Biological Molecules & Flashcards
What is a protein? How many are there? What is the composition of proteins?
One or more polypeptides
There are 20 proteinogenic amino acids each with a different R group.
CHONS
How is a peptide bond formed?
In a condensation reaction between the hydroxyl group of a carbonyl group, and the hydrogen of an amine group.
Molecule of water formed
What are the 3 components of an amino acid?
1) amine group on left ( NH2 )
2) carbonyl group ( C—O C-OH )
3) R group ( variable side chain )
The R group determines how each amino acid differs and why their properties differ
What is a dipeptide? What is a polypeptide? How does a peptide bond look?
2 amino acids joined together by peptide bonds
This a polymer of amino acids, so chains of amino acids joined by amino acids
C - N double bond O H
What is the primary sequence? What is the effect of a change in amino acids?
This is the sequence of amino acids that makes up a polypeptide joined by peptide bonds. This is determined by the DNA of a cell. This is specific for each protein, so a change in amino acids cause a change in the primary structure.
What is the secondary structure? What bonding is present?
The initial folding and coiling of a polypeptide chain
This includes alpha helixes ( between double bond oxygen of carboxyl group and hydrogen of amino group ) and regions of beta pleats
Hydrogen bonding ( between the NH and C double bond o group between nitrogen and hydrogen ) - this forms the beta pleats
This can be broken by high temp or pH changes
What is the tertiary structure? What bonding exists?
The further coiling of the secondary structure which forms the overall 3D shape.
Bonding :
- disulphide bridges between sulfur atoms, more specifically - two cysteine R groups of amino acids
- hydrophobic and hydrophilic interactions ( between polar and non polar R groups )
- hydrogen bonding ( between R groups )
- ionic bonding ( between positively and negatively charged R groups )
What is the quaternary structure?
One or more polypeptide chain
Each polypeptide is a subunit
What is the difference in hydrogen bonding between the secondary and tertiary structure?
Secondary - between amine and carboxyl groups
Tertiary - between R groups
How do plants make amino acids? What does a lack of proteins mean?
Glucose is joined with nitrate ions
Stunted growth
How do we get our proteins?
This is by consumption in our diet. But, many essential amino acids are not needed by our body.
Compare fibrous and globular proteins
Fibrous proteins are :
- strong
- insoluble ( hydrophobic R groups )
- unreactive
Eg. Collagen, keratin etc
Also, long and flexible
Structural roles
Globular proteins :
- soluble ( due to hydrophilic amino acids on outside - hydrophilic R group folded on outside and hydrophobic R group regions folded inside)
- spherical
- compact
- 3D structure
- often complementary to another molecule and therefore specific
- metabolic roles
Eg. Haemoglobin, enzymes, hormones
Why are globular proteins easily transported?
They are soluble
What are thr tests for lipids, proteins and starch?
Lipids :
Ethanol and water
Cloudy white emulsion if present
Proteins :
Bieuret solution
Blue to lilac / purple
Starch :
Iodine
Yellow brown to blue black
How do temp and pH affect structures?
Can cause tertiary and quaternary structure to unravel and go back to primary and secondary
Explain the structure of collagen, and where do we find it?
It is STRONG.
Glycine molecule every third amino acid so polypeptide chains lie close together
Small R group to allow polypeptide chains to wrap tightly
3 polypeptide chains wrap to form a triple left handed helix
CrossLinks between adjacent molecules and hydrogen bonding between chains
Staggered ends so no weak spots
We find it in tendons ( connect muscle to bones ), skin, and ligaments ( bone to bone ). It is suited to this purpose as it has a high tensile strength, flexible, insoluble, does not stretch
Explain the structure of keratin. Where do we find it?
This is made up of 2 polypeptide chains coiled together
It has a high proportion of cysteine so it can form desulfide bridges, making it strong
In hair, nails, claws ( i.e delicate parts of the body )
Outer layer of skin has keratin so impermeable to water
Explain the structure of elastin. Where do we find it?
It has tropoelastin fibres coiled like a spring. It stretches when blood passes through and recoils when blood leaves. It also has cross links between adjacent molecules. It is made up of hydrophobic groups joined together.
We find this in connective tissue and places like blood vessels, cartilage, walls of bladder and alveoli etc
What is the structure of haemoglobin? Describe the structure.
Haemoglobin has 4 polypeptide chains. Each polypeptide chain has a haem group, Fe 2+, which has a high affinity for oxygen - it can hold 4 oxygen molecules. It is a conjugated protein, so a protein with a prosthetic group ( non protein group ).
What molecules make enzymes?
Golgi apparatus, RER, lysosomes, ribosomes
What does Q10 mean? What is the formula for Q10?
The increase in ROR when temp is increased by 10 degrees. Rate of reaction at T+10 degrees / rate of reaction at T degrees
What is an enzyme?
Biological catalysts that increase the ROR by providing an alternative pathway with a lower AE. It is not used up.
Globular proteins with a specific tertiary structure to what it binds to
Active site of enzyme is complementary to the substrate
How are enzymes biological catalysts?
The substrate binds to the enzyme, lowering the activation energy. More substrates exceed the AE barrier so increased ROR
How does temp affect enzyme action?
Increase in temp means :
- enzymes and substrate have MORE KINETIC ENERGY
- move around more quickly and randomly
- more successful collisions between enzyme and substrate
- more ESC formed
Increased initial rate of reaction
An increase in temp can affect the bonds in the tertiary structure. It puts a strain on, and then breaks the hydrogen and ionic bonds. There is a change in tertiary structure so there is a change in the active site. This prevents the substrate binding to the enzyme, so the enzyme denatures. Less product formed. Causes a linear decrease in graph after optimum temp reached
Why are enzymes soluble in water?
