Elements of Life - notesBiomolecules describe the molecules required by living things to build body parts and maintain the biochemical processes required for life functionsThese biomolecules may be classed as either organic or inorganic compounds

Organic compounds are compounds containing carbon that are found in living things  Except for hydrogen carbonates (HCO3

-), carbonates (CO32-) and oxides of carbon (CO, CO2)

Inorganic compounds are all other compounds (there are less different inorganic compounds than organic compounds)

BiomacromoleculesOrganic molecules can form large and complex biomacromolecules when simple recurring subunits (monomers) are joined together to form polymers

Monomers of organic molecules are joined together to form polymers via a condensation reaction, which results in the formation of a water molecule

Polymers can be broken down (or hydrolysed) via a hydrolysis reaction, which requires molecules of water to reverse the condensation process

Condensation and Hydrolysis Reactions

There are four main classes of macromolecules: carbohydrates, lipids, nucleic acids and proteins Autotrophs synthesise their own organic molecules from inorganic compounds they take in from the surrounding environment (e.g.

photosynthesis) Heterotrophs synthesise necessary organic molecules from other organic molecules consumed as part of their diet

Classes of Macromolecules

Fundamentals of Chemistry

The AtomAll substances, living and non-living, are composed of matter; and the fundamental unit of matter is an atomAtoms consist of a central space called a nucleus, which contains both positively charged particles (protons) and neutral particles (neutrons), while negatively charged electrons circle the nucleus in regions known as orbitals

The Periodic Table of ElementsAtoms differ in the number of protons they possess, and different atoms have different chemical properties (i.e. they react differently with different things)Atoms can be grouped together according to key properties as organised into a chart known as the periodic table of elements

The Periodic Table of Elements

Atoms in the same group (columns) share similar chemical properties as they have the same number of electrons in their outer valence shell

Atoms in the same period (rows) have the same number of electron shells but do not share any consistent chemical properties Atoms always have the same number of protons and electrons - when they gain or lose electrons they become charged ions An atom may have a different number of neutrons - these different forms of the atom are called isotopes and can cause radioactive

decay

Types of Bonding Atoms always try to have a full outer shell of electrons - in order to achieve this they will bond with other atoms When atoms bond together they form molecules - those made of one type of atom are elements while those made of many types

are compounds Atoms may join together by either gaining and losing electrons (ionic bonding) or by sharing electrons (covalent bonding) 

Ionic Bonding Ionic bonding occurs between a metal and a non-metal The metal has a nearly empty outer shell and so loses electrons to form a positively charged cation The non-metal has a nearly full outer shell and so gains electrons to form a negatively charged anion The resulting charge of these two ions creates a strong electrostatic attraction between them - an ionic bond

Ionic Bonding

Covalent Bonding Covalent bonding occurs between two non-metals Because both atoms have a large number of electrons in their outer shell, it is not feasible to lose or gain so many and so they

share The number of covalent bonds able to be formed reflects the number of missing electrons from the outer shell (e.g. carbon needs

four electrons and so can form four covalent bonds) Because there is no ionic charge, covalent molecules are not as strongly attracted to each other as ionic molecules (covalent bonds

are weaker)

Covalent Bonding

Metallic Bonding Metallic bonding occurs between two metals The atoms lose their outer shell electrons to become positively charged cations, and the electrons circulate as a delocalised sea This is why metals are good conductors of electricity and usually highly malleable Metallic bonding is not as integral to the structure and function of living organisms as ionic and covalent bonding

Intermolecular Bonding

Intermolecular bonding occurs between covalently bonded molecules and is significantly weaker than intramolecular bonding It results from the weak attraction between electrons and protons of different covalently bonded molecules

