The Chemical Nature of CellsThe Chemical Nature of CellsChapter 1Chapter 1

Unit 3 Biology ~ 2011Unit 3 Biology ~ 2011

KEY KNOWLEDGE KEY KNOWLEDGE The Chemical Nature of CellsThe Chemical Nature of Cells By the end of this chapter, you should:

Enhance your knowledge & understanding of the synthesis of

biomacromolecules such as polysaccharides, lipids, proteins

and nucleic acids.

Enhance your knowledge & understanding of the structure &

function of nucleic acids.

Understand the structural diversity of proteins & how this

diversity relates to the variety of functions that proteins carry

out in living organisms

Develop an understanding of the concept of the proteome of

an individual or a cell.

The Chemical Basis of LifeThe Chemical Basis of Life

All cells are composed of atoms and molecules which interact in thousands of simultaneous chemical reactions.

Organisms are composed of chemicals that react with each other and with the substances in the environment.

BiochemistryBiochemistry

The study of the chemicals involved in living organisms is called ‘biochemistry’.

Investigations in biochemistry allow for the development of pharmaceuticals, vaccines and improvements in medical diagnoses.

GENOMICS & PROTEOMICS are two recent fields of science dealing with the study DNA and proteins.

All the data that is gathered needs to be collated, analysed and stored in a systematic way. Thus the field of BIOINFORMATICS has been developed.

BioinformaticsBioinformatics

BiomoleculesBiomolecules

Living things are made from the following major groups of biological molecules: Proteins Nucleic Acids Carbohydrates Lipids

Cells require these molecules for survival. They are an integral part to the structure &

function of the cell.

Polar vs Non-PolarPolar vs Non-Polar

POLAR: this is when the molecule has an unequal distribution of electrons resulting in an overall negative charge at one end and an overall positive charge at the other.

NON-POLAR: molecules with an equal distribution of charge.

The polarity of the molecule will affect its interaction within the cell, for example a polar molecule can dissolve in water.

WATER ~ why is it so important?WATER ~ why is it so important?

ALL known life forms require water to survive 75% - 85% of a cell’s weight is water Almost all substances and chemical

reactions of biological significance require water.

Cells are constantly bathed by a watery solution

Water is essential for the cycling of matter between the living & non-living parts of ecosystems.

Chemical Properties of WaterChemical Properties of Water

H2O

Water can exist as a solid (ice), a gas (steam) or as a liquid

Water molecules are highly polar. The oxygen part of the molecule is negative so it is

attracted to the positive end of other water molecules. Water molecules join together by HYDROGEN

BONDING Hydrogen bonds involve the bonding between a

hydrogen atom on one molecule and the negative atom of another molecule or element

Water: the versatile solventWater: the versatile solvent

The polarity of water molecules allows substances to dissolve in it.

This ability is due to the water molecules interacting with other charged particles

HYDROPHILIC: Polar molecules can form hydrogen bonds with polar molecules of water and so they dissolve (water loving).

HYDROPHOBIC: Non-polar substances will not dissolve in water because they cannot form hydrogen bonds with water molecules.

Dissolving in Water (cont…)Dissolving in Water (cont…)

The ‘rule’ for substances to form a solution is that “LIKE DISSOLVES LIKE”.

Polar solvent + Polar solute = Solution

Non-polar solvent + Non-polar solute = Solution

Concentration of SolutionsConcentration of Solutions

The functioning of cells is affected by the concentration of fluids in and around the cells.

Movement of water and other substances across the cell membrane depends on the comparative concentration of these substances inside & outside of the cell.

The solute is more concentrated

on this side

The solvent ismore concentratedon this side

Acids & BasesAcids & Bases

ACID: a substance that produces hydrogen ions in solution (low pH).

BASE: a substance that will take hydrogen ions from an acid (high pH)

The acidity of a solution is measured by pH. Chemical reactions within cells can produce acidic

or basic substances. Blood pH must be kept within very strict limits

around 7.4. Cell reactions cannot take place if the pH is too

high or too low.

Buffering SystemBuffering System

In order to maintain a stable pH level, a buffering system is enacted.

