Molecules Flashcards
O=
Oxygen
C=
Carbon
N=
Nitrogen
H=
Hydrogen
S=
Sulfer
Fe=
Iron
Monomer
A single unit which is the most basic a singular sugar, a single amino acid or a glycerol or fatty acid
Dimer
Two monomers chemically bonded together
Polymer
A long chain of monomers chemically bonded together
Metabolism
Is the sum of all chemical processes that take place inside a living organism
2 steps of metabolism
Anabolism
Catabolism
Anabolism
is the synthesis of complex molecules from simple molecules by a condensation reaction. These reactions require energy - building larger molecules
Catabolism
is the synthesis of simple molecules from complex molecules by a
hydrolysis reaction. These reactions release energy - breaking down large molecules
anabolic process
Protein synthesis using ribosomes
DNA synthesis during replication
Synthesis of complex carbohydrates such as starch, cellulose and glycogen
Catabolic processes
Digestion of food in the mouth, stomach and small intestines
Digestion of complex carbon compounds in dread organic matter by decomposers
Monomer-the smallest unit, a single molecule
A single amino acid
A fatty acid or glycerol-smallest component of a lipid
Monosaccharide-one molecule of carbohydrate
Dimer-two monomers joined together
Dipeptide-two protein molecules
Disaccharide-two molecules of carbohydrates-maltose
Triglyceride-three fatty acids and a glycerol molecule
Polymer-many monomers joined together-sometimes with other molecules
Polysaccharide-ie starch
Polypeptide-protein ie haemoglobin
Lipids-ie phospholipid bilayer
Covalent bonding
is a chemical bond that involves the sharing of electrons to form electron pairs between atoms.
Ionic bonding
is a strong electrostatic force of attraction between these oppositely charged ions
Hydrogen bonding
Where electrons are not evenly distributed leading to areas of negative charge - a negatively polarised area of one molecule attracts a positively charged area of another forming a electrostatic bond that is weaker than the other two bonds
Hydrogen bonding explained
The negative charge of the oxygen atom attracts the positive charge of the hydrogen atom.
This creates an electrostatic attraction which is a weak bond
Condensation
A condensation reaction joins two molecules together with the formation of a chemical bond and involves the elimination of a molecule of water.
Hydrolysis
A hydrolysis reaction breaks a chemical bond between two molecules and involves the use of a water molecule.
Monomers to polymers and back to monomers
Each time a monomer is attached it forms a water molecule so water is released – just like when we breath out on a cold day and we breath out water vapour. This is Condensation
The opposite reaction is the addition of water to break down polymers into monomers so a water molecule is used – the is hydrolysis = water splitting in Latin.
Monosaccharides
Glucose (C6H12O6) is a common monosaccharide and an important source of energy.
Other monomers on interest are galactose and fructose
Isomeric monosaccharides
Glucose has two isomers – alpha and beta glucose which has the OH group in a different place which means that polysaccharides made from beta glucose form straight polymers such as cellulose unlike glycogen and starch which form from alpha glucose which is curved.
Disaccharides to polysaccharides
Many monosaccharides can be joined together to make polysaccharides by condensation reactions.
The glucose monomers are joined by 1-4 glyosidic bonds and 1-6 glyosidic bonds
The application of this in the body - Enzymes
During digestion salivary amylase hydrolyses starch (polysaccharide) into maltose (disaccharide)
Salivary amylase is denatured by stomach acid
Pancreatic amylase in added to the intestines after the stomach which continues hydrolysis of starch to maltose
The membrane bound disaccharidases found in the lining of the ilium hydrolyse maltose into alpha glucose for absorption
Lipids
Lipids are insoluble in water
They contain carbon, hydrogen and oxygen.
The two main types for us are triglycerides and phospholipids
Roles of lipids in the body
Phospholipids
Found in cell membranes and membranes around organelles, they provide flexibility and transfer of lipid soluble substances across the membrane.
Energy
Lipids contain more energy for the same mass as carbohydrate and release water when oxidised. Stored in adipocytes
Insulation
slow conductors of heat so storage under the skin helps retain body heat and provide electrical insulation as myelin.
Protection
fat is stored around the body to provide additional protection
Triglycerides
A group of three fatty acids (tri) combined with glycerol (glyceride).
Each fatty acids forms an ester bond with glycerol in a condensation reaction and three molecules of water.
Hydrolysis of a triglyceride produces glycerol and three fatty acids and requires three water molecules.
Differences in molecules come from the range of fatty acids that get attached to the glycerol (over 70 different types can be combined)
Structure and function of triglycerides
Triglycerides have a high ratio of energy storing carbon and hydrogen bonds and so are a richer source of energy than glycogen.
They have a low mass to energy ratio so many can be stored in a small volume as it reduce the mass that needs to be carried as a food source.
They are insoluble and non polar so their storage doesn’t effect osmosis in cells unlike glucose which needs to be stored as glycogen or starch
They have a high ratio of hydrogen to oxygen atoms and release water for when oxidised so provide an important source of water.
