Proteins + enzymes Flashcards
What re the functional groups of amino acids
- amino group
- R group
- carboxyl group
What is the R group
- variable functional group that changes depending on the type of amino acid
How are dipeptides made?
- condensation reaction
- peptide bond formed
- chemical reaction joining two amino acids with a peptide bond forming a dipeptide and releasing a water molecule
What are the similarities between all dipeptides
- all contain carboxyl group
- all contain amino group
- all have two R groups
- all contain C and H and N and O
What is the role of proteins
Enzymes - These proteins are used to breakdown and synthesise molecules
Antibodies - These proteins are involved in the immune response.
Transport - Some proteins can move molecules or ions across membranes.
Structural components - Proteins like keratin and collagen are used to create strong fibres.
Hormones - Some of these are proteins that act as chemical messengers in the body.
Muscle contraction - Muscles are made up of proteins.
Describe the structure of an amino acid
- central carbon
- amino group (NH2)
- carboxyl group (COOH) opposite the amino group
- R group opposite hydrogen
What are the different structures of proteins?
- primary
- secondary
- tertiary
- quaternary
Describe the primary structure
- sequence of amino acids in the polypeptide
- bonded by covalent peptide bonds
- DNA of a cell determines the primary structure of a protein
- specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)
describe the secondary structure
- interactions between localised sections of polypeptide chain
- 2 chains: alpha helix and beta pleated sheets
- held in place by hydrogen bonds
describe the hydrogen bonds in a secondary structure
- weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
- can be broken by pH and temp
Describe alpha helix structure
- hydrogen bonds form between every fourth peptide bond
- between the oxygen of the carboxyl group and the hydrogen of the amine
Describe beta pleated sheet structure
- when the protein folds so that two parts of the polypeptide chain are parallel to each other
- enabling hydrogen bonds to form between parallel peptide bonds
Describe tertiary structure
- overall 3D shape of polypeptide
- Further conformational change of the secondary structure
- additional bonds forming between the R groups (side chains)
- shape varies in the 20 amino acid structures that determine function
- bonds: hydrogen, ionic, hydrophobic interactions, disulphide bridges
what are disulphide bridges?
- occurs between cysteine amino acids
- type of covalent bond
- R group has SH group -> sulphur atoms are bonded and hydrogen atoms are lost
- strong and broken by reducing agents (chemicals)
what are hydrophobic interactions?
- between non polar R groups
- hydrocarbons are hydrophobic (R groups have hydrocarbons) amongst amino acids
- very weak + easily broken
what is a quaternary structure?
- made of >1 polypeptides chain
- formed by interactions between polypeptides
- work together as a functional macromolecule
- each individual polypeptide chains refer to as subunit
bonds: hydrophobic interactions, hydrogen, ionic, disulphide bridges
what is ionic bond here?
- Ionic bonds form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups
- Ionic bonds are stronger than hydrogen bonds but they are not common
- These bonds are broken by pH changes
What are globular proteins
- compact, water soluble, spherical
- formed form overall 3D folded structure into tertiary structure
- bc of non polar hydrophobic R groups oriented toward centre
- bc of polar hydrophilic R groups oriented towards aqueous surroundings
Explain the solubility property of globular proteins
- important physiological roles
- can be transported easily
- involved in metabolic processes
Explain the folding of the protein
- due to interactions between R groups
- have specific shapes
- enables important physiological roles
e.g. enzymes, immunoglobulins respond to specific antigens
What is a conjugated protein
- type of globular protein
- contains non polar component = prosthetic group
What is a prosthetic group
- non protein part of a protein molecule
- permanently attached to the molecule
- vital for normal functioning of molecule
what are the different types of prosthetic groups?
- lipids or carbohydrates combine with proteins -> lipoproteins or glycoproteins
- metal ions + molecules derived from vitamins can form prosthetic groups
what is haemoglobin
- conjugated protein, found in red blood cells
- transports oxygen from lungs to body tissues
What is the structure of haemoglobin
- made of 4 polypeptide chains (quaternary structure)
- 2 alpha globin, 2 beta globin
- has prosthetic group iron ion (Fe^+2) = called haem group
- one oxygen molecule bonds to each haem group (Each haemoglobin transports oxygen = maximises amount transported)
- haem group is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red
what is insulin
- hormone made + secreted by pancreas
- helps maintain blood glucose levels
What is the structure of insulin
- 2 polypeptide chains: alpha and beta
- joined by disulphide links
explain the features of insulin
- shape allows it to specifically bind to receptors on cell membranes –> lower BGLs
- has hydrophilic R groups on outside –> soluble in water –> insulin can dissolve in blood + get transported round the body
Describe pepsin
- catalyses digestion of proteins
- found in stomach (Acidic env, low PH)
describe structure of pepsin
- primary structure, very few basic R groups
= prevents tertiary structure being impacted by low PH - tertiary structure kept stable by hydrogen bonds + disulphide links
why does enzymes get denatured at low PH
- bc of amino acids with basic R group
- basic group acts as base -> accepts Hydrogen ions –> becomes positively charged
- basic R group becomes +vely charges -> changes structure
- affects ionic and hydrogen bonds –> denature protein + alter function
What are fibrous proteins?