They are globular proteins with hydrophilic amino acids on the surface
What is the impact of controlling the factors affecting enzyme action? What are the four factors?
Homeostasis should be maintained. This means enzymes can work at their optimum and function properly for the survival of organisms
These are
- pH
- enzyme conc
- substrate conc
- temp
What is an intracellular enzyme?
This is an enzyme that acts and functions inside the cell. For eg, catalase converts the harmful hydrogen peroxide to water and oxygen
What is an extracellular enzyme?
They are secreted by cells and catalyse reactions outside of cells. Examples of this are amylase which turns starch into maltose. It is secreted in the pancreas and released in the s.i. Also, trypsin turns proteins to peptides.
What is a key feature of enzymes?
It has a high turnover number so can catalyse substrates quickly
What type of pathways do enzymes control?
Metabolic pathways
Anabolic = building up reactions
Catabolic = breaking down reactions
Explain the lock and key theory
Active site of enzyme is complementary to the substrate
The substrate fits into the active site of the enzyme. This forms an ESC due to strains on the bonds. These are held together by amino acids on the surface of the enzyme. The product is a different shape to the enzymes active site, so it can no longer bind. This means it leaves the active site to catalyse another reaction. It remains UNCHANGED
Explain the induced fit theory
When the substrate binds to the active site of the enzyme, it affects and strains the bonds holding the tertiary structure. Therefore, the shape of the active site changes to accommodate to the substrate. It moulds itself around the substrate and is held together by oppositely charged groups. It also weakens the bonds in substrates, lowering the AE.
How does pH affect enzyme action?
An increase in H+ ions interferes and alters the with hydrogen and ionic bonds in the tertiary structure. Changes the charges on r groups. This changes the tertiary structure, changing the shape of the active site. This means the substrate can no longer fit into the active site as the enzyme is no longer complementary. This denatures the enzyme.
Or if more or less, less ESC complexes formed
The conc of H+ ions can give the best shape.
Use the phrase H+ ions
How does substrate conc affect enzyme action?
When the substrate conc is higher, there is a greater chance of substrate entering active site and hence collisions between the enzyme and the substrate. More ESC formed so higher rate of reaction.
However, once all the active sites are occupied, increasing substrate concentration no longer has an effect on the rate of reaction. This means enzyme conc is now the limiting factor.
How does enzyme conc affect enzyme action?
Increase enzyme conc = more active sites available
Greater chance of enzyme and substrate colliding, increased frequency of successful collisions, more ESC complexes formed, increased rate of reaction.
When all active sites occupied, increasing enzyme conc no longer has an effect on the rate of reaction. Substrate conc becomes the limiting factor
Extremes of pH and temp causes the conc of enzymes to reduce
What controls should we consider when carrying out the enzyme practical?
- Volume and conc of enzyme solution
- Volume and conc of substrate solution
- Controlling of temp ( use a thermostatic water bath )
- Control of pH ( buffer solution controls pH )
What is coenzymes and cofactors? Give examples.
Coenzymes are large organic molecules which transfer reactants between enzymes. Example of coenzyme is NAD. A cofactor is an inorganic ion that increase the activity of an enzyme and allow the enzyme to catalyse reactions. Examples of Cl- in amylase.
What is an competitive inhibitors? How does this affect rate of reaction?
This has a similar structure to the substrate and competes with substrate. This binds to the active site. This prevents the substrate binding to the enzyme. This reduces frequency of successful collisions, so there was ESC formed. This reduces the rate of reaction temporarily
How do we reduce the effect of a competitive inhibitor?
This is by increasing the substrate conc.
What affects the rate of inhibition?
The conc of inhibitors and substrates
What is a non competitive inhibitor? What is the effect on the rate of reaction?
The substrate binds to the allosteric site. This alters the tertiary structure of the enzyme, which changes the active site. This means the substrate can no longer fit into the active site of the enzyme. Reduced rate of reaction
What is a prosthetic group?
A non protein group permanently bound.
For eg, zn2+ in carbonic anahydrase
What is the key difference between inhibitors?
Competitive = binds temporarily
Non competitive = binds permanently
What does DNA and RNA stand for? What is its composition?
RNA - ribonucleic acid
DNA - deoxyribonucleic acid
CHOPS
What does DNA do?
Codes for sequences of amino acids which determine the final 3D structure of the protein
What is the monomer of DNA? Describe the structure of a DNA nucleotide, and how does this differ to a RNA nucleotide?
Nucleotides
Phosphate group attached to deoxyribose sugar ( ribose sugar ) attached to a nitrogenous base
DNA has a deoxyribose sugar, but RNA has a ribose sugar
What are polynucleotides, and how are they formed?
Polymers of nucleotides
They are formed via a condensation reaction between the deoxyribose sugar and phosphate group forming a phosphodiester bond and therefore, forms a sugar phosphate backbone. The bases stick out of the chain. These are strong covalent bonds, and ensure the genetic code is not damaged and passed onto other cells.
What are phosphorylated nucleotides? Give examples
ADP and ATP
More than one phosphate group
ADP ( 2 P )
ATP ( 3 P )
Where does the phosphodiester bond form specifically?
Between H on the carbon 3 of deoxyribose sugar, and hydroxyl group on phosphate group
