Biological Molecules Flashcards
Describe the structure of a water molecule
- One oxygen atom and 2 hydrogen atoms
- Polar molecule, contains a positive and negative charge
- Oxygen atom is delta negative, hydrogen atoms are delta positive
How are hydrogen bonds formed in water?
An oxygen atom from one water molecule bonds with the hydrogen atom of another water molecule, quite a lot of energy is required to break hydrogen bonds so water has a high specific heat capacity making water a stable habitat
What are the main properties of water?
- High specific heat capacity (thermal stability) - provides a stable environment for aquatic organisms
- Forms a liquid - transport medium in animals and plants
- Ice has a low density - ice floats on water, insulating the water below
- High surface tension - small animals can move across the surface of the water
- Water is cohesive - water molecules form a strong water column that moves up the xylem in plants
- Transparent - allows aquatic plants to photosynthesise
- Assists with metabolism, breaks bonds in hydrolysis reactions and makes bonds in condensation reactions (overall process is called metabolism)
- Water is a solvent meaning chemicals can dissolve in it and take place in reactions in the cytoplasm
What is a monomer?
A single molecule
What is a polymer?
A chain of monomers bonded together, monomers bond together through a condensation reaction - a covalent bond forms between two adjacent monomers and a molecule of water is produced
What happens during a condensation reaction?
A covalent bond forms between adjacent monomers by removing the OH molecule from one monomer and the H molecule from the other monomer, this forms a water molecule
What happens in a hydrolysis reaction?
A covalent bond between two monomers is broken by the addition of a water molecule, OH is added to one monomer and H is added to another
What are the monosaccharides that make up maltose?
Glucose + glucose
What are the monosaccharides that make up Sucrose?
Glucose + fructose
What are the monosaccharides that make up Lactose?
Glucose + galactose
Which bond joins two monosaccharides to form disaccharides?
- A glycosidic bond joins two monosaccharides together and a water molecule is formed, the same mechanism is used to add a monosaccharide onto a polysaccharide
- In maltose, a 1-4 glycosidic bond is formed, this is where a bond is formed between carbon 1 on one alpha glucose and carbon 4 on the other alpha glucose molecule
How are glycosidic bonds broken down?
A hydrolysis reaction takes place, the OH bonds to carbon 1 on one glucose and the H bonds to carbon 4 on the other glucose
What is starch composed of?
- 2 polysaccharides: amylopectin and amylose, amylose has a coiled structure and amylopectin has a branched structure with few long branches
- Amylopectin and amylose are both alpha glucose monomers
What is starch?
An energy storage molecule found in plants, it is the source of carbohydrates our food
What is glycogen?
- An energy storage molecule found in animals and people, any excess glucose in our diet is stored as glycogen in the liver and muscles. When glucose levels are low, glycogen is converted back into glucose
- Glycogen has a branched structure with any short branches
- Made of alpha glucose monomers, has a similar structure to amylopectin
What is cellulose?
- A molecule that is found in the cell walls of plant cells, it gives structure and support
- Made of beta glucose monomers
- Hydrogen bonds form between glucose molecules on adjacent cellulose chains to give strength to the whole structure
- Hydrogen bonds also form between beta glucose molecules in the same chain to stop the chain from spiralling and to give it additional strength
What are the properties and functions of starch?
- Energy store in plants
- Insoluble
- Doesn’t affect water potential of the plant
- Branches can be easily broken so glucose can be used in respiration (it is oxidised in respiration to release energy)
What are the properties and functions of glycogen?
- Energy store in humans and animals
- Insoluble
- Doesn’t affect the water potential of the animal cell
- Branches can be easily broken so that glucose can be used in respiration
What are the properties and functions of cellulose?
- Structural carbohydrate in plant cell walls
- Gives strength to cell walls (due to hydrogen bonds between different cellulose chains)
What is a triglyceride?
A type of lipid that is an energy source, digested in our small intestines into fatty acids and glycerol
If a fatty acid chain contains a double bond, is it saturated or unsaturated?
Unsaturated, saturated fatty acids are more compact due to the absence of any double bonds
How are triglycerides synthesised?
Fatty acids and glycerol are added together, 3 ester bonds form between the fatty acids and glycerol in a condensation reaction where 3 water molecules are produced
What are the main properties of lipids?
- Large organic molecules
- Non-polar
- Insoluble in water
- Soluble in alcohol
What are the main uses of lipids/triglycerides?
