Unit 1 Biological Molecules (Proteins) Flashcards
What do amino acids join together to form before they become proteins?
They become polypeptides.
How are dipeptides formed?
Dipeptides are formed from the condensation reaction of two amino acids.
How are polypeptides formed?
Polypeptides are formed from the condensation of many amino acids.
What atom is the central part of each amino acid?
The alpha carbon atom is the central of each amino acid.
What are the 4 groups bonded to the central carbon atom within a amino acid?
Amine, carboxyl, hydrogen and an R group
What is the R group?
A different group within each individual amino acid.
Why is the R group essential for each amino acid?
The R group determines how each amino acid interacts and bonds with other amino acids in the polypeptide chain.
How many types of amino acids are there that are common between most organisms?
20 amino acids
How many amino acids cannot be produced by the human body and need to be digested?
10 amino acids
What is different about glycine compared to all the other amino acids?
Glycine is the only amino acid that contains a hydrogen bond within its R group as well not a carbon atom within its R group.
What is the name of the bond formed between amino acids called?
A peptide bond
What do the 2 amino acids at each end of the polypeptide chain form?
They form terminals at each end.
What are the 2 amino acid terminals at each ends of the polypeptide chain called?
The N-Terminal = The amine terminal
The C-Terminal = The carboxyl terminal
Describe the bonding when amino acids join together?
A bond forms between the carboxyl group of one amino acid and the amine group on another amino acid.
What is released as a by-product of the bonding of 2 amino acids?
Water
What type of bond is the peptide bond?
Covalent bond
What type of structure is the antibody?
Protein
What are antibodies made up of because they are proteins?
Polypeptide chains.
What are antibodies used up in?
The immune response
What type of proteins are antibodies?
Diverse proteins
What is the difference about each individual protein?
Each individual protein has its own difference sequence of amino acids.
What do transport proteins include?
They include channel proteins.
What are the roles of transport proteins?
Transport proteins transport molecules along the cell membranes.
What are different about the molecules that transport proteins, transport along cell membranes?
They transport molecules that are too large to diffuse across freely or molecules that carry a charge.
Describe structural proteins?
Structural Proteins are long, strong polypeptide chains.
What are a special feature that structural proteins have when forming chains?
Structural proteins are connected by cross-links that are held together by parallel sides.
Give 2 examples of structural proteins?
Collagen and keratin
What are Enzymes?
They are biological catalysts.
What are the roles of enzymes?
They increase the rate of a reaction without being used up.
Describe the structure of enzymes?
They are usually tightly folded, complex proteins that are soluble.
What test is used to test for proteins?
The Biuret Test
What are the steps within the Biuret Test?
1) Add sample to distilled water and biuret solution.
2) Shake and leave upright for 5 mins
If the protein is present within the sample what is the colour change of the solution?
The solution changes from blue to violet.
What has to happen to the amino acids in order for them to be present within the solution?
The amino acids were joined together to be present within the solution which means it would be able to create the protein.
What does the primary structure of a protein means?
The primary structure is the order of amino acids within a polypeptide chain.
What is the primary structure determined by?
The gene encoding the protein.
What can a change in the nucleotide sequence of the gene’s coding DNA do?
A new amino acid being added to the growing polypeptide chain.
What else could a change in the amino acids lead to?
A change in the protein’s structure, shape and function.
What forms the secondary structure?
The primary polypeptide chain.
What do amino acids in a polypeptide chain form between other amino acids in the chain?
Hydrogen bonds.
What do the hydrogen bonds cause the protein to do?
The hydrogen bonds cause the proteins to fold into specific structures.
What determines the secondary structure of a protein?
The folding of the polypeptide chain determines its secondary structure.
What are the 2 most common secondary structures?
The beta- pleated sheet and the alpha-helix.
What is one word that describes the secondary structure of a protein?
Stable
What is the difference between individual hydrogen bonds and many hydrogen bonds joined together?
Individual hydrogen bonds are weak but many hydrogen bonds are very stable.
What factors can decrease the stability of the secondary structure?
pH and Temperature
What forms the tertiary structure?
The secondary polypeptide chain is folded into a tertiary polypeptide chain.
What is structurally different about the tertiary structure compared to the secondary and primary structures?
Tertiary structures are 3D
What groups form the side chains on amino acids?
R groups
What are 2 words that are used to describe the 3D tertiary structure?
Coiled or folded.
What happens when a protein loses its 3D shape?
It may not be able to function at an optimum level or even at all.
