1. 1. Chemical elements are joined together to form biological compounds Flashcards
carbs contain 3 elements
carbon
hydrogen
oxygen
monosaccharide
The simplest sugars, consist of a single monomer
General formula (CH2O)n
All carbohydrates contain the elements carbon, hydrogen and oxygen.
two isomers of glucose (a monosaccharide)
1. alpha
two isomers of glucose (a monosaccharide)
2. beta
difference of hydroxyl group alpha vs beta glucose
difference of hydroxyl group alpha vs beta glucose
The only difference in the alpha (α) and beta (β) ring isomers is the position of the OH group on carbon atom 1.
To remember which ring form is which, use ABBA:
Alpha OH Below – Beta OH Above
glucose
Glucose is a polar molecule – hydrogen bonds can form between the Oδ- on C2 of one glucose molecule and C3δ+ of the next glucose molecule in the chain. As a result, the amylose molecule coils up to form a helix.
This makes starch a compact molecule that is less soluble in water - an ideal properties for storage of glucose.
Also, because starch is insoluble it does not affect the water potential of the cell in which it is stored. This means that starch is osmotically stable.
alpha glucose function
function
- energy storage (found in starch)
- energy source (easily broken down in cellular respiration, providing ATP)
beta glucose function
function
-structural component in plants, found in cellulose, beta links create long, straight chains which are rigid
-fiber in diet, in cellulose, aids digestion
EDITTTT glucose in nature
36% α glucose
-more reactive as more hydroxyl groups on bottom
-delta charge on O and H
-charge is unevely distributed on molecule
64% β glucose
classification of monosaccharides
3 carbons Triose
5 carbons, pentose eg ribose, deoxyribose
6 carbons, hexose eg glucose
eg of monosaccharide
glucose
fructose
galactose
structural isomers
Molecules with the same molecular formula but with different arrangements of their atoms are called structural isomers.
fructose vs glucose vs galactose
- Glucose: The -OH group on carbon 4 is on the right side in the Fischer projection.
- Galactose: The -OH group on carbon 4 is on the left side in the Fischer projection.
all types of carbs diagram
glycosidic bonds
And their roles
type of covalent bond, forms between two monosaccharides,
formed by condensation
two types
-Alpha Glycosidic Bond
- Beta Glycosidic Bond
roles
-allow molecules to store energy efficiently
-create rigid structures, essential for plant cell walls
-breakdown via hydrolysis releases monosaccharides, used for energy production in cellular respiration
naming glycosidic bonds
glucose
fructose
galactose
isomers
C6H12O6
same molecular formula
different structural formula
disaccharide
class of carbohydrates made up of two monosaccharide subunits
general molecular formula is C 12 H 22 O 11 .
formed by a condensation reaction (i.e., loss of water)
The bond that holds them together is called a glycosidic bond.
hydrolysis reaction.
The glycosidic bond can be broken by the chemical insertion of water – this reforms the OH groups and is called a hydrolysis reaction.
eg of disaccharide
sucrose = α glucose + fructose
maltose = α glucose + α glucose
lactose = α or β glucose + galactose
condensastion reaction of two monosaccharides
condensation reaction of two molecules of alpha glucose
polysaccharide
Polysaccharides are complex carbohydrates. They are large molecules, or polymers, consisting of chains of monosaccharides linked together by glycosidic bonds.
formed by condensation reactions, to form chains
2 functions of polysaccharides
Some polysaccharides have metabolic functions and others have structural functions in cells and organisms.
metabolic eg starch (plants) and glycogen (animals) made of a-glucose
function of polysaccharides
energy storage (starch in plants, glycogen in animals)
structural (cellulose) (chitin)n
oligosaccharides
short chain polysaccharides
3-10 monosacharide residues
eg of polysaccharide
Starch
glycogen
cellulose
heparin
peptidoglycan
starch
consists of polymers:
amylose
-polymer of α glucose, linked by 1,4 glycosidic bonds
-unbranched helical molecule
-most -OH groups are capable of forming H bonds with H2O in aqueous environments
-forms coiled molecules
amylopectin
- the bonds between glucose molecules within a branch are α-1,4 glycosidic bonds but at branching points, the bonds are α-1,6 glycosidic bonds.