Phospholipids
Phospholipids are really important molecules in your body because all of your cell membranes and some of the organelles are made of them!
They are made of one molecule of glycerol, two fatty acid chains and one phosphate molecule – hence the name.
Fatty acid chains are hydrophobic. Phosphate molecules are hydrophilic. In water they orientate into a layer facing towards and away from the water.
Phospholipids in the cell membrane
The hydrophobic and hydrophilic properties of the lipids mean that they orientate to create a bilayer in an aqueous solution.
This is our cell membrane, the micelles (that you will look at in digestion) and our lysosomes and endosomes as well as other sub cellular structures.
Phospholipids
The heads will face towards water and tails away from water so will form a bilayer in an aqueous environment
The head is also negatively charged and the tail is neutral so this creates an electrochemical barrier to ionic material entering the cell. They are polar molecules
Some phospholipids are made of two different fatty acid chains. The ‘kink’ caused by the unsaturated fatty acid chain prevents packing too closely together so helps the cell membrane remain fluid.
Protein monomers
Amino acids are the monomers that make up polymers of proteins – polypeptides - which in turn can be combined to form proteins.
There are 20 amino acids that occur in all living organisms and they have the same basic structure with a single change (the R group) that makes them different. They contain nitrogen (N).
Of the 20 amino acids we cannot form all of them in our bodies so we must ingest the 9 essential ones from food sources.
Structure of an amino acid
Every amino acid has a central carbon atom (C) to which are attached four chemical groups:
Amino group (-NH2) the basic group where amino part of the name comes from.
Carboxyl group (-COOH) an acidic group which gives the acid part of the name.
A Hydrogen atom (H)
R (side ) group - each one has a different R group and the 20 naturally occurring ones all have a different side group but are otherwise identical.
Bonding monomers
Just like carbohydrates – condensation and hydrolysis can bond and split protein monomers
The combination is from an OH group on one amino acid and the –H from the other amino acid (H20). They then form a peptide bond from the carbon atom of one and the nitrogen atom from the other.
Proteins and structures
Proteins form together into polypeptides through a series of condensation reactions and this is the primary structure of the protein.
The primary structure determines its three dimensional shape and therefore its function and change in the amino acid sequence can change the shape which means the protein cannot carry out its function.
Proteins have a primary, secondary, tertiary and quaternary structure – this is quite complex but essential to understand so stick with it.
Primary structure
The primary structure of the protein is the amino acids that make it up.
These are joined by peptide bonds
This is the structure as it is assembled by the ribosome
Secondary structure
As we saw with water molecules the hydrogen on the NH bond has a slightly positive charge and the oxygen in the –C=H has an slightly negative charge.
These hydrogen bonds cause the polypeptide to twist into a 3d shape such as the alpha helix or beta sheets where the chains becomes folded.
Tertiary structure
The alpha-helices of the secondary protein structure can be twisted and folded again into specific 3d shapes which form the tertiary structure which is held together through an range of additional bonds and areas that are hydrophilic and hydrophobic.
Disulphide bridges – are strong so not easily broken between amino acids
Ionic bonds – formed between the carboxyl and amino groups, less strong so can be broken by pH changes
Hydrogen bonds – numerous and easily broken
Quaternary structure
Large molecules can often form complex polypeptides with non protein structures such as the iron contain haem group where the globin protein complex shape also include the haem group.
The primary structure always determines that 3d shape
Bonding and final shape
In the initial order of the amino acids some will be positive charged, some negative, some hydrophilic, some hydrophobic, some that will create hydrogen bonds, others disulphide bonds and so on.
So to get the desired 3D shape of the final protein the order of the amino acids must be correct.
Globular proteins
Enzymes and hormones are usually ‘globular’ proteins, meaning they are more or less spherical, or globe- shaped such as haemoglobin.
Globular proteins that are water soluble have hydrophilic R groups on the outside and those that are not have Hydrophobic R groups on the outside.
Denaturalisation of proteins
Most bonds that hold the 3d shape are fairly weak and can be broken by heat or changes in pH. Heat and pH can break the bonds causing an unravelling of the 3d shape so the protein no longer functions as it is the wrong shape.
Denaturalisation
Denaturing means changing shape from the original structure and it is not reversible which is why egg white doesn’t become clear again as the cooked egg cools.
Creating proteins
Two key processes:
Transcription
Translation
Transcription
A copy is made of the genetic code of the DNA inside the nucleus
Translation
The code is translated from DNA instructions into an amino acid sequence by the ribosome.
Functions of proteins in the body
.Enzymes catalysis reactions – pepsin for example
• Actin and myosin cause muscle contraction
• Cytoskeleton of cells – tubulin and microtubules
• Fibrous proteins give strength – collagen, tendons, ligaments • Blood clotting – plasms proteins act as clotting factors
• Transport of oxygen and carbon dioxide via haemoglobin • Cell adhesion – membranes proteins linking to other cells
• Membrane transport channels and pumps
• Hormones and receptors on cell membranes
• Packing of DNA around histones