What are different about the side chains of charged amino acids?
The charged amino acids have either a positive or negatively charged ion on either side of the side chain.
This happens due to hydrophobic interactions
What can happen due to charged amino acid side chains?
They can form relatively strong ionic bonds with other amino acids.
What are the 3 ways sulphur bonds are expressed?
S-S, Disulphide bridges and disulphide bonds.
What type of bond is a disulphide bond?
It is a covalent bond.
Where are S-S bonds found?
In CYS Proteins (cysteine amino acids).
What does the overall stability of the tertiary structure increase due to?
Hydrogen bonds
What creates the complex 3D structure of a protein?
R group interactions
What forms a quaternary structure?
Many 3D polypeptides bonded together
How many polypeptides does haemoglobin contain?
Quaternary structured proteins may have a prosthetic group (inorganic compound) they are called?
4
The conjugated protein
What is the R group within haemoglobin?
The haem group
What is collagen?
A fibrous protein found within the skin.
What do the weak interactions between the subunits in insulin help with?
The weak interactions between the subunits in insulin polypeptide chain help with the overall stability of the quaternary structure.
What are the 2 main combination bonds within insulin
Hydrogen bonds and Disulphide bonds
The combination of hydrogen and disulphide bonds can make insulin into what type of shape?
A Clumped, globular (ball) shape
What type of reactions do enzymes catalyse?
Enzymes catalyse biochemical reactions
Where around the cell can enzymes catalyse reactions?
Enzymes catalyse reactions inside and outside of cells.
What is the activation energy?
A specific amount of energy needed to start a chemical reaction.
Can the Activation energy for different types of reactions?
Yes
How do enzymes increase the rate of the reactions? (General answer)
Enzymes reduce the activation energies of chemical reactions inside the cell which in turn increase the rate of chemical reactions.
Describe how enzymes increase the rate of reactions? (Greater Depth)
Enzymes bind to the reactant molecule and allow bond-breaking and bond forming processes to form more easily.
What are the chemical reactants that bind easily called?
Substrates
What is different about the active site for each enzyme?
The active site for each enzyme is different based on each substrate binding to it.
What is the enzyme-substrate complex?
The enzyme-substrate complex is formed when the substrates are complementary to the active site of the enzyme.
What is the shape of the enzyme determined by?
The shape of the enzyme is determined by the tertiary structure of the polypeptide chain.
What model was used to describe the enzyme action?
The Lock and Key Hypothesis
Explain the lock and key hypothesis in terms of the enzyme action?
The substrate is the key that fits into the lock which is the active sit of the enzyme.
What is the alternative model to the lock and key model?
The Induced fit model
Describe how the Induced fit model works?
The enzyme and the substrate come together and when they interact it causes a small shift in the enzyme structure.
What does the shift in the enzyme structure do?
The shift allows the enzyme and the substrate to bind and catalyse a reaction.
What is a denatured enzyme?
External factors that can affect the tertiary polypeptide chain within an enzyme that can affect its shape and how it can function.
Explain how changing the pH affects the enzyme? (1st step)
Changing the pH means that the number of hydroxide and hydrogen ions around the enzyme.
Explain how changing the pH affects the enzyme? (2nd step)
These hydrogen and hydroxide ions interact with the charges on the enzymes amino acids which change the ionic and hydrogen bonding which can affect the tertiary structure of the enzyme’s shape.
What does increasing the temperature do to the energy of the molecules.
Temperature increases the kinetic energy of the molecules.
Explain how increasing the temperature allows the rate of reaction to be faster?
Increasing the temperature increases the chance of a collision between the enzyme an the substrate so more collisions happens in a shorter amount of time which means increased rate of reaction.
What happens to the rate of the reaction if the temperature is increased by 10C?
Usually the rate of reaction will double for most enzyme controlled reactions.
What happens to reaction rate if enzyme concentration was increased?
Increasing the enzyme concentration means thee are more available enzymes ready to catalyse substrates in a set time. So reaction rate increases
What happens to the reaction rate if substrate concentration was increased?
Substrate concentration increases the number of enzyme-substrate complexes until all the substrates have formed Enzyme-Substrate complexes in which the rate of the reaction starts to stay the same.
When the rate of reaction starts to stay the same it is called?
Saturation of the enzyme
What are inhibitors?
Chemicals that slow down or stop the rate of a chemical reaction.
Through what feature are both the inhibitors and substrate similar?
The shape of the inhibitors are the same as the substrate that fit into the enzymes active site blocking the entry of the substrate.