Polarity While covalent bonding represents sharing of electrons between atoms, the sharing may not always be equal and will depend on: The number of protons in an atom (more protons equals a greater attraction for electrons) The number of electron shells in an atom (electrons in higher shell numbers are a further distance from the nucleus = less attraction

to nucleus) Atoms that have a stronger affinity for electrons are said to have a higher electronegativity Covalently shared electrons will orbit closer to atoms with a higher electronegativity, resulting in a slight charge difference between

atoms These molecules are said to be polar and can form weak electrostatic associations, while molecules that do not have polarity are

non-polar

Polarity

Hydrogen Bonds

A polar association that occurs between the hydrogen atom of a polar molecule and a fluorine, oxygen or nitrogen atom (F, O, N) of another polar molecule is called a hydrogen bond

This is because fluorine, oxygen and nitrogen have the highest electronegativities, while hydrogen has the lowest - this results in the greatest polar associations between these atoms

Dispersion Forces Non-polar substances cannot form permanent polar associations but will still be attracted to each other by temporary attractions Because electrons are moving within an orbit, at any particular instant it will closer to the nucleus or further away, creating

momentary associations due to uneven electron distributions called dispersion forces (or Van der Waals forces)

INORGANIC MOLECULES

Inorganic molecules do not contain carbon and were not synthesised from a biological origin (oxides of carbon and carbonates are exceptions) Certain inorganic molecules play important roles in maintaining living organisms

Oxygen and Carbon Dioxide Oxygen is needed in most organisms to release energy from organic molecules (via aerobic respiration) Organic molecules are synthesised by plants from an inorganic stock of atmospheric carbon dioxide (via photosynthesis) These two processes are in many ways inter-related, with O2 being released by photosynthesis and CO2 being released by

respiration

The Role of Oxygen and Carbon Dioxide in Living Organisms

Minerals Mineral nutrients are the chemical elements required by living things other than the four main elements of organic molecules (C, H,

O, N) Phosphorus is a part of nucleic acids, cell membranes and ATP Sulphur is found in certain amino acids and can play an important role in the structure and function of proteins Calcium is important in the growth and development of bones and teeth Sodium and potassium are involved in neuronal signalling (nervous communication) Iron is found in red blood cells and is necessary for the transport of oxygen in blood Magnesium is found in chlorophyll, which is required for photosynthesis

Water

Living organisms usually consist of approximately 70 - 90% water as it functions as the fluid medium that bathes the cells and tissues

Water has a specific structure with associated properties that are critical for the maintenance of living organisms

Structure of a Water Molecule:

Water (H2O) is made up of two hydrogen atoms covalently bound to an oxygen atom While this bonding involves the sharing of electrons, they are not shared equally  The oxygen atom, having more protons (+ve), attract the electrons (-ve) more strongly (i.e. the oxygen has a higher

electronegativity) Thus the oxygen atom becomes slightly negative and the hydrogen atoms become slightly positive

Hydrogen Bonding between Water Molecules: Covalently bonded molecules that have a slight potential charge are said to be polar The slightly charged regions of the water molecule can attract other polar or charged compounds Water molecules can associate via weak hydrogen bonds (F/O/N bonding with H)

Structure and Bonding of Water Molecules

Properties of Water: Water has a high specific heat capacity It can absorb a lot of energy with little change in form due to the extensive hydrogen bonding, making water a good medium for

metabolic reactions It also has a high heat of vaporisation - this allows sweat to be an efficient form of evaporative cooling Water is very cohesive Because water molecules are polar, they will form intermolecular associations with each other (cohesion) and other polar molecules

