Biological Molecules Flashcards
How does hydrogen bonding occur
1) A molecule of water is one atom of oxygen covalently bonded with two atoms of hydrogen by shared electrons.
2) The shared negative hydrogen electrons are pulled towards the positive oxygen atom, each hydrogen is left with a slightly positive charge.
3) The unshared negative electrons on the oxgen atom give it a slightly negative charge
4) This creates a polar molecule (partial negative on one side and partial positive on the other)
5) The slightly negative charged oxygen atoms attract the slightly positively charged hydrogen atoms of other water molecule. This attraction is called hydrogen bonding.
What is the unit of ‘delta positive’ and ‘delta negative’
δ+ delta positive
δ- delta negative
Explain the function of water
Water is a reactant in many chemical reactions e.g hydrolysis reactions
Water is a solvent, many substances dissolve in it e.g ions in water in the bloodstream. Most biological reactions require a solution.
Water transport substances e.g glucose, mineral ions, oxygen gas
Water is involved in temperature control because it has a high specific heat capacity and large latent heat of evaporation
Water is a habitat. Nutrients can be dissolved in water . Contains oxygen gas which is essential for life. Forms an insulating layer for organisms when formed into ice
How does the structure of water relates to its function
• Hydrogen bonds give water a high specific heat capacity
• Hydrogen bonds also give water a high latent heat of evaporation
• Water’s polarity makes it very cohesive
• Water’s polarity also makes it a good solvent
• Water is less dense when it’s solid - makes a good habitat
Explain how hydrogen bonds gives water a high specific heat capacity
Specific heat capacity (SHC) is the energy needed to raise the temperature of 1 gram of a substances 1c
The hydrogen bonds between water molecule absorb a lot of energy so water has a high SHC- requires a lot of energy to heat up.
How can the SHC of water contribute for the survival of organism
Water doesn’t experience rapid temperature change due to having a high SHC.
This property makes water a buffer against rapid temperature change thus a good habitat- the temperature under water is more stable than on land.
Explain how hydrogen bonds gives water a large latent heat of evaporation
It takes a lot of (heat) energy to break the bonds between water molecules.
As a result water has a high latent heat of evaporation- a lot of energy is used when water evaporate
How can the large latent heat of evaporation of water contribute for the survival of organism
Large latent heat of evaporation is useful for living organisms because it means water great for cooling things:
This is why some mammals like u sweat when they’re too hot. When sweat evaporates they cool the surface of the skin
Explain how waters polarity makes it very cohesive
Cohesion is the attraction between molecules of the same type .
Water molecules are very cohesive because they’re polar. Water molecules are cohesive as there are hydrogen bonds between water molecules.
How can the cohesion of water contribute for the survival of organism
Cohesion of water helps water to flow making it great for transporting substances.
It helps columns of water to be transported up by plant stems in the transpiration stream
Explain how water polarity makes it a good solvent
Many biological molecules are ionic. This means they’re made from one positively charged atom or molecule and one negatively charged atom or molecule.
Water is polar, the slightly positive end of the water molecule will be attracted to the negative ion and the slightly negative end of a water molecule will be attracted to the positive ion.
Thus , Ions will get surrounded by water molecules (dissolve)
How can the water being a good solvent contribute for the survival of organism
Water’s polarity makes it useful as a solvent in living organism - water is an excellent transport medium
E.g in humans, important ions can dissolve in the water in blood and then be transported around the body (blood plasma- transport carbon dioxide, mineral acid and amino acids).
Water is used to transport substances in xylem vessels of plants. Water in the xylem contains dissolved mineral ions such as magnesium ion.
Explain how water is less dense when solid
At low temperature water freezes and turn from liquid to solid.
Water molecules are held further apart in ice than they are in liquid water because each water molecule forms four hydrogen bonds to other water molecules, making a lattice.
This makes ice less dense and float
How can the density of water when solid contribute for the survival of organism
This is useful for living organisms because, in freezing temperatures, ice forms an insulating layer on top of water- the water below doesn’t freeze. So organisms that live in the water, like fish, don’t freeze and can still move around,
What is the element composition of carbohydrates
C , H , O
What is the element composition of lipids
C, , H , O
What is the element composition of proteins
C , H , O , N , S
What is the element composition of Nuclei acids (DNA and RNA)
C , H , O , N , P
Explain what a monomer is
Monomers are small units which are the components of larger molecules
What are examples of a polymer
Starch and cellulose
Explain what a polymer is
Polymers are molecules made from many monomers joined together
Explain what is the condensation reaction
A reaction with two molecules joined together by a chemical bond with the release of a water molecule.
E.g when two glucose molecules bond together
Explain what is the Hydrolysis reaction
Hydrolysis is the opposite of a condensation reaction.
It is when water is added to break a chemical bond within a molecule.
Draw a diagram of a condensation and Hydrolysis reaction
What are single, paired and large chain of monomers called
Monosaccharide
Disaccharide
Polysaccharide
What are the bonds in carbohydrates called
Glycosidic bonds
Examples of monosaccharides
Glucose (hexose monosaccharide)
Ribose (Pentose monosaccharide)
Galactose
Fructose
What are the different forms of glucose
Alpha-glucose
Beta- glucose
What are the similarities differences between a-glucose and b-glucose
They have the same chemical formula but have slightly different structures.
If the carbon 1 hydroxyl pointes above the ring we call this isomer beta glucose
If the carbon 1 hydroxyl points below the ring we call this isomer alpha glucose
Draw the structure of a Glucose and Ribose
Draw the structure of Alpha glucose and Beta Glucose
What is an isomer
Isomers are molecules with the same chemical formula but have different structures.