- Energy source, used in respiration to produce ATP
- Energy storage, mammals store triglycerides in adipose tissue. The triglycerides can be used later on as an energy source
- Protection, body organs are surrounded by fats which protects them from damage during sudden movement
- Insulation, animals that live in cold climates have a layer of adipose tissue called ‘blubber’ that insulates them from the cold
- Buoyancy, Animals use their blubber to help keep them afloat, they float because triglycerides are less dense than water
What is the main use of cholesterol?
Cholesterol adds stability to the plasma membrane, animals in colder regions have more cholesterol in their membranes to prevent them from freezing
What are the main uses of steroids?
Steroids are hormones such as oestrogen and testosterone, they are large but can cross the plasma membrane easily as they’re non-polar
What are the main uses of phospholipids?
Phospholipids are the main component of the plasma membrane, they form a bilayer because the phosphate head is hydrophilic and attracts water and the fatty acid tail is hydrophobic and repels water. The phospholipid bilayer is a partially permeable membrane as it only allows small or non-polar molecules into the cell
What are amino acids?
Molecules that make up proteins, there are 20 different amino acids that make up amino proteins and they all have a similar structure
What are amino acids made up of?
Oxygen, nitrogen, carbon and hydrogen, some also contain sulfur
What do two amino acids joined together by a peptide bond form?
A dipeptide, many amino acids join together to form a polypeptide which can then fold into a protein, a peptide bond is formed after a condensation reaction takes place. A condensation reaction happens when the OH from the carboxyl group on the first amino acid and a hydrogen from the amine group on the second amino acid are removed, forming a water molecule, a peptide bond forms between the carboxyl and amine groups, the amino acids are now a dipeptide, this is a condensation reaction
How can a peptide bond be broken?
By the addition of a water molecule, the OH is added to the carboxyl group of the first amino acid and the hydrogen is added to the amine group on the second amino acid, this is a hydrolysis reaction
Which bonds are formed between these molecules?
Glucose, Lipids, Protein
Glucose - glycosidic bond
Lipid - ester bond
Protein - peptide bond
What is the primary structure of a protein?
A chain of amino acids all joined together by peptide bonds, each protein is different because the amino acid sequence is different in each polypeptide
What determines how a polypeptide will fold?
The properties of each amino acid in the sequence, some amino acids are polar and some are non-polar some are negatively or positively charged, they all vary in size
Which two structures can a polypeptide chain fold into?
- An alpha helix or a beta pleated sheet
- An alpha helix is a coiled structure with 36 amino acids per turn of the helix, the alpha helix is held together by hydrogen bonds between the NH of one amino acid and the CO of another amino acids 4 places ahead of it in the chain
- A beta pleated sheet is a zig zag structure, when a chain folds over itself it forms a beta pleated sheet, hydorgen bonds form between the NH on one amino acid and the CO on another amino acid further down the chain
What is the tertiary structure of a protein?
A 3d structure that is formed when alpha helices, beta pleated sheets and areas of straight chains of amino acids fold together. The tertiary structure contains one polypeptide chain, tertiary structure consists of secondary structures such as alpha helices and beta pleated sheets, it can consist of both as chains can fold into both alpha helices and beta pleated sheets. These are connected by turns in the chains
Which bonds hold together a protein’s tertiary structure?
Ionic bonds, hydrogen bonds, disulphide bridges (only cysteine amino acids can form disulfide bridges) and hydrophilic and hydrophobic interactions, hydrophobic portions are in the centre of the protein and the hydrophilic portions are on the outside
What is the quaternary structure of a protein?
- Made up of multiple polypeptide chains in their tertiary structure that are held together by the same bonds that hold together the tertiary structure of a protein
Describe the structure of collagen
Collagen has three polypeptide chains that are all wound around each other to form a triple helix, this triple helix is held together by hydrogen bonds
How are collagen fibrils formed?
Cross-links are formed between adjacent triple helices to form collagen fibrils, the cross-links are covalent bonds
How is collagen fibre formed?
Many collagen fibrils are joined together by cross-links (covalent bonds) to form a collagen fibre
Are fibrous proteins soluble?
No, they are insoluble
What are the main properties of collagen?
- They are mechanically strong
- Part of bones, cartilage, tendon and connective tissue
- Allow blood vessels to withstand high pressure
- Insoluble
What are the main properties of keratin?
- Many disulfide bridges
- Hard and strong
- Part of fingernails, hair, horns, hooves and feathers
- Insoluble
What are the main properties of elastin?
