Quarternary: interactions between protein subunits that result in the protein being classified as fibrous, globular or conjugated

+ProteinsPrimary structure

+ProteinsSecondary structure

+ProteinsTertiary structure

+ProteinsQuaternary structure

+Nucleic Acid

+Nucleic acids•Stores info (chemical code) to produce proteins).•Organised as DNA or RNA.•DNA is 2 strands of nucleotides.•RNA is single strand.

+The building blocks of DNA and RNAThree types of chemicals make up the building blocks for nucleic acids.PhosphatesSugarsOrganic bases

+

The nucleic acids are very large molecules that have two main parts.

The backbone of a nucleic acid is made of alternating sugar and phosphate molecules bonded together in a long chain

Each of the sugar groups in the backbone is attached (via the bond shown in red) to a third type of molecule called a nucleotide base

+The basic structure of a nucleotide is shown below

+

Nucleic acids have at least two functions:

to pass on hereditary characteristics from one generation to the next, and

to trigger the manufacture of specific proteins.

2 rings in their structure

1 ring in their structure

+

Therefore they can only link with the opposite base pair

A -> TC-> GWhich shows that one strand is a

template for the other.

+Nucleic acid to DNA

+

+Nucleic acidsDNA • The double helix

structure and dimensions of DNA.

• The two chains are held together by hydrogen bonds between complementary bases.