Explain the structure of glucose
Glucose is a hexose sugar- a monosaccharide with six carbon atoms in each molecule
There are two types of glucose, glucose A and B which have the same chemical formula but have different structures
What are examples of Disaccharides
Maltose
Sucrose
Lactose
How is maltose , sucrose and lactose formed
Maltose is a disaccharide formed by condensation of two glucose molecules
Sucrose is a disaccharide formed by condensation of glucose and fructose
Lactose is a disaccharide formed by condensation of glucose and galactose
Explain a polysaccharide
A polysaccharide is a macromolecule consisting of more than 2 sugars - often a long chain of polymers joined together by glycosidic bonds
What are example of Polysaccharides
Glycogen
Starch
cellulose
How is Glycogen , starch and Cellulose formed
- Glycogen is formed by the condensation of alpha glucose molecules.
- Starch is formed by the condensation of alpha glucose molecules.
- Cellulose is formed by the condensation of beta glucose molecules.
Polysaccharide chains may be:
• These chains may be:
• Branched or unbranched.
• Folded (making the molecule compact which is ideal for storage eg. starch and glycogen).
• Straight (making the molecules suitable to construct cellular structures e.g. cellulose) or coiled.
Explain what glycogen is
The glucose storage molecule is glycogen and the major stores of glycogen are found in the liver and in the muscle cells
Explain the structure of Glycogen
- It is a multi-branched alpha glucose polymer joined together by 1, 4 and 1, 6 glycosidic bond. It is stored in the muscle and liver
- It has a large number of side branches meaning that energy can be released quickly as enzymes can act simultaneously on these branches.
-Glycogen is more branched than amylopectin which makes glycogen a very compact molecule .
-Glycogen has large number of branches thus a lot of free ends. This means that enzymes can convert glycogen back to glucose very rapidly
-Glycogen is insoluble in water. Glycogen does not draw water into the cell by osmosis . Additionally, being a a large molecule glycogen cannot diffuse out of the cell
Explain the function of Glycogen
-Glycogen is the main energy storage molecule in animals which is stored in the muscles and in the liver. In times of high energy usage, these organs hydrolyse the glycogen stored and break it down into glucose molecules which can be used in respiration
-It is a relatively large but compact molecule thus maximising the amount of energy it can store. Makes it optimal for an energy storage molecule.
-Finally being insoluble means it will not affect the water potential of cells and cannot diffuse out of cells being a large molecule .
-Glycogen has a a large number of branches + free ends thus enzymes can convert glucose very rapidly
What is starch made from
• Starch is constructed from two different polysaccharides:
- Amylose (10 - 30% of starch)
• Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-glucose molecules
• The helix shape enables it to be more compact and thus it is more resistant to digestion - Amylopectin (70 - 90% of starch)
• 1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic bonds form between glucose molecules creating a branched molecule
How does the structure of starch relate to its function
Amylose forms a tight helix which make starch compact.. Thus the starch can store a large amount of glucose molecule for its size.
Amylopectin and amylose are polymers which are too large to diffuse through the cell membrane and pass out of the cell. Thus starch is insoluble in water and does not cause water to enter the cell by osmosis.
As amylopectin has a large number of branches it has a large number of ends thus enzymes can break down starch rapidly by breaking the glycosidic bonds at the end of molecules.
Explain the structure of Amylose
Amylose is a polymer of alpha glucose molecules.
The amylose molecule twists into a compact helix with hydrogen bonds forming between glucose molecules along the chain.
Amylose contain hundreds or thousands of alpha glucose molecules which are joined together by 1,4 glycosidic bonds.
Explain the structure of Amylopectin
Amylopectin is a polymer of alpha glucose joined together by 1,4 glycosidic bonds. However, amylopectin chains have a branch every 25-30 glucose molecules.
The branch is connected to the main chain by a glycosidic bond which is connected to carbon 1 of one glucose molecule and carbon 6 of another (1,6 glycosidic bond).
What is the structure of cellulose
Cellulose is a polymer of beta glucose
The structure of beta glucose is similar to alpha glucose. However, the hydroxyl on carbon 1 points above the plane of the ring.
Glycosidic bonds cannot form between carbon 1 and 4 as the hydroxyl groups point in different directions. As a result when a molecule of cellulose is formed every second beta glucose molecule flips. Thus a 1,4 glycosidic bond is formed
Cellulose is an unbranched polysaccharide joined by glycosidic bonds in a condensation reaction
What is the function of cellulose
Cellulose forms a straight chain without any branches. This allows cellulose molecules to get close together.
Hydrogen bonds can now form between neighbouring chains. As a result a large number of hydrogen bonds are formed which makes cellulose extremely strong.
Cellulose cell wall is permeable to molecules
The contents of the plant cell push against the turgid cell of the cellulose cell wall. The strength of the cell wall resists the outwards pressure due to the cells contents, This prevents plants cell from bursting.
Plant cells filled with water become rigid. These turgid cells give the plant an upright structure.
What are some examples of monomers
Monosaccharides such as glucose, amino acids and nucleotides
What is the structure of water
Molecule of water contains one atom of oxygen chemically bonded to two atoms of hydrogen.
The bonds between atoms are covalent bonds
What is the structure of water
Molecule of water contains one atom of oxygen chemically bonded to two atoms of hydrogen.
The bonds between atoms are covalent bonds
Explain how waters polarity make it useful for metabolic reactions
Water’s polarity makes it a very good polar solvent for many biological molecules.
E.g: in ionic calcium chloride, the positive Ca2+ will be attracted to the negative pole of a water molecule, and Cl- will be attracted to the positive pole.
Many metabolic reactions occur in water.
Explain how water being a good metabolic reactant can ensure the survival of an organism
water is a reactant in many different reactions such as hydrolysis reactions and photosynthesis
Water is also produced in certain metabolic reactions. These include condensation reactions and aerobic respiration
Explain the key features of monosaccharides
They are soluble in water. This is because they contain a large number of OH groups within their structure (hydroxyl groups). As a result the hydroxyl group will form hydrogen bonds with water molecules which cause the molecule to be soluble (hydrophilic)
Hydrophilic= water loving (hydrophilic molecules dissolve in water)
What is the word equation of glucose
C6H12O6
What product are made when creating a disaccharide
A molecule of water is produced which is formed from hydrogen atom from one of the monosaccharides and a hydroxyl group from the other
What alternative products are created when a disaccharide is formed
A molecule of water is produced which is formed from hydrogen atom from one of the monosaccharides and a hydroxyl group from the other
How can a disaccharide be formed into a monosaccharide
If water is added to a disaccharide we can break the glycosidic bond. This converts the disaccharide back to the original monosaccharides This is called hydrolysis reaction.