This involves maintaining a steady pH by either releasing more hydrogen ions or using up excess hydrogen ions.

ACID BASE

Physical Properties of WaterPhysical Properties of Water

BIOLOGICAL MACROMOLECULESBIOLOGICAL MACROMOLECULES

EVERY living cell is involved in synthesising macromolecules for the following: Building up body parts of the organism Maintain biochemical processes, including:

CommunicationTransforming energyRelaying genetic information

The four main classes of macromolecules are: Proteins, Nucleic Acids, Carbohydrates & Lipids.

Organic molecules are made up of smaller subunits

The subunits are called monomers

Polymers are formed when the monomers are bonded together

Organic Organic MoleculesMolecules

Synthesis of BiomacromoleculesSynthesis of Biomacromolecules

Some organisms can synthesise their own biomacromolecules whereas others must rely on the substances they have taken in.

AUTOTROPH: an organism that is able to synthesise organic molecules from inorganic materials.

CHEMOTROPH: an organism that is able to synthesise organic molecules from specific chemicals.

HETEROTROPH: an organism that must synthesise their organic molecules from existing organic molecules that are taken in as food.

PolymerisationPolymerisation

Biomacromolecules are synthesised inside the cell. Polymerisation is the process of smaller repeating

units (monomers) being linked together to form long chains called polymers.

Proteins, carbohydrates & nucleic acids are synthesised in this way and are classed as polymers.

Lipids do not form polymers. They are composed of distinct chemical groups of atoms.

Condensation PolymerisationCondensation Polymerisation

When monomers link together, a water molecule is generated. The hydroxyl group of one monomer reacts with

the hydrogen atom of another monomer. This reaction is called Condensation

Polymerisation.

Monomers Polymers single units/subunits many

linked units/ macromolecules

polymerisation

CARBOHYDRATESCARBOHYDRATES

Carbohydrates are the most common compounds in living things.

Organisms use carbohydrates as an energy source and for structural components.

Each molecule is composed of the following atoms in the ratio of 1:2:1 1Carbon atom : 2Hydrogen atoms : 1 Oxygen atom CH2O is the formula

Carbohydrates are classified as: Monosaccharides Disaccharides Polysaccharides

Classification of CarbohydratesClassification of Carbohydrates

CARBOHYDRATE CLASSES

Monosaccharides

Disaccharides

Polysaccharides

Triose

Pentose

Hexose

Maltose

Sucrose

Lactose

Cellulose

Starch

Glycogen

Chitin

MonosaccharidesMonosaccharides

Molecules contain a single sugar unit Usually has the formula C6H12O6

Monosaccharides with the same molecular formula have differing structural formula (arrangement of atoms)

Soluble in water Usually known as ‘sugars’ Most important example is GLUCOSE Other examples:

Fructose Galactose

DisaccharidesDisaccharides

Disaccharides form when two monosaccharides combine.

Examples include: Sucrose = glucose + fructose Lactose = glucose + galactose Maltose = glucose + glucose

PolysaccharidesPolysaccharides

Between ten & several thousand monosaccharides that have joined together

The most common sugar component is glucose The differences in properties relate to the ways in

which the glucose molecules are linked together. Many polysaccharides are INSOLUBLE in water Examples:

Cellulose: structural component of every plant cell wall Starch: main form of storage by most plants Glycogen: energy storage in animals

PROTEINSPROTEINS

Almost everything a cell is made up of or does depends on PROTEIN.

Proteins contribute to building many different structures and control the thousands of chemical reactions that maintain life processes.

Building Blocks of ProteinsBuilding Blocks of Proteins

Proteins are made up of AMINO ACIDS. There are 20 different amino acids that

contribute to the proteins found in cells. The basic structure of proteins includes up to

thousands of amino acids bonded together to form linear polymers that are folded, twisted or coiled.

Plants synthesise their own amino acids. Animals rely on their diet to obtain their

amino acids.

Amino AcidsAmino Acids

All amino acids have the same basic chemical structure: A central carbon atom A hydrogen atom A carboxyl acid group

(COOH) An amine group (NH2) An “R” group this

group is different for each type of amino acid

CarbonAtom

AmineAcid

Carboxylgroup

R Group

HydrogenAtom

Amino Acids & ‘R’ GroupsAmino Acids & ‘R’ Groups

The R group can either give the protein molecule a polar region or a non-polar region.