Give 2 examples of a competitive inhibitor?
Succinate ions
Malonate ions
What enzyme does the malonate ions have to block?
Succinate dehydrogenase
What cycle is succinate dehydrogenase important in?
The Krebs cycle
What is the basic explanation of The Krebs Cycle?
It is a cycle that is used in the process of releasing the energy during respiration.
What 2 effects do non-competitive inhibitors have on the enzyme?
A reversible and non-reversible effect.
What substance denatures enzymes required to synthesise haemoglobin?
Lead
What is an additional feature to non-competitive inhibitors that competitive inhibitors cannot do?
Non-competitive inhibitors can change the shape of an Enzyme’s active site so that it is no longer complementary to the substrate.
Where are the non-competitive inhibitors attached to on a Enzyme?
Not the active site of the enzyme but another site.
What are 2 ways the rates of reactions can be calculated?
The decrease in reactants
The increase in products
What is the y-axis on the rate of reaction labelled as?
Enzyme Activity
What is the x-axis on the rate of reaction labelled as?
Time
Give 1 examples of what the y-axis can be?
Seconds
Give 2 examples of what the x-axis can be?
Decimetre cubed and centimetre cubed
What does the optimum conditions of an enzyme mean?
The level at which an enzyme works at its maximum rate.
Where is pepsin found?
It is a digestive enzyme found in the stomach.
What is the optimal condition of pepsin?
pH of 1.5
What is the optimal conditions for lipase?
pH of 8
(E) What class of protein enzymes is protease included within?
Endopeptidase
(E) Give an explanation about Endopeptidases?
It cleaves proteins in the middle of proteins and not at the ends.
Explain why pepsin can only be an Endopeptidase? (1st step)
1) Proteins are polymers made of amino acids monomers, connected by peptide bonds.
Explain why pepsin can only be an Endopeptidase? (2nd step)
2) The ends of the protein do not have a peptide bond but an amine group on on end and a carboxyl group on another.
Explain why pepsin can only be an Endopeptidase? (3nd step)
3) The active site of pepsin has a specific shape. The tertiary structure of the enzyme is complementary to the peptide bonds formed by other amino acids.
Explain why pepsin can only be an Endopeptidase? (3nd step)
4) This means the ends of the protein can’t fit into the active site of the enzyme. As only the middle of the protein can bind to the enzyme’s active site to form the enzyme-substrate complex.
Explain the basic temperature dependence trend in enzymes?
Activity initially increases with temperature. The energy of the reactants increases so protein and enzyme collision chances increases. Therefore increasing the activation energy.
Explain the basic temperature dependence (Denaturation) trend in enzymes?
When the temperature eventually crosses the optimum temp, enzyme activity decreases. An increase or decrease in the pH of the enzyme can also decrease which results in the decreasing activity of enzymes.
Why does sudden pH change affect enzyme activity?
Enzyme activity would suddenly decrease due to the tertiary structure of the protein changing causing denaturation.
(E**) What causes the changes in protein structure through the three or four levels of structure?
The primary chain folds to form secondary structures of alpha helix and beta pleated sheets which then fold onto each other to form the tertiary structure.
(E**) What structural level of proteins is functional? Why?
The tertiary structure is functional as it contains the geometric shape showing the necessary loops and bends.
(E**) What are chaperones?
Chaperones are proteins that help with folding or unfolding of larger proteins.
(E**) What two elements are used in the formation of amino acids?
Hydrogen and Nitrogen
(E**) What types of amino acids would you expect to find on the surface of a soluble protein and which would you expect to find in the interior?
Polar and charged amino acids will be found on the surface of a membrane protein however non-polar in the interior. The inner membrane protein will be polar and hydrophilic.
(E**) What would happen if even one amino acid is substituted for another in a polypeptide?
The amino acid may or may or not have any significant effect on the protein structure and function.
(E**)What would happen if even one amino acid is substituted for another in a polypeptide? Give an example if there may be a mutation.
In the case of haemoglobin, the sickle cell trait can occur due to a mutation in the gene sequence.
Describe the shape of globular proteins?
They are sperical in a ball shape and are tightly folded in 3D polypeptide chains
Describe the polarity within the globular proteins?
Hydrophobic - inside
Hydrophyllic - outside
Describe the properties of globular protein?
Soluble in water
Like hormones such as insulin
Like Transport proteins such as haemoglobin and or myoglobin
Like enzymes such as lipase
What are fibrous proteins?
Parallel polypeptide chains held by cross fibres