Explain why glucose is soluble and why this is a problem
Glucose is extremely soluble in water. It contains a large number of hydroxyl groups which are polar. As a result hydroxyl groups can form hydrogen bonds with water molecules. This makes glucose soluble in water.
However,if a cell contains a large amount of dissolved glucose this can cause water to move into the cell through osmosis. As a result plant store glucose as starch.
What is a microfibril
Polymer of 10,000 beta glucose molecules in a long unbranched chain is called a microfibril (long cellulose chains)
What is a macrofibril
Microfibrils group together to form a larger structures called macofibrils
What is a microfibril
Polymer of 10,000 beta glucose molecules in a long unbranched chain is called a microfibril (long cellulose chains)
What is a cellulose fibre
Macrofibrils grouped together form a cellulose fibre
What is a cellulose fibre
Macrofibrils grouped together form a cellulose fibre
What four elements are primarily found in living organisms
Carbon-C
Hydrogen-H
oxygen-O
Nitrogen-N
Describe a covalent bond
A covalent bond is the sharing of two or more electrons between two atoms
The electrons can be shared equally forming a nonpolar covalent bond or unequally (where an atom can be more electronegative δ-) to form a polar covalent bond
How are covalent bond formed
Covalent bonding occurs when pairs of electrons are shared by atoms. Atoms will covalently bond with other atoms in order to gain more stability, which is gained by forming a full electron shell (valence shell is formed)
What is an ion
An atom or molecule in which the total number of electrons is not equal to the total number of protons is called an ion.
What are cation and anions
Cations are ions with a positive charge, meaning they have lost electrons.
Anions are ions with a negative charge, meaning they have gained electrons.
Describe an ionic bond
Ionic bonds form between a positively charge atom and a negatively charged atom
How are ionic bonds formed
Ionic bonds are formed between two or more atoms by the transfer of one or more electrons between atoms. Electron transfer produces negative ions called anions and positive ions called cations
What is an organic and inorganic substance
Organic substances contain carbon covalently bonded to a hydrogen atom. (CH4)
Inorganic substances lack C-H bonds. (NH4)
What are lipids
Lipids are macromolecules that contains carbon, hydrogen and oxygen atoms.
Unlike carbohydrate, lipids contain a lower proportion of oxygen
What are the groups of lipids
Triglycerides (main components of fats and oils)
Phospholipid
Explain the Properties of lipids
They contain carbon, hydrogen and oxygen- lots of of energy can be released
The proportion of carbon to oxygen and hydrogen is smaller than in carbohydrates
They are insoluble in water
They are soluble in organic solvents such as alcohol and acetone
Explain the function of lipids
Storage of energy for long term use (e.g triglycerides) or adipose tissue in humans.
Hormonal roles (e.g steroid such as oestrogen and testosterone)
Insulation- both thermal (triglycerides) and electrical (sphingolipids). Furthermore, adipose tissue in humans help to insulate the body, reducing heat loss to the environment.
Protection of internal organs (triglycerides and waxes). Furthermore, adipose tissue is found around organs to protect it from injury
Structural components of cells (phospholipids , cholesterol, mitochondria, )
Lipids are used for water proofing- oils which coat the feathers of aquatic birds ( this is because the molecule is uncharged therefore non-polar. This means it is hydrophobic adn does not dissolve in water)
Explain how are triglycerides formed
Triglycerides form when a condensation reaction occurs between one glycerol and three fatty acid chains
-the 3 hydroxyl group of the glycerol molecule combine with a carboxylic group of 3 fatty acid molecules to form an ester linkage (esterfication)
This condensation reaction results in the formation of three water molecules
Explain how triglycerides are used in animals compared to plants
Animals tend to store triglycerides as fat (solids)
plants tend to store triglycerides as oils (liquids)
Explain the structure of saturated fatty acids
Fatty acids are long hydrocarbon chains that are found in certain types of lipids (triglycerides and phospholipids)
They differ in length (2-24 carbons) and in the number of double bonds
Contains a carboxylic group on one end
Fatty acids with no double bonds are saturated
Explain the properties of saturated fatty acids
This generates fats that are usually solid at room temp
Saturated fats are usually linear in structure, originate from animal sources (I.e fats)
Explain the structure of unsaturated fatty acids
Fatty acids with double bonds are unsaturated- either monounsaturated (1 double bonds) or polyunsaturated (> 1 double bond)
Contains a carboxylic group on one end
Explain the properties of unsaturated fatty acids
Unsaturated fatty aids are bent in structure, originate from plant sources (I.e oils)
Unsaturated fatty acids are usually liquid at room temperature and are called oils
what are example of real life items which contain trans fats
Hydrogenated vegetable oils
Fast foods
Cakes/pastries
Chocolate
Deep fried food
what are example of real life items which contain saturated fats
Vegetable fats:
Coconut
Palm oil
Condensed milk
Animal fats:
Poultry skin
Fatty meat
Butter
Ghee
what are example of real life items which contain unsaturated fats
Polyunsaturated:
Com oil
Soybean oil
Sunflower oil
Seeds
Monounsaturated:
Olive oil
Cannoli oil
Peanut oil
Explain the structure for phospholipids
Structure similar to triglyceride, but one Fatty acid chain is replace with a Phosphate group PO4^3-group
Explain the properties of phospholipids
Phospholipids are amphipathic (contain both a hydrophobic and hydrophilic)- the phosphate head is negatively charged and thus is polar (hydrophilic) whereas the two fatty acids tails these are non-polar (hydrophobic)
Phospholipids have both mono layers and bilayers
Explain the function of phospholipids
Phospholipids play a crucial role in forming the plasma membrane of cells:
• In an aqueous environment being polar means a bilayer can be formed.