-gives more ends to hydrolyse, enables faster metabolic rate
glycogen
has side branches
glycosidic bonds forming between OH groups on C1 and C4 but also C1 and C6. Glycogen can form granules in cells and act as a carbohydrate/energy store.
supports higher metabolic rate of animals (as more ends avaliable to hydrolyse)
branches in amylopectin and glycogen
make them better for the release of glucose. This is because there are more ‘ends’ where glycosidic bonds can be hydrolysed and glucose released, which can be used in respiration to produce ATP.
cellulose
ellulose is a complex carbohydrate made of a polymer of β-glucose molecules. The β-1,4 glycosidic linkages result in the −CH2OH groups being on opposite sides of the chain of adjacent glucose molecules.
Within a cellulose chain, adjacent glucose molecules are rotated 180° relative to each other. This means that OH groups are aligned and a water molecule can be removed to form a glycosidic bond.
Therefore, hydrogen bonds do not form between glucose molecules within the same chain, but between glucose molecules in different chains.
The hydrogen bonds form cross-linkages which hold the chains together. This makes cellulose form into long threads called microfibrils.
Cellulose is completely insoluble and the microfibrils are laid down in overlapping layers in plant cell walls.
most abundant structural polysaccharide in plant cell walls
distribution of hydroxyl groups, means cross links between cellulose molecules can occur, procides support and strength
hydrogen bonds form between adjacent -OH groups on cellulose molecules
cellulose is what type of polysaccharide
Cellulose is called a structural polysaccharide. It is very difficult to digest because of the very high numbers of hydrogen bonds between the chains of beta glucose. This also gives cellulose very high tensile strength; it is difficult to break when stretched. This means that cells with cellulose in their cell wall are more resistant to osmotic lysis (they are not likely to burst because cellulose stops too much water entering the cell).
chitin
amino acid side chains
used for exoskeletons
Chitin is found in the cell walls of fungi and in the exoskeletons of insects. It is not a true polysaccharide as it contains the element nitrogen – it is called a heteropolysaccharide.
It has a similar structure and function as cellulose but because it contains side groups containing N, more hydrogen bonds can form. Chitin microfibrils, therefore, have greater tensile strength than those of cellulose.
The diagram shows two of the monosaccharides (N-acetyl glucosamine) found in chitin joined together by a β-glycosidic bond.
why is cellulose less reactive than other polysaccharides
due to hydrigen bonds and cross linking between chains
hydroxyl groups on adjacent cellulose molecules form hydrogen bonds
strong cross links between cellulose fibers makes structure rigid
lignin
polymer of sugar and amino acids
deposited between cellulose molecules to lignify tissue
macromolecules
giant molecules
some are polymers
labelled lipid
triglyceride
three condensation reactions, forming ester bonds
Triglycerides have key roles in respiration and energy storage due to its insolubility and high carbon to hydrogen ratio.
lipids
Lipids are organic compounds made of carbon, hydrogen and oxygen. All lipids contain a high proportion of CH2 groups. Phospholipids also contain phosphorus.
All lipids have a low solubility in water but a high solubility in organic solvents (e.g., ethanol, tetrachloromethane).
long term store of energy (high energy density 9kcal per gram, hydrophobic, stored compactly)
not polymers
made of glycerol and fatty acids
too small to be macromolecules
Triglycerides
molecules that form fats or oils depending on the size of the molecule. The more carbon atoms, the higher the melting point because the intermolecular forces are stronger and more energy is required to overcome them.
Each triglyceride is made from glycerol combined with three fatty acids through a condensation reaction with the release of three molecules of water.