(adhesion) This allows water to travel up the stems of plants (against gravity) without requiring high levels of energy for transport It also means water has a high surface tension, allowing small insects to walk along the surface of water without disturbing its

integrity

Water is the 'universal' solvent Water, due to its polarity, can dissolve other polar substances as well as ionic compounds (but not non-polar substances) While individual water molecules cannot sufficiently weaken and break the intramolecular attraction between ions, large enough

quantities can  This makes water a very efficient transport medium for hydrophilic ('water-loving') substances, but not hydrophobic substances Water is less dense as a solid Unlike most substances, water expands when frozen to ice (the arrangement of water molecules in an ice crystal creates empty

spaces) This is important as it means ice will float on water - this prevents the oceans from freezing over when surface temperatures are

sub-zero

CarbohydratesCarbohydrates are the most abundant of the four main classes of organic molecules found in natureThey contain carbon, hydrogen and oxygen in an approximate ratio of (CH2O)n with the number of carbons usually ranging from 3 - 7 per monomerMonomers usually adopt a cyclic ring structure in aqueous solutions and their names often end with the suffix 'ose'

Structure of Glucose

Types of Carbohydrates Monosaccharides:  Simple monomeric sugars, forms the basic subunits of more complex sugars Examples include glucose, fructose and galactose Disaccharides:  Two sugar subunits joined together (often used for transport as contains twice the energy yield while still

remaining soluble) Examples include maltose (glucose + glucose), sucrose (glucose + fructose) and lactose (glucose + galactose) Polysaccharides:  Many sugar subunits joined together in a long chain or polymer (are typically insoluble in water due to their

size) Examples include glycogen (glucose storage in animals), starch (glucose storage in plants) and cellulose (component of plant cell

wall) Complex polysaccharides are those that consist of different monosaccharide subunits (e.g. murein in bacterial cell walls)

Different Polymers of Glucose

Functions of CarbohydratesCarbohydrates can serve many functions within the cell, including:

Principle source of chemical energy for living organisms (e.g. glucose) Storage of energy reserves in plant and animal tissue (e.g. starch and glycogen respectively) Structural components of cells (e.g. cellulose in the cell wall of plants) Function as cell membrane receptors for cell recognition and communication (e.g. glycoproteins and glycolipids)

Biosynthesis of Carbohydrates In carbohydrates, monosaccharides can be joined together in a condensation reaction to form a disaccharide and water This results in the formation of a covalent bond known as a glycosidic link Under appropriate conditions, monosaccharides may link up via glycosidic bonds to form polysaccharides The synthesis of polysaccharides can occur at various locations within a cell, such as the smooth ER, the golgi apparatus or

plastids (in plants) Polysaccharides and disaccharides can be broken down into monosaccharides via a hydrolysis reaction, which requires water to

reverse the process

A Condensation Reaction between Two Monosaccharides

LipidsLipids are primarily composed of carbon, hydrogen and oxygen, although some forms of lipids may include additional elements (e.g. N and P)Unlike the other three types of organic molecules, lipids do not form polymers (although they may be constructed from identifiable subunits)Lipids are synthesised in the smooth endoplasmic reticulum and come in a wide variety of structural and chemical forms

Types of Lipids Triglycerides:  Function as a long-term energy source in animals (fats) and plants (oils) Phospholipids:  Structural component of cell membranes Steroids:  Act as hormones in plants and animals, and is a structural component of animal cell membranes (cholesterol) Waxes:  Act as a protective layer against water loss in plant leaves and animal skin Carotenoids:  Light-absorbing accessory pigment in plants (involved in photosynthesis) Glycolipids:  Complex of carbohydrate and lipid that acts a cell receptor molecule

Function of LipidsLipids can serve many functions within the cell, including:

Storage of energy for long-term use (e.g. triglycerides) Hormonal roles (e.g. steroids such as estrogen and testosterone) Insulation (retention of thermal energy) Protection of internal organs (e.g. triglycerides and waxes) Structural components (e.g. phospholipids, cholesterol)

Biosynthesis of Lipids Triglycerides are formed when glycerol is joined to three fatty acid chains via condensation reactions (producing three molecules of

water) Animals tend to store triglycerides as fats (solid form) while plants tend to store triglycerides as oils (liquid form) Triglycerides can be either saturated (fatty acids have no double bonds) or unsaturated (fatty acids have double bonds) Phospholipids are synthesised when a phosphate group is bonded to glycerol instead of a third fatty acid Because the phosphate is polar and the fatty acids are non-polar, phospholipids contain both hydrophilic and hydrophobic regions