• They form a bilayer with the FA tails facing into each other, and the polar heads facing outwards and dissolving in the aqueous intra- and extracellular fluids.
• The hydrophilic heads of the phospholipids can be used to hold at the surface of the cell surface membrane.
• Their structure allows them to form glycolipids with carbohydrates which are important on the cell surface membrane for cell recognition.
• They are ideal for forming cell surface membranes as they enable integration of other molecules into the ‘mosaic’ and help to regulate the movement of molecules in and out of
the cell.
Compare phospholipids with triglycerides
No. Fatty acids tails: 2 / 3
Presence of phosphate: yes / no
Polar / non-polar: polar phosphate head / non-polar
No,water molecules released when formed :
3 / 3
Function:
Cell membrane components / energy storage
What is cholesterol
Cholesterol is an important component of the cell membrane and helps to regulate its fluidity:
High levels of cholesterol in the membrane can lead to a decrease in fluidity and stability.
Low levels of cholesterol can cause the membrane to become more fluid and lead to disruptions in cell function.
Explain the structure of cholesterol
Has a 4 carbon ring structure with a hydroxyl (OH) group at one end
Comes from the family of sterols
Explain the function of cholesterol
• Cholesterol is important in the formation and fluidity of cell surface membranes and in theproduction of certain hormones e.g.testosterone and oestrogen .
Hormones (oestrogen and testosterone) are able to pass through cell membranes and interact with receptors inside the cell as they are based on cholesterol
Cholesterol creates vitamin D in the skin in response to UV light (needed for the development of bones)
Cholesterol is used in the liver to create bile which increase the rate of digestion of lipids by the enzyme lipase
Forms a small, thin molecule that fits into a lipid bilayer giving strength and stability
Cholesterol can insert into cell membranes by using its hydrophilic hydroxyl group to interact with the head groups of phospholipids. While the rest of it interacts with the hydrophobic fatty acids tails
Explain the properties of cholesterol
The hydroxyl group is hydrophilic. However the rest of the molecule is hydrophobic.
Therefore, the cholesterol can insert itself into the cell membrane. The hydrophilic hydroxyl group on the cholesterol molecule can interact with the heads of the phospholipids. While the rest of the cholesterol molecule can interact with the hydrophobic fatty acid tails. (Not soluble in water)
What are the two different major lipoproteins
Low-density lipoproteins (LDL)
High-density lipoproteins (HDL)
Draw the structure of a triglyceride
Draw the structure of a phospholipids
Explain the function of LDLs
• Low density lipoproteins (LDL) carry cholesterol from the liver to the rest of the body
• LDLs bind to receptors on cell surface membranes before being taken up by the cells where the cholesterol is involved in the synthesis and maintenance of cell membranes.
Explain how LDLs form
• Triglycerides (from fats in our diet) combine with cholesterol and proteins to form LDLs
which transport the cholesterol to our body cells.
Explain the problem with LDLS
Excess LDL overload on these membrane receptors, results in high blood cholesterol levels, which may be deposited in the artery walls forming atheromas.
Therefore it is desirable to maintain a higher HDL:LDL ratio in the blood. As HDLs reduce blood cholesterol deposition
Explain how HDLs form
HDLs are made when triglycerides (from fats in diet) combine with cholesterol and proteins.
Explain the function of HDLs
High density lipoproteins (HDL) scavenge excess cholesterol in the body tissues and carry it back to the liver where it is broken down.
• This lowers blood cholesterol levels, and helps to remove the fatty plaques of atherosclerosis.
Dietary factors that increase cholesterol levels
High intake of certain types of fast will differently affect cholesterol levels in the blood:
• Saturated fats increase LDL levels within the body, raising blood cholesterol levels
• Trans fats increase LDL levels and decrease HDL levels within the body, significantly raising blood cholesterol levels
• Unsaturated (cis) fats increase HDL levels within the body, lowering blood cholesterol
levels
How do Saturated/mono-saturated and polyunsaturated fats contribute to cholesterol levels
Saturated fats: studies have shown they increase LDL and HDL cholesterol, however increase in LDL cholesterol is greater.
Monounsaturated fats:Help the removal of LDLs from the blood
Polyunsaturated fats: Increase the activity of the LDL receptor sites so the LDLs are actively removed from the blood
Describe the general structure of amino acids
Amino aids are formed from an amine group and a carboxyl group attached to a single carbon atom.
The R group attached to the carbon is different for each of the 20 amino acids
What are the general elements within a amino acid
Carbon,hydrogen, nitrogen and oxygen
Some contain sulfur
Explain how amino acids can bond together
Two amino acids can react together and form a chemical bond. This is known as a ** peptide bond **.
A molecule of water is produced from this reaction (condensation reaction)
The molecule formed is called a dipeptide as it contains two amino acids which are bonded together
If three or more amino acids bond together what is formed
If three or more amino acids bond together a polypeptide is formed
(Consist of hundred of amino acids formed together)
Explain how we can reverse a peptide bond
A peptide bond is formed through a condensation reaction where water is produced.
The peptide bond can be broken by adding a molecule of water (hydrolysis reaction)
This reaction is carried out by protease enzymes in the digestive system
Explain the difference between a polypeptide and a protein
In order to be classed as a protein a polypeptide has to fold into a complex, 3-dimensional shape
Once a polypeptide has folded into the correct shape it carries out its function e.g as an enzyme or hormone. It is then considered to be a protein molecule.