The fatty acids bind to the glycerol by means of ester bonds.
Triglycerides are broken down in a hydrolysis reaction with the chemical insertion of three molecules of water.
The diagram shows how triglycerides are formed and are broken down.
fatty acids diagram
R group can be saturated or unsaturated
glycerol diagram
condensation glycérol and fatty acids
phospholipid
hydrophillic head - allows exchange of substances between cell and environment
hydrophobic tail
fat and water soluble, can form lipid bilayer, crucial for role in cell membranes
function of a phospholipid
The different properties of the phosphate heads and the fatty acids affect how easily different molecules can cross a cell membrane (see Unit 1.3: Cell membranes and transport).
If phospholipids are poured into water, the molecules arrange themselves in a single layer. But in cell membranes, phospholipids form a bilayer.
The hydrophilic phosphate groups are attracted to water molecules in the cytoplasm and outside the cell.
The hydrophobic tails are repelled by water molecules and ‘hide’ from water in the cytoplasm and outside the cell.
what affects fluidity of membrane
The different properties of the phosphate heads and the fatty acids affect how easily different molecules can cross a cell membrane (see Unit 1.3: Cell membranes and transport).
If phospholipids are poured into water, the molecules arrange themselves in a single layer. But in cell membranes, phospholipids form a bilayer.
The hydrophilic phosphate groups are attracted to water molecules in the cytoplasm and outside the cell.
The hydrophobic tails are repelled by water molecules and ‘hide’ from water in the cytoplasm and outside the cell.
difference between phospholipid and triglyceride
triglyceride - 3 fatty acids, and no phosphate
phospholipid - 2 fatty acids and a phosphate group
elements in aminoacids
N
C
H
O
amino acids
essential - obtained in diet
non-essential - synthesised
zwitterion
condensation réaction of amino acids
condensation réaction of amino acids
hydrogen bonding
weak
ionic bonding
between R groups
disulphide bridge
amino acids oxidise to form disulphide bridge
hydrophobic interactions
non-covalent bonds
between water and hydrophobes
protein
Proteins are polymers made up of about 20 naturally occurring subunits called amino acids.
Each amino acid has a central carbon atom with four different functional groups attached:
the amino/-NH2 group, which has basic properties and can gain a H+ in acidic conditions to form an -NH3+group
the carboxylic acid/-COOH group, which has acidic properties and can lose a H+ in alkaline conditions to form a -COO- group
an atom of hydrogen, H
a variable group, R.
IMPORTANT: you don’t have to learn these but it’s useful to realise how the R group can change the property of an amino acid and protein.
A highly important R group is found in the amino acid cysteine where R = -CH2-SH2
The -SH group of one cysteine can form a covalent bond with the -SH group of another cysteine. This bond is called a disulfide bridge and plays an important role in maintaining the 3D structure of proteins.
primary structure of proteins
sequence of amino acids in a polypeptide chain determined by DNA coding
based on:
which amino acids are present
the number of each type of amino acid present
the sequence of amino acids in the polypeptide chain.
secondary structure of proteins
alpha
Secondary structure - interactions with peptide backbone forms beta pleated sheets and alpha helices
Alpha helices - have a helical structure, formed by hydrogen bonds between layers of the helix, creating a spiral shape (hydrogen bonds stabilise the helical structure)
Proteins with a secondary structure play important structural roles in organisms.
The alpha helix gives rise to fibrous proteins where several strands of alpha helices can be coiled together to give a rope-like arrangement. These are insoluble in water and have a structural function in organisms.
E.g., α-keratin in wool
collagen in skin and blood vessels.
Beta pleated sheets form layers of protein.