Non-polar regions are hydrophobic and will usually be tucked inside the protein molecule so as not to be exposed to the watery environment.

Polar regions are hydrophilic and tend to be on the surface of protein molecules.

Structural Structural Formulae Formulae of the 20 of the 20 Amino AcidsAmino Acidsused to makeused to makeproteins in proteins in living living organismsorganisms

Protein StructureProtein Structure

Primary Structure: refers to the sequence of amino acids that form

the polypeptide chain. Secondary Structure:

coiling (α-helices) & folding (β-sheets) of the polypeptide chain.

Other parts remain unchanged (random loops) Hydrogen bonds form between segments of the

folded chain that are close together and help stabilise the 3-D shape

PRIMARY STRUCTURE

SECONDARY STRUCTURE

Protein StructureProtein Structure (cont…) (cont…) Tertiary Structure:

Interactions between R groups Results in hydrogen bonds, ionic bonds or disulfide

bridges between cysteine amino acids. Interactions follow the ‘like attracts like’ rule:

hydrophilic + hydrophilic; hydrophobic + hydrophobic.

The polypeptide chain is folded, coiled or twisted into the protein’s functional shape (conformation).

Protein molecules with the same sequence of amino acids will fold into the same shape.

If an incorrect amino acid is present this will alter the shape of the protein making it non-functional.

Tertiary Structure (cont…)

Protein Structure Protein Structure (cont…)(cont…)

Quaternary Structure: Many large complex

protein molecules consist of two or more polypeptide chains.

Hydrogen bonds, ionic bonds and/or covalent bonds hold the polypeptide chains together and gives the overall shape to the molecule.

Protein Protein Structure Structure (cont…)(cont…)

Functional Diversity of ProteinsFunctional Diversity of Proteins

Motility: movement of cells & organelles Structural: support, strength protection Enzymes: speed up reactions Transport: carry molecules around cell or across

membrane Hormones: chemical messengers Cell-Surface Receptors: act as a ‘label’ to provide

identification of the cell Neurotransmitters: chemical messengers between

neurons Immunoglobulins: antigens Poisons/toxins: chemicals for defence or capturing

food

Conjugated ProteinsConjugated Proteins

Proteins whereby the chains of amino acids ‘conjugate’ with other groups

Occurs most commonly in the nucleus Nucleoproteins – contain both protein & nucleic

acid Haemoglobin is another example of a

conjugated protein The tertiary structure associates with a heme

group

Activating ProteinsActivating Proteins

When proteins, such as insulin, are produced they are inactive

The protein molecule needs to be activated in some way, usually by an ‘activating enzyme’

Changes in ProteinsChanges in Proteins

Proteins are non-functional if the DNA code is translated incorrectly.

Other factors that can cause protein molecules to change are: High temperatures Strong salty solutions Very acidic or very alkaline conditions

Protein molecules will DENATURE under such conditions. The shape of the protein molecule will alter. If the change is minor it could be reversed and the protein

resumes its function. If the change is major the protein will no longer be

functional.

ProteomeProteome

PROTEOME: the whole set of proteins produced by a cell.

PROTEOMICS: the study of proteomes. FUNCTIONAL PROTEOMICS: what

proteins do in different cells and tissues.

LIPIDSLIPIDS

Lipids have three important functions: Energy storage Structural component of cell membranes Specific biological processes (eg: transmission of

chemical signals both within and between cells). All lipid molecules contain carbon, hydrogen &

oxygen Lipids contain relatively little water Lipid molecules carry more energy per

molecule than any other kind of compound found in plants or animals.