- Elastic
- Part of skin, lungs, blood vessels and bladder
- Allows structures to stretch and recoil
- Insoluble
What are cross-links?
Covalent bonds
What is the role of haemoglobin?
In the lungs, each haem group of each haemoglobin molecule attaches to one oxygen molecule, the haemoglobin then transports the oxygen to cells in the body by carrying it in the blood
Does haemoglobin have a quaternary structure?
Yes, it is made up of four polypeptide chains
Why is haemoglobin a conjugated protein?
It contains a prosthetic group (the haem group), the haem group is not made up of amino acids, therefore, it’s not a protein. It also contains an iron ion (Fe^2+)
Give some examples of globular proteins
Enzymes such as pepsin, hormones such as insulin
What are the main properties of globular proteins
- They are soluble due to their polar, hydrophilic amino acids that are on their outside surface.
- Easily transported into cells and can move easily in the cytoplasm of the cell
How does haemoglobin’s structure aid its function?
It has polar, hydrophilic amino acids on its outside surface meaning it’s soluble in red blood cell/erythrocyte cytoplasm so it can carry oxygen in the blood
What is a disaccharide?
2 monosaccharides joined together by a glycosidic bond
What is the molecular formula of glucose?
C6H12O6
What is the molecular formula of ribose?
C5H10O5
What is the molecular formula of deoxyribose?
C5H10O4
On alpha glucose, is the OH on the first carbon above the carbon or below the carbon?
Below the carbon
On beta glucose is the OH on the first carbon below or above the carbon?
Above the carbon
What is a 1-4 glycosidic bond?
Where the hydroxyl group on carbon 1 and carbon 4 line up and a condensation reaction takes place, a water molecule is produced and a glycosidic bond is formed. Carbon 1 and 4 on adjacent glucose molecules are linked by an oxygen molecule, this is a glycosidic bond
How is a glycosidic bond broken?
By adding a water molecule to the bond, this hydrolyses the bond
How is glucose a source of energy?
It is used in respiration to synthesise ATP, this ATP can then be hydrolysed to release energy for active processes in the cells
Which polysaccharides are found in plants?
Amylose and amylopectin
Which polysaccharides are found in humans?
Glycogen
What are the monomers for glycogen, amylopectin and amylose?
alpha-Glucose
Which polysaccharides are branched?
Amylopectin and glycogen
Describe the structure of amylose
Amylose coils into a spiral shape, forming glycosidic bonds between carbons 1 and 4 on different glucose monomers. The hydroxyl groups on carbon 2 face inwards which reduces solubility and allows hydrogen bonds to form between glucose monomers which holds the structure together
Describe the structure of amylopectin
- Amylopectin has 1-4 glycosidic bonds and also coils into a spiral shape with hydroxyl groups on the 2nd carbon facing inwards to reduce solubility, hydrogen bonds are formed between glucose monomers which holds the structure together
- Amylopectin forms branches by forming 1-6 glycosidic bonds between separate glucose monomers on separate chains
- The branches have 1-4 glycosidic bonds between glucose monomers within the branch, 1-6 glycosidic bonds are only between one glucose monomer on one branch and another glucose monomer on another branch
Describe the structure of glycogen
- The structure of glucose is very similar to the structure of amylopectin
- Glycogen has more branches than amylopectin which makes it more compact
- Glycogen is a smaller molecule meaning it has less tendency to spiral
- It is easier to remove monomer units as there are more ends
Where is amylopectin and amylose stored?
In starch granules in cells
Describe the structure of cellulose
- Cellulose makes up the cell walls in plants, it is made up of beta-Glucose monomers
- It forms 1-4 glycosidic bonds between monomers but every other glucose molecule is flipped as the hydroxyl groups on the first carbon in beta glucose don’t align when next to each other, this is why they have to be flipped, so they can form a glycosidic bond
- Hydrogen bonding occurs between glucose monomers in a chain as adjacent monomers are flipped 180º, this helps keep give the chain additional strength and also prevents the chain from spiralling
- Hydrogen bonds are formed between different chains, this gives the overall structure additional strength. These bonds will primarily be formed between the delta positive hydrogen from the OH group on carbon 2 as the hydroxyl group sticks out and the oxygen in the glycosidic bond between two glucose monomers
How many cellulose chains have to from hydrogen bonds between each other to form a microfibril?