Protein consist of several different polypeptides forming a large and complex molecule. It also contains other molecules to support its function (eg haemoglobin)
Explain the primary structure of proteins
The primary structure is simply the specific order of amino acids in a polypeptide
It helps to determine the final 3 dimensional shape of the protein molecule which is critical for its function
Explain how the primary structure of a polypeptide is determined
The primary structure for a polypeptide is determined by the DNA sequence of the gene which encodes the polypeptide
Explain how the secondary structure of a protein is formed
Within a polypeptide chain there are C=O groups and N-H groups
The oxygen atoms in C=+O groups have a small negative charge and the hydrogen atoms in the N-H groups have a small positive charge.
This means they attract to each other and a hydrogen bonds form between amino acids all along the polypeptide chain
The polypeptide chain will twist and fold into shapes and scientists call this the secondary structure
What are examples of secondary structures
Alpha-helix
Beta-pleated sheet
Describe the structure of Alpha-helix
The polypeptide chain is twisted into a helical shape held in place by hydrogen bonds
Describe the structure of the Beta-pleated sheet
The polypeptide chain folds into a flatter, sheet-like structure. The hydrogen bonds between the amino acids hold the shape into place.
What is the secondary structure determined by
The type of secondary structure formed depends on the primary structure in that region
How do amino acid sequences influence the formation of alpha helices and beta pleated sheets in protein structures?
Many proteins have regions with alpha helices and regions with beta pleated sheets.
Certain amino acid tend to be found in alpha helices and other in beta-pleated sheets
Explain how the tertiary structure of a protein is formed
The regions of secondary structure determines how the tertiary structure continues folding forming the final tertiary structure
Explain what is the tertiary structure of a protein
It is the overall 3-dimensional shape of a polypeptide chain
Explain what is the tertiary structure of a protein
It is the overall 3-dimensional shape of a polypeptide chain
It is critical for how a protein function e.g the active site of an enzyme depends on the protein forming a very specific tertiary structure
If the tertiary structure of an enzyme is changed (e.g by heating) the shape of the active site changes. Thus the enzyme no longer function effectively (denatured)
Explain why the tertiary structure important
It is critical for how a protein function e.g the active site of an enzyme depends on the protein forming a very specific tertiary structure
If the tertiary structure of an enzyme is changed (e.g by heating) the shape of the active site changes. Thus the enzyme no longer function effectively (denatured)
Explain the quaternary structure of a protein
The quaternary structure shows how the individual subunits are arranged to form a larger three dimensional structure
It only applies to proteins with at least two subunits
Some protein contain other non-protein molecules forming part of the structure. These are called prosthetic groups and they help the protein to carry out its role
Protein with a prosthetic group are called conjugated proteins.
They show the arrangement of subunits and the position of any prosthetic group
Explain what prosthetic group support RBCs
RBCs contains the prosthetic group haemoglobin which binds to oxygen
Explain hydrogen bonding in proteins
A polypeptide chain will have two amino acids with R groups containing a hydroxyl
Due to the slight positive and negative changes present on the hydroxyl a hydrogen bond can form these two R groups and this contributes to the 3 dimensional shape of the polypeptide chain
Hydrogen bonds are weak and are easily broken by high temperature or by pH changes
Explain hydrophobic and hydrophilic interaction within bonding proteins
Several amino acids have uncharged R groups we call these non-polar amino acids which aren’t attracted to water (hydrophobic). These cluster work to exclude water molecules (hydrophobic interactions). These tend to be in the centre of proteins away from water molecules
Hydrophilic amino acids tend to be found on the surface of proteins where they can interact with water molecules.
Both hydrophobic and hydrophilic interactions are relatively weak bonds
Explain ionic bonding during bonding of proteins
Ionic bonding occurss between amino acids with charged R groups
An amino acid will be a positively charged R group and the other will be a negatively charged R group
These opposite charges attract each other and form an ionic bond. This holds different parts of the polypeptide chain together and contributes to protein structure
Ionic bonds are broken by pH. This is why enzymes can denature under acidic or alkaline conditions
Explain disulfide bonds in the bonding of proteins
A polypeptide contains two molecules of an amino acid called cysteine. The R group of cysteine contains a sulfur atom.
The sulfur atom in the two cysteine molecule form a covalent bond. This is called a disulfide bond.
Disulfide bonds are relatively strong and are not broken by high temperatures or pH changes
Explain what happens when these bonds form between amino acids on the same polypeptide chain
They’ll be involved in tertiary structure
Explain what happens when these bonds form between amino acids on the same polypeptide chain and different subunits
They’ll be involved in quaternary structure
Why is the structure of a protein significant
The structure of a protein is critical to its function
What 2 different protein groups are there based on a proteins structure
Globular proteins
fibrous proteins
Explain the structure of a globular protein
They have an approximately spherical shape
They are surrounded by hydrophilic amino acids
There are hydrophobic amino acids deep in the centre of the protein away from water molecules
Explain the key features of globular proteins
They are soluble in water - This is due to hydrophilic amino acids surrounding the surface. This means that hydrophilic R groups can interact with water molecules. Therefore, globular proteins are soluble in water
Contains hydrophobic amino acids within the centre of the protein away from water molecules.
Describe how the structure of haemoglobin link to its function
Each haem group contains a fe2+ ion where the oxygen binds. Thus one haemoglobin molecule can bind to four oxygen molecules. This supports the function of haemoglobin in the RBC as it role is to bind reversibly to oxygen in the lungs to release oxygen in the body tissue.
Furthermore, as oxygen attaches to the haemoglobin, the quaternary structure of the protein changes slightly. This makes it easier for more oxygen to attach. Thus more oxygen traveling across the body to muscle tissue
Explain the structure of haemoglobin
Haemoglobin is a polypeptide with four polypeptide subunits.
Two are called the alpha subunit and the other two are called the beta subunit .
Each subunit contains a prosthetic group haem. Therefore, haemoglobin is a conjugated protein.
Each haem group contains a fe2+ ion where the oxygen binds.
Explain the structure of insulin
Insulin consist of two polypetide chains. The chains are linked by a disulfide bonds.