Triglycerides and Phospholipids

Nucleic AcidsNucleic acids are the basic unit of inheritance, they constitute all the genetic material of living thingsThis genetic information determines how individual cells and entire organisms develop and function (by encoding for protein synthesis)

Structure of Nucleotides The monomeric unit of a nucleic acid is a nucleotide, which is comprised of a 5C-sugar, a phosphate group and a nitrogenous base The carbon atoms of the sugar molecule are numbered (1 - 5), the base connects to the 1'-C while the phosphate connects to the

5'-C of the sugar

Structure of a Nucleotide (Sugar, Phosphate & Base)

The nucleotide will contain one of four different nitrogenous bases, and when nucleotides are joined into chains, the order of these bases will determine the specific genetic information encoded by that sequence of nucleic acid

The four bases in DNA are:

        Adenine                                             Guanine                                   Thymine                                Cytosine

Adenine (A) and guanine (G) are purines (double ring bases)

Thymine (T) and cytosine (C) are pyrimidines (single ring bases)

Biosynthesis of Nucleic Acids

Nucleotides a linked into a single strand via a condensation reaction The phosphate group (attached to the 5'-C of the sugar) joins with the hydroxyl (OH) group attached to the 3'-C of the sugar This results in a phosphodiester bond between the two nucleotides and the formation of a water molecule Successive condensation reactions between nucleotides results in the formation of a long single strand

Types of Nucleic AcidsThere are two main types of nucleic acids:

DNA:  DNA (or deoxyribonucleic acid) is found in the nucleus and carries the genetic instructions for coding proteins on sequences called genes

RNA:  RNA (or ribonucleic acid) functions to transfer the genetic information from the nucleus to the rest of the cell mRNA (messenger RNA) is a transcript copy of a gene which encodes a specific polypeptide tRNA (transfer RNA) carries the polypeptide subunits (amino acids) to the organelle responsible for protein synthesis (ribosome) rRNA (ribosomal RNA) is a primary component of the ribosome and is responsible for its catalytic function

Differences Between DNA and RNA

Organisation of DNA Two polynucleotide chains of DNA are held together by hydrogen bonds between complementary base pairs: Adenine pairs with thymine (A=T) via two hydrogen bonds Guanine pairs with cytosine (G=C) via three hydrogen bonds

                           

Thymine                                   Adenine                                              Cytosine                                      Guanine

In order for bases to be facing each other and thus able to pair, the two strands must run in opposite directions (i.e. they are anti-parallel)

As the polynucleotide chain lengthens, the atoms that make up the molecule will arrange themselves in an optimal energy configuration 

This position of least resistance results in the double-stranded DNA twisting to form a double helix with approximately 10 - 15 bases per twist

Structure of the Double Helix

Packaging of DNA Eukaryotic chromosomes consist of DNA wrapped around histone proteins This forms the basic structure of the nucleosome, which is packed together to form chromatin (in a 'beads on a string' arrangement) Chromatin will supercoil and condense during prophase to form chromosomes that can be visualised under a light microscope Prokaryotic DNA is not wrapped around proteins and is thus considered to be 'naked'

Arrangement of DNA into Chromosomes

Function of Nucleic Acids The code carried by DNA is organised into triplets of bases (i.e. three nucleotides) called codons Each codon codes for an amino acid according to a set of rules known as the genetic code A sequence of codons which determines the sequence of a polypeptide is called a gene As the DNA is confined to the nucleus and the ribosomes responsible for protein synthesis are in the cytoplasm, an RNA copy is

made (mRNA) This process by which DNA is transcribed into an RNA copy is called transcription The mRNA goes to the ribosome, which synthesises a polypeptide sequence based on the order of codons in the gene This process by which mRNA is translated into a polypeptide sequence is called translation

