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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