Describe how the structure of insulin link to its function
The hormones like insulin carry out their function by binding to specific receptor molecules. These receptor are proteins found on the cell membrane of target cells
The shape of the insulin molecule mean that it fits perfectly within its receptor even slight changes to the shape of the molecule could prevent it from binding effectively .
The shape of protein hormones such as insulin are critical for how they bind to receptor and carry out their effects.
Insulin can support blood glucose concentration
Explain the structure of lysozyme
Lysozyme consist of a single polypeptide chain. The chain folds to form a groove along the surface. This groove is called the active site. The shape of active site fits perfectly to substrate molecule in the bacterial cell wall.
Describe how the structure of lysozyme link to its function
Found in Saliva and tears
Enzymes (lysozyme) can only react with a specific substrate molecule. This specificity is due to the structure of the enzyme.
Lysozyme consist of a single polypeptide chain. The chain folds to form a groove along the surface (active site). The shape of active site fits perfectly to substrate molecule in the bacterial cell wall.
As a result the lysozyme and the active site work together to catalyse the breakdown of a molecule in the bacterial cell wall. This helps defend the body against bacteria
Surrounding the substrate are amino acids which work to hold the substrate in place.
Lysozymes contain regions where amino acids catalyse reaction.
What role do fibrous protein mainly play
They play a structural role e.g bones, tendons or wall of blood vessels
Explain the structure of fibrous proteins
Forms long, rope like molecules e.g collagen
Explain the properties of fibrous proteins
Fibrous proteins are insoluble in water
Where is collagen found
Collagen is found in tendon, which connects muscle to bones and ligaments which connects bones to each other
It is also found in skin
Explain the key features in collagen
It is a strong molecule due to its structure. The polypeptide chains in collagen wrap tightly together to form a triple helix.
Explain the structure of collagen and how it relates to its strength
The polypeptide chains in collagen wrap tightly together to form a triple helix.
In collagen polypeptides every third amino acid is glycine. The R group of glycerin is a hydrogen atom. Thus glycine has the smallest R group of any amino acid.
This allows collagen polypeptides to wrap tightly around each other
As it wraps around each other a large number of hydrogen bonds form between the polypeptide chains. This helps to stabilise the quaternary structure of the proteins. They are also joined to each other by strong crosslinks.
A large number of these triple helical molecules join together to form large structures called microfibrils and fibrils. The molecules are staggered thus have no weak spots
Cross linking between different triple helical molecules further strengthens collagen
Where is keratin found
It is found in hair, fingernails and the outer surface of skin
Explain the key features in keratin
Keratin is extremely strong and insoluble in water
Explain the structure of keratin and how it relates to its strength
keratin consists of long stranded molecules with a high proportion of the amino acid cysteine. This is used to form disulfide bonds which are strong covalent bonds.
Due to the high proportion of cysteine keratin molecules contains a large number of disulfide bonds which contributes to the strength of keratin molecules
Where is elastin found
The skin and walls of arteries
Explain the key features in elastin
Elastin fibers stretch when blood passes through the artery and then recoil in between pulses, helping the artery to return to its original shape.
Explain the structure of elastin and how it relates to its elasticity
Elastin molecules are long strands, containing hydrophobic regions. These strands are cross linked to each other.
The hydrophobic regions on different strands associated causing the elastin molecules to group together. However, when stretched the strands move apart but remain attached at the cross link.
After stretching, the elastin molecules reassociate, springing back together.
This makes elastin a very elastic molecule
Why do we carry test for non-reducing or reducing sugars
We often carry out these test to determine which chemicals are present in different foods. However, these can be used for different purposes
E.g: test plants for starch to see if they have carried out photosynthesis.
Or
Test urine for protein to diagnose kidney problems or for glucose to check diabetes.
What safety measures should be considered when carrying out chemical tests for food
Safety googles should be worn as potentially harmful chemicals are being used. To avoid contamination.
Spills need to be cleaned with distilled water.
Describe the initial stages of the food test
We have to grind our food with a small amount of distilled water in a mortar and pestle
Once we have turned the food into a paste, we then add more distilled water and we stir the mixture (the mixture is going to be full of solid food particles and these could make the test results difficult to see)
Therefore, we need to filter our mixture to remove these solid food particles. We carry out out test on the filtrate (food solutions which passes the filter)
Describe the food test for starch
We place 3cm^3 of our food tube into a solution into a test tube
We then add 1cm^3 of a solution containing iodine adn potassium iodide.
In the presence of starch, the iodine solution turns a blue-black colour. In the absence of starch the solution remain orange
Describe the food test for protein
We place 3cm^3 of our food tube into a solution into a test tube
We then add 3cm^3 of dilute sodium hydroxide solution and mix
Next we add ten drops of dilute copper (II) sulfate solution and mix again
If protein is present then the solution turns purple or lilac. If protein is absent then the solution will remain blue.
Important details:
The sodium hydroxide solution and the copper (II) sulfate are premixed. This is called a blurted solution. This test detected peptide bonds therefore you get a positive results either proteins. However, a solution of amino acids would give a negative result as these do not contain any.
Describe the food test for lipids
In this test the food mixture must not be filtered. That’s because the lipids can stick to the filter paper. Therefore, we can leave to food mixture for a while to allow the particles to settle.
We add 3cm^3 of our food solution into a test tube
We then add 3cm^3 of ethanol and water. We then shake the solution
If lipids are present, then a white cloudy emulsion will form. If the solution stays clear, then lipids are not present .
Be aware as the ethanol is flammable therefore the experiment must not be carried near any opens flames.
Define reducing sugars
Reducing sugars can donate an electron to another molecule
What monosaccharides and disaccharides are reducing sugars
All monosaccharides are reducing sugars
Some disaccharides are reducing sugars (maltose , lactose)
What is an example of a non-reducing sugar
Sucrose
Describe the test for reducing sugars
- safety goggles should always be worn
We should first grind the food with a mortar and pestle in distilled water. We should then filter away the solid food particles.