E.g., fibroin in silk.
secondary structure of proteins
beta
Beta pleated sheets are parallel or antiparallel depending on direction of polypeptide chain
secondary structure of proteins
Hydrogen bonds are crucial for the formations of secondary proteins
tertiary structure of proteins
Tertiary structure - influenced by interactions of the side chains, inc hydrophobic and hydrogen bonds
depends on the properties of the R groups.
inc
ionic
covalent
hydrogen
hydrophobic interactions
tertiary structure folding
The additional folding of the protein gives rise to a compact, globular, three-dimensional shape that makes the protein soluble in water – charged groups on the outside and hydrophobic groups on the inside. The tertiary structure gives globular proteins a specific 3D shape which gives the protein its function.
Many globular proteins have a metabolic function in organisms:
enzymes – active sites to bind to a substrate
antibodies – sites for binding to antigens
hormones – sites for binding to specific receptors.
label the bonds
ionic bonds
Ionic bonds are formed from charged variable groups and can interact with water, which helps a protein to dissolve.
covalent bonds in disulphide bridge
Covalent bonds are formed from variable groups containing sulfur atoms – two of these can bond together to form a disulfide bridge. As they are covalent bonds, disulfide bridges are strong and more difficult to break. A higher temperature or more extreme pH would be needed to break these bonds.
hydrogen bonds
Additional hydrogen bonds can also form between polar variable groups.
hydrophobic interactions
Hydrophobic interactions take place when the variable groups are non-polar. They are repelled by water and are usually found on the inside of the protein as far away from water as possible; a protein rich in non-polar side groups will be less soluble in water.
quarternary structure of proteins
Quaternary structure - involves arrangement of multiple polypeptide chains
These are fibrous proteins which have a structural role in the body.
polypeptide chains held together by:
-disulphide bridges eg insulin, haemoglobin
-hydrogen bonds eg collagen, silk These are fibrous proteins which have a structural role in the body.
denaturation of proteins
breaking down of weak bonds
covalend bonds between amino acids
hydrogen bonds
active site changes shape, interactions can’t occur
BUT peptide bonds not broken
secondary and tertiary structures not destoryed
primary structure destroyed - proteins can refold
renaturation of proteins
hydroken bonds reformed
if primary structure disrupted, can’t occur
factors affecting denaturation
change in pH
increase in temp
heavy metals
ionising radiation
carbs and triglycerides
long term energy store
Adenine Triphosphate
ATP captures chemical energy obtained from the breakdown of food molecules and releases it to fuel other cellular process
nucleotide of ATP
hydrolysis of ATP
breaks last covalent bond between phosphate groups
releases chemical energy
energy used for: active transport, muscle contraction, formation of large molecules
uses of ATP
muscle contraction
active transport
DNA replication
cell divison
nucleotide
nucleotide
polynucleotide
While ions are all charged, molecules can have:
no charge – non-polar
or a slight charge – polar.
ions, non-polar and polar behaviour
Ions and polar compounds attract oppositely charged particles and play important roles in the structure of molecules.
Non-polar compounds do not dissolve in water but will dissolve in lipids (fats/oils) – they are said to be lipid-soluble.
ions
Organic compounds
Organic compounds always contain the elements carbon and hydrogen, and many contain oxygen and/or nitrogen.
Inorganic compounds
also contain carbon, hydrogen, oxygen and nitrogen, but can be made without the involvement of living organisms.
water properties
Water is a polar molecule – it has no overall charge, but the hydrogen atoms have a partial positive charge and the oxygen atoms have a partial negative charge.
A water molecule is usually drawn using solid lines for the bonds between the hydrogen and oxygen atoms.
The partial charges are shown as δ+, delta positive and δ−, delta negative.
Because of their polarity, water molecules attract each other by forming hydrogen bonds. This is usually represented by a series of vertical lines as shown in the diagram.
water properties 2
water diagram
why is water known as a universal solvent
Because of their polarity, water molecules are attracted to other water molecules and charged particles. This helps charged particles dissolve in water.