Around 60-70 cellulose chains have to form hydrogen bonds between chains to form a microfibril
How many microfibrils have to bundle together to form a macrofibril?
Around 400
How does the structure of plant cell walls assist their function?
- Macrofibrils and microfibrils have very tensile strength, because of the strength of the glycosidic bonds and also the hydrogen bonds within each chain between rotated beta-glucose molecules and also because of the hydrogen bonds between chains
- Macrofibrils run in all directions, criss crossing the wall fro extra strength
- Cellulose is difficult to digest, animals don’t even have an enzyme to break it down
- Each cell needs to support the plant because plants don’t have a rigid skeleton, cellulose in the cell wall makes each cell stronger so it can support the cell
- There is space between macrofibrils meaning that mineral ions and water can pass through the cell wall when they need to, this means the cell wall is fully permeable
- The high tensile strength prevents the cell from bursting when turgid and the cell wall also protects the cell membrane
- Macrofibril structure can be reinforced by other substances such as cutin and suberin, this makes the cell wall waterproof
- In the tree trunks, cell walls are extra thick to withstand the weight
What is a bacterial cell wall made out of?
Peptidoglycan
What are insect and crustacean exoskeletons made out of?
Chitin
What is a fungal cell wall made up of?
Chitin
How does chitin’s structure differ to cellulose’s?
It has a NHCOCH3 group in place of the OH group on carbon 2
How does chitin increases the strength of its structure?
It forms cross-links between long parallel chains of acetylglucosamine, in a similar way to cellulose
How does a disulfide linkage form?
It forms between the R groups of two cysteine amino acids in a polypeptide chain, two SH molecules join together to form an S-S bond
What is the structural formula of glycerol?
CH2OHCHOHCH2OH
How is a fatty acid structured?
It has a carboxyl group on one end of the molecule, the rest of a molecule is an alkyl chain, if the alkyl chain contains a C=C bond then it is an unsaturated fatty acid, if it doesn’t then it’s a saturated fatty acid
Which type of bond forms between a fatty acid and glycerol?
An ester bond, the OH from the carboxyl group on each fatty acid molecule and the oxygen from the Oh group on each carbon of the glycerol molecule are removed to form a water molecule, 3 ester bonds are formed, one between each fatty acid and each carbon atom on the glycerol molecule. Each ester bond has an oxygen linking the 2 molecules.
What is the structure of the phosphate group in a phospholipid?
P(OH)3O
What is the structure of a phospholipid in comparison to a triglyceride?
It is the same except it has a phosphate group (P(OH)3O) in place of one of the fatty acid tails
Which part of the phospholipid molecule is polar and which part is non-polar
The phosphate group which is the head of the molecule is polar (hydrophilic) and the fatty acid tail is non-polar (hydrophobic)
What is cholesterol?
- A steroid alcohol, a type of lipid that is not made out of glycerol and fatty acids
- Cholesterol is a non-polar molecule meaning it can sit in the centre of the hydrophobic part of the bilayer and
- Cholesterol regulates the fluidity of the membrane, preventing it from becoming too fluid of too stiff
What type of molecules can pass through the phospholipid bilayer?
Non-polar and small molecules
Which type of bond is formed between two amino acids?
Peptide bond
How is a peptide bond broken?
By adding water to the C-N bond, this breaks the bond and forms two separate amino acids. An OH is added to the carbon and an H is added to the N. This is a hydrolysis reaction
How is a peptide bond formed?
Two amino acids are added together, a condensation reaction occurs between the OH from the carboxylic acid group and the H from the amine group, this forms a peptide bond between the two amino acids
What makes beta pleated sheets and alpha helices stable structures at optimal temperature and pH?
Many hydrogen bonds that are formed between NH groups and CO groups
How do ionic bonds form between amino acids?
Ionic bonds can form between carboxyl groups and amino groups that are part of R groups. The NH2 group ionises into NH3+ and the COOH ionises into COO-. The NH3+ group and the COO- group are strongly attracted to each other
How do hydrophobic and hydrophilic interactions affect the shape of the protein?
Hydrophobic regions of the R group associate in the centre of the polypeptide to avoid water and similarly hydrophilic regions are found towards the edge of the polypeptide. Hydrophobic and hydrophilic interactions cause twisting of the polypeptide chain which changes the shape of the protein
Are fibrous proteins hydrophobic or hydrophilic?
Hydrophobic as they have regular repetitive amino acid sequences
Why is being insoluble in water an advantage to a fibrous protein?