The Role of DNA and RNA in Protein Synthesis

The Genome

Not all DNA sequences code for proteins (i.e. not every sequence of DNA is a gene) The totality of genes in a cell or organism is called the genome and the study of the way genes interact is called genomics The human genome consists of ~ 20,000 - 25,000 genes

ProteinsProteins occupy ~ 50% of the cell's dry mass and contain the elements carbon, hydrogen, oxygen and nitrogen (and usually sulphur)Proteins are composed of monomeric subunits called amino acids - there are 20 different types of amino acids

Structure of Amino Acids All amino acids contain a central carbon atom which is bonded to:  a hydrogen atom (H)  an amine group (NH2)  a carboxylic acid group (COOH)  a variable group (R) which differs between amino acids, resulting in distinct chemical properties

Structure of an Amino Acid

Types of ProteinsThere are two main classes of proteins:

Fibrous proteins are generally composed of long and narrow strands, which are insoluble in water and have a structural role within the cell

Globular proteins are generally have a more compact and rounded shape, they are soluble in water and have functional roles within the cell

Differences Between Fibrous and Globular Proteins

Functions of ProteinsProteins are very diverse and serve a number of different roles within the cell, including:

Structure:  Support for body tissue (e.g. collagen, elastin, keratin) Hormones:  Regulation of blood glucose (e.g. insulin, glucagon) Immunity:  Bind antigens (e.g. antibodies / immunoglobulins) Transport:  Oxygen transport (e.g. haemoglobin, myoglobin) Movement:  Muscle contraction (e.g. actin / myosin, troponin / tropomyosin) Enzymes:  Speeding up metabolic reactions (e.g. catalase, lipase, pepsin) 

Biosynthesis of Polypeptides Amino acids can be joined together in a condensation reaction to form a dipeptide and water

This results in the formation of a peptide bond, and for this reason long chains of covalently bonded amino acids are called polypeptides

Proteins destined for use within the cell are synthesised at ribosomes freely located in the cytoplasm Proteins destined for use outside of the cell (via secretion) are synthesised at ribosomes that are bound to the endoplasmic

reticulum (i.e. rough ER) Polypeptide chains can be broken down via a hydrolysis reaction, which requires water to reverse the process and cleave the

peptide bond

Formation of a Dipeptide

Organisation of ProteinsPrimary (1°) Structure

The order / sequence of the amino acids of which the protein is composed Formed by covalent peptide bonds between adjacent amino acids Controls all subsequent levels of structure because it determines the nature of the interactions between R groups of different amino

acids

Secondary (2°) Structure The way the chains of amino acids fold or turn upon themselves Held together by hydrogen bonds between non-adjacent amine (N-H) and carboxylic (C-O) groups

May form an alpha helix, a beta-pleated sheet or a random coil Secondary structure provides a level of structural stability (due to H-bond formation)

Tertiary (3°) Structure The way a polypeptide folds and coils to form a complex molecular shape (e.g. 3D shape) Caused by interactions between R groups; including H-bonds, disulphide bridges, ionic bonds and hydrophilic / hydrophobic

interactions  Tertiary structure may be important for the function of the enzyme (e.g. specificity of active site in enzymes)

Quaternary (4°) Structure The interaction between multiple polypeptides or prosthetic groups that results in a single, larger, biologically active protein A prosthetic group is an inorganic compound involved in protein structure or function (e.g. the heme group in haemoglobin) A protein containing a prosthetic group is called a conjugated protein Quaternary structure may be held together by a variety of bonds (similar to tertiary structure) Not all proteins will necessarily have a quaternary structure

Levels of Protein Organisation

The Proteome The totality of proteins in a cell or organism is called the proteome and the study of the way proteins function and interact is called

proteomics Because proteins can be modified to produce multiple functional forms, there are many more proteins than genes Examples of post-translational modifications to proteins include glycosylation, phosphorylation, cleavage, etc.