For this reason, water is sometimes referred to as the universal solvent as a large number of substances can dissolve in water.
letter R
The carbon chain in fatty acids is often represented by the letter R, a variable group containing a chain of between 4 and 24 carbon atoms.
state of lipid at room temp
Lipids with long hydrocarbon chain fatty acids are more likely to be solid at room temperature – these are fats.
Those with short hydrocarbon chains form oils which are liquid at room temperature.
This is because there are weak forces of attraction between the fatty acid chains – the longer the carbon chain, the greater the force of attraction, so the higher the melting point. Some examples of different fatty acids and their melting points are shown below.
Functions of triglycerides
Triglycerides are efficient energy storage molecules. They are more efficient than carbohydrates:
1 g fat provides about 38 kJ energy
1 g carbohydrate provides about 17 kJ energy.
Because of this, fats and oils are the preferred energy storage molecule in animals and many seeds (lipids store twice as much energy per gram than carbohydrates).
Triglycerides are also good thermal insulators and provide mechanical protection for delicate organs.
Because fats are less dense than water, they are used to provide buoyancy for many aquatic animals.
Some animals spread oil onto their fur or feathers because this makes them waterproof. This is because fats are hydrophobic and repel water.
Saturated fatty acids
They can also be saturated, with only single bonds between carbon atoms. They contain the maximum number of hydrogen atoms.
Lipids containing only saturated fatty acids generally form fats at room temperature. This is because the fatty acid tails are straight and can pack closely together. Stronger forces of attraction can form which means more energy is needed to break the bonds and melt the fat – the melting point is higher.
Unsaturated fatty acids
Fatty acids can also be unsaturated, with one or more double bonds between carbon atoms.
They do not contain the maximum number of hydrogen atoms. For each carbon-carbon double bond, the fatty acid will contain two fewer hydrogen atoms.
Lipids containing unsaturated fatty acids are usually oils at room temperature.
The double bonds make the fatty acid tails less straight (they kink) so they cannot pack as closely together.
The forces of attraction between the fatty acids are weaker, so less energy is needed to break the bonds and melt the fat – they have a lower melting point.
A high intake of fat by humans, notably saturated fats, is a contributory factor in heart disease.
It raises the low-density lipoprotein (LDL) cholesterol level, which increases the incidence of atheromas in coronary arteries (and in other arteries).
This leads to blockages and eventually, heart disease.
POLYUNSATURATED FAT
An essential fat that we must get from food because our bodies cannot produce it. It lowers LDL (bad cholesterol). Found in: most cooking oils, pumpkin seeds, pine nuts, sesame seeds, fatty fish. Also known as: omega-3 and omega-6 fatty acids.
MONOUNSATURATED FAT
Considered a healthy fat: it lowers LDL (bad cholesterol) and maintains HDL (good cholesterol). Found in: olive oil, avocado and avocado oil, most nuts and nut butters.
SATURATED FAT
Increases total cholesterol and LDL (bad cholesterol). Best to consume in moderation. Found in: red meat, whole milk, cheese, coconut, butter, processed meat, many baked goods, and deep fried foods.
TRANS FAT
A by-product of processing healthier fats to give them a longer shelf life. Raises your LDL (bad cholesterol) and lowers your HDL (good cholesterol). Intake should be limited. Also known as: partially hydrogenated oil
Amino acids can polymerise through a condensation reaction to give
dipeptides and polypeptides.
linkage between 2 amino acids
The linkage between two amino acids is called the peptide bond. Peptide bonds form between the carboxyl group of one amino acid and the amino group of another.
two different dipeptides can be formed from two different amino acids
This means that the dipeptides can have different properties because of the arrangement of the amino acids on either side of the peptide bond.
how do different R groups affect amino acids
This can affect the charges on the amino acid and therefore the properties of the dipeptide. This is also shown in the diagram.
polypeptide
a series of peptide bonds holding amino acids together - form a chain
how does order of aminoacids affect molecule (polypeptide)
The sequence or order of amino acids in a polypeptide affects the organisation of the molecule as it is processed to form a functional protein.
