1.4 proteins and enzymes Flashcards
What is the structure of an amino acid?
Centra carbon atom
H atom
amino group - NH3
Carboxyl group - HO-C=O
and the r (variable) group
What bond is formed in condenation reaction of amino acids?
peptide bond
Where is the peptide bond formed in an amino acid?
the C of the carboxyl group of one amino acid and the N of the amino group of another amino acid
What is the N terminal of a polypeptide?
the amino group is at the end of the peptide chain
What is the C terminal of a polypeptide chain?
the carboxyl group is at the end of the polypeptide chain
What is the primary structure of a protein?
the sequence of amino acids in a polypeptide chain that is held in place by peptide bonds
What happens if the amino acid sequence was changed?
would change the structure of the protein
What is a secondary structure protein?
twisting of secondary structure into regular arrangement
it is either a alpha helix or a beta pleated sheet
What is a tertiary structure protein?
further folding of secondary structure into a 3D gobluar shape
What bonding occurs in a secondary structue protein?
H bonds between the carboxyl group and amino group
What bonding occurs in a tertiarty structure protein?
ionic bonds
h bonds
disulphide bridges occurs between r groups
What is a quaternary structure protein?
functional protein composed oof more then 1 polypeptide
the polypeptide might be a 2 or 3 structure
Where is the water removed from two amino acids in a condensation reaction?
The OH from the carboxyl group of one amino acid and the H from an amino group from the other amino acid
What is the bond formed in the condensation reaction between amino acids?
A peptide bond
What is a peptide bond?
The bond between the C from the carboxyl group of one amino acid and the nitrogen from the amino group of the other amino acid
What is the ‘N terminal’?
The amino group at the end of the polypeptide chain
What is the ‘C terminal’?
The carboxyl group at the end of the polypeptide chain
What is the structure of a fibrous protein?
Multiple secondary structure proteins that make a functional protein, folded to make a quaternary structure protein
What is the function of a fibrous protein?
Structural function
What are the properties of fibrous proteins?
High tensile strength
Insoluble in water
What are two examples of fibrous proteins?
Collagen
Keratin
What is Collagen’ structure (fibrous protein structure)?
Quaternary = 3 polypeptide chains which are secondary structure alpha helixes that are held in place by H bonds
What is the structure of a globular protein?
Single tertiary structure polypeptide
Or
Multiple tertiary polypeptide so a quaternary structure protein
What makes a globular protein soluble in water?
Hydrophobic interactions cause the R groups to face centre
What are the functions of a globular protein?
Biochemical
Enzymes
Pigments
Receptors
Antibodies
What does the function of a globular protein depend on?
The specific 3D shape
What is a congregate protein and an example of one?
A protein that contains a non-protein group which is called the prosthetic group eg: haemoglobin contains iron
What causes proteins to denature?
High temperatures breaks H bonds
pH breaks ionic bonds
What does denaturing a protein mean?
The bonds have been broken so it changes shape therefore stops functioning properly
What is the impact of fibrous proteins denaturing?
They lose their structural strength
What is the impact of globular proteins denaturing?
They become inactive and/or insoluble because the R groups move
What are the 4 bonds that maintain a proteins shape?
Peptide bonds
Ionic bonds
Hydrogen bonds
Disulphide bridges
What is a biological catalyst?
A substance that is produced by living tissue, that speeds up the rate of reaction without altering and being used up.
It does not cause a reaction to happen
What is catabolic enzyme action?
Breaks down something in the reaction
What is anabolic enzyme action?
Builds up something in the reaction
What does it mean by enzyme specificity?
The active site is specific to the substrate as they are complementary in shape. The enzymes are specific to 1 reaction for multiple similar groups of reactions
What is intracellular enzyme action and examples?
Happens inside the cell
Eg:
Lysosomes
Cytoplasm
Organelles like the mitochondrial membrane
What is extra cellular enzyme action and examples?
Happens outside of the cell
Eg:
The alimentary canal in the digestive system
How does an enzyme catalyse a reaction?
Does not react with the substrate and is not involved in the reaction
It provides the environment for reaction to occur
It lowers the activation energy
What is an exergonic reaction?
Products have less energy than reactants - energy is released
What is an endergonic reaction?
The reaction requires energy
What must the substrate shape be like to join the active site?
The substrate shape must be complementary to the active site and the shape must be maintained and specific
What is is called when the subtracted joins the enzyme?
Enzyme-substrate complex
What is the lock and key model of enzyme action?
The substrates shape is specific to the active site and will only fit in the active site of one specific site enzyme
The enzyme is unaltered by the reaction
What is the induced fit theory?
Initially the active site is not complementary in shape to the substrate
When the substrate fits, the active site alters and changes shape to fit the substrate
When the substrate leaves, the active site returns to original shape
What type of reaction is the formation of enzyme-substrate complexes?
Catabolic
What is an example of the induced fit model?
Lysosymes in lysosomes digest bacterial cell wall
What type of protein are enzymes?
Globular
What makes the substrate more stable ?
Forming an enzyme-substrate complex
What type of reaction is ATP hydrolysis?
Exergonic
What might you observe in an enzyme controlled reaction?
The product appearing
The substrate disappearing
Bubbles - O2
What effect does temperature have on enzyme action?