We then place 3cm^3 of our food solution into a boiling tube and add 3cm^3 of Benedict’s solution. ( contains Cu2+ make the solution blue)
We then place the boiling tube into a beaker of boiling water and leave it for five minutes.
If the solution remains blue then there is no reducing sugar present . However, if reducing sugar is present then this adds an electron to the copper 2+ ion. This form a copper 1+ ion forming a red precipitate.
If there is a very small amount of reducing sugar then only a very small amount of red precipitate forms. This causes the Benedict’ solution to turn green.
If more reducing sugar is present then the colour yellow. A higher level of reducing sugar produces an orange colour.
If a lot of reducing sugar is present then we see a brick red colour.
Key ideas of the Benedict’s test
It only gives us a very appropriate idea of the amount of reducing sugar. This is because the Benedict’s test only shows a narrow range of colour changes and all humans perceive colour slightly differently - semi-quantitative.
Goggles should always be worn during the test
Describe the test for non-reducing sugars
First we should take a small amount of our unknown solution and carry out the Benedict’s test to check if it contains non-reducing sugars.
( we need to note down any colour changes and which takes place)
We take a fresh boiling tube and add 3cm^3 of our unknown solution. Next we add 3cm^3 of dilute hydrochloric acid and gently boil the solution in the water bath for five minutes,
If a non-reducing sugar is present then the acid hydrolyses the glycosidic bonds releasing the monosaccharides.
Next we add 3cm^3 of a dilute alkali such as sodium hydroxide solution. We then use the pH paper to check the our solution is alkaline. That is because the Benedict’s test cannot work under acidic conditions.
Finally we add 3cm^3 of Benedict’s solution and then hear it in the boiling water for five minutes. (Then note down any colour change)
Key ideas of non-reducing sugar
We cannot test non-reducing sugars directly. We need to break the glycosidic bond releasing the monosaccharides. Because all monosaccharides reducing sugars we can test for them using the Benedict’s solution
Explain the outcome if the first Benedict test is blue and the Second Benedict’s test is orange when trying to find if non-reducing sugars are present in a solution
Blue= negative ( reducing sugar not present)
Orange= positive (non-reducing sugar present)
Explain the outcome if the first Benedict test is green and the Second Benedict’s test is red when trying to find if non-reducing sugars are present in a solution
Green= positive ( very small amount of reducing sugar not present)
Red = positive (non-reducing sugar present)
Explain the outcome if the first Benedict test is red when trying to find if non-reducing sugars are present in a solution
Red- positive (large amount of reducing sugar)
Second Benedict’s solution test (not possible)- even if non-reducing sugar was present we would not be able to see a colour change beyond red.
( only can test for non-reducing sugar when there is either no reducing sugar present or a small amount)
Explain the science Benedict’s test works
Benedict’s reagent contains Cu^2= ions which make the solution blue
When reducing in sugars such as glucose donate an electron it reduces the Cu^2+ ion to the Cu^+ ion forming a red precipitate.
The red precipitate and the blue of the Benedict’s solution leads to a colour change. If the solution was left for several hours then the red precipitate would settle at the bottom. (Allows us to see the blue Benedict’s solution at the top)
The Benedict’s solution will be less blue than it was before the test. That’s because some of the Cu2+ ions have reacted and are no longer in the solution ( a greater concentration of glucose would result in the solution to appear less blue at the end as there will be fewer cu^+ ions remaining in the solution0
Explain a problem with the Benedict’s solution test when attempting to quantify glucose
Small changes to the blueness of the solution in the Benedict’ test are too subtle to be able to detect by the eye. Therefore, we quantify the blueness of the solution in by using a machine called a colorimeter.
Describe how a colorimeter works
Before we use a colorimeter, we first need to filter off the red precipitate leaving just the Blue Benedict’s solution
If we shine white light than all colour will be absorbed apart from blue. That’s because Benedict’s solution allows blue light to pass through therefore is why it has a blue colour.
This absorption of light can be used to quantify the levels of blueness- as it transmits through teh solution as is detected by a photoelectric cell (form of light detector)
However, red light is the best as Benedict’s solution allows blue absorbs red most out of all the different colours as it is on the opposite end of the spectrum then blue. (Red is the complementary colour to blue)
We can place a red filter in front of our lamp. This only allows red to pass through.
Explain the results if a sample of Benedict’s solution which is a very pale blue is used
The sample could have been reacted with a very large amount of glucose. Therefore, has a small amount of Cu^+ ions.
Little red light is absorbed by the solution therefore a lot is transmitted through and detected by the photoelectric cell ( light detector)
The less red light is absorbed the greater the amount of glucose that must have reacted with out Benedict’s solution.
Why is the Benedicts test and a colorimeter used
In order to accurately determine the concentration of glucose in a sample.
Explain a problem with the colorimeter when attempting to tell us the actual concentration of glucose
We need to prepare a whole range of glucose concentrations. We then react each solution with Benedict’s solution and filter off the red precipitate.
We then use the colorimeter to see how much red light is absorbed by each solution.
We carry out the same procedure with our unknown solution. By comparing our unknown solution with our known solution we can determine the concentration of glucose in our unknown solution. This is called a calibration curve.
Explain the method of the experiment to create a calibration curve in order to find the concentration of glucose in our unknown solution.
We get six test tubes then start with a known concentration ( stock solution) of glucose (5mmol /dm^3) and create a range of dilutions from that.
Using a syringe we use 5cm^3 of our stock solution into test tube
This test tube contains a glucose solution with a concentration of 5mmol / dm^3.