FatsFats

Made up of two kinds of molecules: Fatty acid Glycerol

Triglycerides are a common form of fats

TriglyceridesTriglycerides

Triglycerides: subunits of fats & oils Three fatty acids attach to the glycerol backbone. SATURATED fats:

Found in animals Solid Fatty acids are packed closely in a straight line

UNSATURATED fats: Found in plants Liquid Fatty acids form double bonds and are not packed closely

together

PhospholipidPhospholipid

Two fatty acids attached to a glycerol

Also have a phosphate group attached to the glycerol

Phospholipids are the major component of cell membranes

Classification of LipidsClassification of Lipids

Lipids are classified according to their solubility The solubility of lipids is dependent on the shape

of their molecules and the intramolecular bonding. Lipid molecules have large non-polar hydrophobic

regions meaning they are insoluble in water. Non-polar lipid molecules CAN dissolve in other

non-polar substances. Some other types of lipid molecules have both a

hydrophilic region and a hydrophobic region.

TYPES OF LIPIDS

Fats & Oils

Terpenes

Waxes & Cutins

Oils in plants; Fat deposits under the skin

Essential oils giving plants their colour & odour

Waterproof coating on leaves, fruits, insects

Phospholipids

Glycolipids

Steroids

Form part of cell membranes

Provide energy; marker on cell membrane

Hormones, vitamin D, cholesterol

NUCLEIC ACIDSNUCLEIC ACIDS

Nucleic acids are long molecules made up of three distinct chemical parts.

Nucleic acids store information in a chemical code for the production of proteins.

Nucleic acids are the GENETIC MATERIAL for every living organism.

DNA = deoxyribonucleic acid RNA = ribonucleic acid

DNA & RNADNA & RNA

DNA Linear molecule Double stranded The two strands wind around

each other to form a double helix Made up of nucleotides Located in the nucleus Deoxyribose is the sugar

component Nitrogenous bases:

Adenine Guanine Cytosine Thymine

RNA Linear molecule - shorter than

DNA Single stranded Made up of nucleotides Formed in the nucleus then

moves to the ribosomes in the cytoplasm to function.

Ribose is the sugar component – ribose has one less oxygen atom than deoxyribose

Nitrogenous bases: Adenine Guanine Cytosine Uracil

NucleotidesNucleotides

Nucleotides are the monomers that bond together to make the nucleic acid polymers.

Nucleotides have 3 distinct chemical parts: A 5-carbon sugar (ribose or deoxyribose) A Negatively charged phosphate group An organic nitrogenous base

Adenine - AGuanine - GCytosine - CThymine - T

Nucleotides Nucleotides (cont…)(cont…)

The sugar molecule of one nucleotide binds with the phosphate group of the next nucleotide.

The nitrogenous base is left sticking out and faces the opposite nitrogenous base from the adjoining DNA strand

Hydrogen bonds hold the nitrogenous base pairs together forming the ‘rungs’ of the helix.

The bases pair according to the following rule: A pairs with T G pairs with C

Chemical Chemical structure structure of DNAof DNA

DNA ~ functionDNA ~ function

The sequence of nucleotides in DNA codes for amino acids that will form a particular protein.

GENES: the segments of DNA that code for protein formation

GENOME: the total set of genes that each cell of an organism carries.

GENOMICS: the study of genes and the way they interact with each other.

DNA ~ function DNA ~ function (cont…)(cont…)

DNA passes on information from one generation to the next.

DNA, usually in the form of chromosomes, is located in the nucleus of cells.

One of the strands of DNA acts as a template so that the complimentary strand of DNA can be formed (following the base pairing rule).

DNA is also used as a template for the formation of RNA.

Some DNA is located in mitochondria & in chloroplasts.

Biotechnology has allowed for the manipulation & modification of DNA.

RNA ~ functionRNA ~ function

The major function of RNA is to produce proteins. GENE EXPRESSION: the information from the DNA strand is

taken by the RNA and the appropriate proteins produced. mRNA: messenger RNA – the code from DNA is transferred to

mRNA in a process called transcription. The mRNA strand moves out of the nucleus into the cytoplasm and attaches to the ribosomes.

rRNA: ribosomal RNA – ribosomes are composed of rRNA and other proteins.

tRNA: transfer RNA – each tRNA molecule has an amino acid attached at one end and an anti-codon on the other end. The anti-codon pairs up with the corresponding codon on the mRNA. This ensures the correct sequence of amino acids for the polypeptide chain.

tRNA moleculetRNA molecule