As fibrous proteins are required to form fibres, if they were insoluble they would be unable to carry out their function
How are globular proteins structured?
- They roll into an almost spherical shape, they have their hydrophobic R groups on the inside of the molecule and their hydrophilic R groups on the outside of the molecule, this makes globular proteins soluble in water
- They often have a very specific shape which enables them to act as enzymes, hormones and haemoglobin
Is collagen a fibrous or globular protein? Describe its function
- Collagen is a fibrous protein, its function is to provide mechanical strength
- In artery walls a layer of collagen is present to prevent the artery from bursting due to the high pressure blood being umped from the heart
- Tendons are made from collagen, tendons connect muscle to bone and enable muscle to pull on bone
- Bones are made of collagen and layered with calcium phosphate which reinforces them and makes bones hard
- Cartilage and connective tissue are also made out of collagen
Is keratin a fibrous or globular protein and what is its function?
- Keratin is a fibrous that is rich in cysteine, this means that is has many disulfide bridges between polypeptide chains (inter-molecular bonding) and also within the same polypeptide chain if it is folded (intra-molecular bonding)
- Keratin also has many hydrogen bonds between and within polypeptide chain
- Keratin is found wherever a body part needs to be hard and strong, it is found in nails, fur, horns, claws, hooves, feathers, hair and scales
- Keratin provides mechanical protection, an impermeable barrier to infection and also as it’s insoluble, a barrier to water-borne pollutants
Is elastin a fibrous or globular protein and what is its function?
- Elastin is a fibrous protein, it has many cross-links between chains and it also has a coiled structure which makes it able to stretch
- Elastin is a key component in skin, it enables skin to stretch around our bones and muscles
- Elastin is contained in our lungs to help them inflate and deflate and also in our bladder to help it expand to contain urine
- Elastin is also contained in blood vessels to help them stretch and recoil as blood is pumped through them, this helps maintain the pressure of the blood
Describe the structure of haemoglobin
- The quaternary structure of haemoglobin is comprised of 4 polypeptide chains, 2 alpha globin chains and 2 beta globin chains
- Each polypeptide chain has its own tertiary structure but when these polypeptide chains are fitted together, they form one haemoglobin molecule, the quaternary structure of haemoglobin is held together by hydrogen bonds, disulphide bridges and ionic bonds
- On each chain is a haem group, a haem group is a prosthetic group which is a cofactor that is covalently bonded to a protein molecule
- The haem group contains an Fe2+ ion that carries oxygen
- A protein that contains a prosthetic group is known as a conjugated protein
- Haemoglobin’s function is to carry oxygen from the lungs to the tissues, an oxygen molecule (O2) binds to the iron in the haem group, when the oxygen molecule binds, the haemoglobin turns from purple red to bright red. The oxygen is released when it reaches the tissues
Can a polypeptide chain fold into both beta-pleated sheets as well as alpha-helices in the same polypeptide chain?
Yes, the alpha helices and beta pleated sheets are connected by turns in the polypeptide chain
Is insulin a fibrous or globular protein? Describe its structure
- Insulin is a globular protein, the A chain starts with an alpha helix and the B chain ends with a beta-pleated sheet
- Both chains fold into their tertiary structure and their tertiary structures are then joined together by disulphide bridges. Amino acids with hydrophilic R groups are on the outside of the molecule, this makes it soluble in water. Insulin binds to glycoprotein receptors on the outside of muscle and fat cells, this increases their uptake of glucose from the blood and increases their consumption rate of glucose for processes such as respiration.
Is pepsin a fibrous or globular protein?
- A globular protein, pepsin is an enzyme that digests protein in the stomach, pepsin is made up of a single amino acid chain containing 327 amino acids, it folds into a symmetrical tertiary structure
- Pepsin has very few amino acids with R groups that can act as bases (NH2) and many R groups that can act as acids (COOH), this is why it is very stable in the acidic conditions as there are few basic R groups to accept H+ ions and therefore, the acidic conditions have very little affect on the structure of the enzyme
- The tertiary structure of pepsin is held together by hydrogen bonds and two disulfide bridges
What is AB initio protein modelling?
- A model is built based on the physical and electrical properties of the atoms in each amino acid in the sequence, with this method there can be multiple solutions to the same amino acid sequence
What is comparative protein modelling?
The amino acid sequence is scanned against a database of solved structures and produces a set of possible models that would match the sequence