In test tube 2 we add 4cm^3 of our stock solution plus 1 cm^3 of distilled water. This contains a glucose solution of 4mmol / dm^3
In test tube 3 we add 3cm^3 of our stock solution plus 2 cm^3 of distilled water. This contains a glucose solution of 3mmol / dm^3
In test tube 4 we add 2cm^3 of our stock solution plus 3 cm^3 of distilled water. This contains a glucose solution of 2mmol / dm^3
In test tube 5 we add 1cm^3 of our stock solution plus 2 cm^3 of distilled water. This contains a glucose solution of 1mmol / dm^3
In test tube 6 we add 5cm^3 of our stock solution plus 6cm^3 of distilled water. This contains no glucose at all
Next we set up a test tube containing 5cm^3 of our unknown concentration of glucose. At this stage we add 5cm63 of Benedict’s solution to each test tube and mix them thoroughly.
We then place all the test tubes in a boiling water bath for five minutes. During this time the Benedict’s solution will react with the glucose producing a red precipitate.
Finally, we filter each solution into a fresh test tube. This removes the precipitate, leaving the remaining Benedicts solution (a centrifuge can be used instead of a filer funnel)
Explain how to use a colorimeter
Some colorimeters have test tube which can be directly placed inside. However, in other colorimeters we need to transfer all your solutions into small plastic containers called cuvettes
Curettes have two clear transparent sides and two sides which are translucent . We always place the cuvettes into the colorimeter so that the light passes through the transparent sides.
First we should set the colorimeter on the red filter. That’s because red is the complementary colour to blue. (Red will be the colour most absorbed by the blue solution)
We then set the colorimeter to measure absorption. In other words to see how much red light is absorbed by the solution. We then place a cuvettes contains just distilled water into the colorimeter and set the colorimeter to zero ( we telling the colorimeter to consider water to absorb zero red light)
We then use the colorimeter to read the absorbances of all our solutions. We plot this information on a dilution serve on a graph. We use the calibration curve to determine the concentration of glucose in our unknown sample
If the absorbance of the unknown sample is too great to read off the calibration curve then you need to dilute the solution and read the absorbance again. ( take the dilution factor into account when determining the concentration of glucose)
Draw the synthesis of the disaccharide sucrose
Draw the synthesis of the disaccharide lactose
Draw the synthesis of the disaccharide maltose
Draw the synthesis of starch
Draw the synthesis of cellulose
What is the function of glucose
Glucose is used as the primary energy source in animals and plants.
Explain how the properties of glucose support it’s function
It is soluble - The hydroxyl groups can form hydrogen bonds with water, so it can be transported around organisms.
Its bonds store lots of energy - This energy is released when the bonds are broken.
What are the the symbols for the following ions: calcium , sodium , pottasium. Hydrogen , ammonium, nitrate, hydrogen carbonate, chloride , phosphate, hydroxide
Calcium ions: Ca^2+
Sodium ions: Na^+
Potassium ions: K^+
Hydrogen ions: H^+
Ammonium ions: NH4^+
Nitrate: NO3^-
Hydrogen carbonate: HCO3^-
Chloride: Cl^-
Phosphate: PO4^3-
Hydroxide: OH^-
What is chromatography used for
Chromatography is a technique that can be used to separate a mixture into its individual components
This method can be used to separate mixtures containing proteins, carbohydrates, vitamins and nucleic acids
Explain the principle of chromatography
Chromatography relies on differences in the solubility of the different chemicals (called ‘solutes’) within a mixture
All chromatography techniques use two phases:
The mobile phase
The stationary phase
The components in the mixture separate as the mobile phase travels over the stationary phase
Differences in the solubility of each component in the mobile phase affects how far each component can travel
Those components with higher solubility will travel further than the others
This is because they spend more time in the mobile phase and are thus carried further up the paper than the less soluble components
Explain the method behind paper chromatography
A spot of the mixture (that you want to separate) is placed on chromatography paper and left to dry
The chromatography paper is then suspended in a solvent
As the solvent travels up through the chromatography paper, the different components within the mixture begin to move up the paper at different speeds. Larger molecules move slower than smaller ones
This causes the original mixture to separate out into different spots or bands on the chromatography paper
This produces what is known as a chromatogram
Explain how we can chromatography to separate a mixture of monosaccharides
Paper chromatography can be used to separate a mixture of monosaccharides. Mixtures containing coloured molecules, such as ink or chlorophyll, do not have to be stained as they are already coloured
Mixtures of colourless molecules, such as a mixture of monosaccharides, have to be stained first. A spot of the stained monosaccharide sample mixture is placed on a line at the bottom of the chromatography paper
Spots of known standard solutions of different monosaccharides are then placed on the line beside the sample spot
The chromatography paper is then suspended in a solvent.As the solvent travels up through the chromatography paper, the different monosaccharides within the mixture separate out at different distances from the line
The unknown monosaccharides can then be identified by comparing and matching them with the chromatograms of the known standard solutions of different monosaccharides
If a spot from the monosaccharide sample mixture is at the same distance from the line as a spot from one of the known standard solutions, then the mixture must contain this monosaccharides
Explain Howe we can use chromatography to separate a mixture of amino acids
Paper chromatography can be used to separate a mixture of amino acids. A spot of the unknown amino acid sample mixture is placed on a line at the bottom of the chromatography paper
Spots of known standard solutions of different amino acids are then placed on the line beside the unknown sample spot
The chromatography paper is then suspended in a solvent. Each amino acid will be more or less soluble in the mobile phase than others and will therefore separate out of the mixture travelling with the solvent at different times/distances from the line, depending on their: charge and size
The unknown amino acid(s) can then be identified by comparing and matching them with the chromatograms of the known standard solutions of different amino acids.If a spot from the amino acid sample mixture is at the same distance from the line as a spot from one the known standard solutions, then the mixture must contain this amino acid
In order to view the spots from the different amino acids, it may be necessary to first dry the chromatography paper and then spray it with ninhydrin solution (this chemical reacts with amino acids, producing an easily visible blue-violet colour)
How can we calcauet Rf valve
Distance moved by solute
————————————- = Rf
Distance moved by solvent
