Elements of Life - notes
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Biomolecules describe the molecules required by living things to build body parts and maintain the biochemical processes required
for life functions
These 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)
Biomacromolecules
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Organic 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
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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 Atom
All substances, living and non-living, are composed of matter; and the fundamental unit of matter is an atom
Atoms 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 Elements
Atoms 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
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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
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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)
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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
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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
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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
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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
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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
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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
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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
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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:
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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
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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
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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
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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
Carbohydrates
Carbohydrates are the most abundant of the four main classes of organic molecules found in nature
They contain carbon, hydrogen and oxygen in an approximate ratio of (CH 2O)n with the number of carbons usually ranging from 3 7 per monomer
Monomers usually adopt a cyclic ring structure in aqueous solutions and their names often end with the suffix 'ose'
Structure of Glucose
Types of Carbohydrates
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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 Carbohydrates
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Carbohydrates 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
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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
Lipids
Lipids 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
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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 Lipids
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Lipids 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
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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 Acids
Nucleic acids are the basic unit of inheritance, they constitute all the genetic material of living things
This genetic information determines how individual cells and entire organisms develop and function (by encoding for protein
synthesis)
Structure of Nucleotides
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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)
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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
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Adenine (A) and guanine (G) are purines (double ring bases)
Thymine (T) and cytosine (C) are pyrimidines (single ring bases)
Biosynthesis of Nucleic Acids
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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 Acids
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There 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
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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
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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
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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 antiparallel)
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
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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
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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
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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
Proteins
Proteins 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
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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 Proteins
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There 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 Proteins
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Proteins 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
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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 Proteins
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Primary (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
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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)
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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)
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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
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Levels of Protein Organisation
The Proteome
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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.