Increases KE
More successful collisions between substrate and active site
What happens if there is excess substrate in an enzyme controlled reaction?
The no. Of active sites becomes a limiting factor because all the active sites are occupied
Why does substrate conc become a limiting factor in an enzyme controlled reaction?
Because it has been converted into product
How do you calculate the rate of production of a product from a graph?
Change in y/ change in x
What is the units for rate?
Mg dm-3 min-1
How do you calculate the percentage change in a reaction?
Original - new / original
X100
How do you calculate the initial rate of reaction?
Draw a tangent and y/x
Tangent starts from 0
What does it mean if the reaction has stopped?
Not all the substrate was converted into product
What does it mean if the reaction has finished?
All the substrate has been converted into product
How do you calculate rate of reaction from the time taken?
1/T
What are the units for rate of reaction calculated from time?
S-1 x10-3
How do you calculate rate of reaction from mass or volume?
Volume/ T
Mass/T
What are the units for rate of reaction calculated from volume?
Cm3s-1
Describe the graph showing the effect of temp on rate of reaction in an enzyme controlled reaction.
- Initially, as temp increases, ROR increases
- Max ROR occurs at the optimum temp
- As temp increases beyond optimum, ROR decreases
Why does ROR initially increase with temp?
Increase in KE of enzymes and substrate so more successful collisions and more enzyme-substrate complexes formed so more product is formed per unit or time
Why does ROR decrease as temp increases beyond the optimum?
Increase KE amino acids vibrate, H bonds between R groups break in the tertiary structure so the active site changes shape, denatures when not complementary to substrate
Describe the graph showing the effect of pH on ROR in exams controlled reactions
A slight change in pH decreases or increases the ROR
1. Optimum ph - lots of product produced
2. Inactivation - less product produced between 2 phs
3. Denaturing at lowest and highest pH on x axis
Explain the pH and ROR graph with enzyme action
- Optimum- complementary to active site
- Different enzymes work at different pHs, during inactivation, the active site changes shape so it is less complementary
- At extreme pHs the tertiary structure changes shape as it breaks the ionic bonds
Describe the the ROR and substrate conc graph
Substrate conc increases so ROR increases
After a certain substrate conc, a further increase in substrate conc the ROR remains constant
Describe the enzyme conc and ROR graph
Enzyme conc increases so ROR increases
After a certain enzyme conc, a further increase in enzyme conc the ROR remains constant
Explain the substrate conc and ROR graph
Substrate conc is the limiting factor initially
Then the conc of enzymes becomes the limiting factor as there is excess substrate past the point of saturation
Explain the enzyme conc and ROR graph?
Initially the enzyme conc is the limiting factor
Then the substrate conc becomes the limiting factor as there are excess enzymes to bind to
What is an enzyme inhibitor?
A chemical or molecules that slows down enzyme activity
What are the two types on enzyme inhibitors?
Competitive and non-competitive
What is competitive inhibition?
It is complementary to the active site
It binds to the active site and blocks the substrate
The substrate and inhibitor are similar in shape
What is an example of a competitive inhibitor?
The resp inhibitor - malonate
What is non-competitive inhibition?
The substrate and inhibitor have different shapes, it binds to the enzyme in a different place than the active site - the allosteric site
The tertiary structure changes shape so the active site changes shape - substrate does not fit - enzyme denatured
What is the allosteric site?
Once the inhibitor has bonded this is the area it is bonded to is called
How can you get max ROR with a competitive inhibitor present?
Increase substrate conc
What is an example of a non-competitive inhibitor?
The resp inhibitor - cyanide
How can you reach max ROR with non-competitive enzymes present?
Max ROR cannot be reached
What is a metabolic pathway?
A series of reactions in which each step is catalysed by an enzyme
What is end-product inhibition?
The product from one enzyme catalyst, acts as a regulator in excess and can become an inhibitor to a different enzyme step in the metabolic pathway
What is a conjugated protein?
a protein to which another chemical group (e.g., carbohydrate) is attached by either covalent bonding or other interactions
What organelle helps translate the primary structure of a protein?
Ribosomes
How does an enzyme act as a catalyst by the induced fit model?
substrate binds to the active site
active site changed shape so it is complementary to the substrate
reduces the activation energy
How can you stop an enzyme catalysed reaction?
boil - denature enzyme
put in freezer - reduces KE
add high conc of inhibitor - E-S complexes do not form
How does a competitive inhibitor reduce ROR?
inhibitor is similar in shape to substrate
binds to the active site
prevents E-S complexes forming
How does a structure of a protein depend on the amino acids?
Structure determined by position of the amino acids
Primary structure is the sequence of amino acids
Secondary structure formed by hydrogen bonding between amino acids
Tertiary structure formed by interactions between R groups
Creates active sites on enzyme
Quaternary structure formed by interactions between polypeptide chains
How does non-competitive inhibition reduce ROR?
Attaches to the enzyme at a site other than the active site
Changes shape of active site
No longer complementary so no more binding
How is there always a NH2 and COOH at the end of a polypeptide?
peptide bonds join amino acids
there is a free NH2 and COOH at either end
Why do enzymes denature at a faster rate at higher temps?
more kinetic energy