- long strands of polypeptide chains
- have repeating sequences of amino acids
- have long cross linkages due to hydrogen bonds
- have little or no tertiary structure
- amino acids have non polar R groups –> insoluble in water (suitable for structural roles)
- polypeptide chains form fibres –> tough and strong protein
Describe collagen
- forms strong fibres
- connective tissue sound in skin, tendons, ligaments, biomes, blood vessels
- found in artery walls to prevent vessels from from high pressure
- used to make tendons which connect muscle to bone = allows skeleton to move
- used to make bone
- provide structural support and stable and flexible and tough
what is the structure of collagen?
- formed from three polypeptide chains closely held by hydrogen bonds
- triple helix shape (not alpha helix)
- every 3rd amino acid in primary structure = glycine
Describe keratin role
- hard, strong
- makes up nails, horns, hooves, hairs, feathers
- protects epithelial cells
- strengthens skin + internal organs
- controls hrowth of epithelial cells
- maintains elasticity in skin
what is the structure of keratin
- primary structure = high amounts of of cysteine (amino acid sulfur)
- disulphide links between two polypeptide chains = hard + strong
- intertwined to form coils, join to make a-keratin / pleated sheets (beta pleated sheets)
Describe the role of elastin
- elastic properties = stretch + recoil (bc of coiling and crosslinks that keep them together
- found in lungs –> to inflate and deflate
- in arteries –> easier to pump blood for heart
- in bladder –> expand and hold urine
- in blood vessels –> maintain pressure by stretch and recoil
what is the structure of elastin?
- many molecules of large flexible molecules
- made of tropoelastin
- many amino acids
- grouped in short, repeated sequences of 3-9 amino acids
- hydrophobic amino acids –> hydrophobic domains
Describe how the structure of a protein depends on the amino acids it
contains.
- Structure is determined by position of amino acid/R
group - Accept for ‘interactions’, hydrogen bonds / disulphide
bridges / ionic bonds / hydrophobic hydrophilic
interactions - Primary structure is sequence/order of amino acids
- Secondary structure formed by hydrogen bonding between amino
acids - Tertiary structure formed by interactions between R groups
- Creates active site in enzymes
- Quaternary structure contains >1 polypeptide chain
Describe how amino acids join to form a polypeptide so there is always
NH2 at one end and COOH at the other end.
- One amine/NH2 group joins to a carboxyl/COOH group to form a
peptide bond - there is a free amine/NH2 group at one end
and a free carboxyl/COOH group at the other
Describe a biochemical test to confirm the presence of protein in a
solution.
- Add biuret (reagent) = sodium hydroxide solution and copper sulphate solution
- Positive result = lilac
Explain what the positions of the spots in the diagram show about these
amino acids
- Moved to negative electrode because positively charged
- Spots move different distances bc amino acids
different charge/mass - Two spots not three because amino acids same charge/mass
Describe how a peptide bond is formed between two amino acids to form a dipeptide.
- Condensation reaction/ loss of water
- Between amine / NH2 and carboxyl / COOH;
The secondary structure of a polypeptide is produced by bonds between amino acids.
Describe how.
- Hydrogen bonds;
- Between NH group of one amino acid and C=O group
- Forming β pleated sheets / α helix;
A change from Glu to Lys at amino acid 300 had no effect on the rate of
reaction catalysed by the enzyme. The same change at amino acid 279
significantly reduced the rate of reaction catalysed by the enzyme.
Use all the information and your knowledge of protein structure to suggest
reasons for the differences between the effects of these two changes.
- Both negatively charged to positively charged change in amino
acid - Change at amino acid 300 does not change the shape of the active
site bc does not change the tertiary structure - Amino acid 279 may have been involved in a bond and so the shape of the active site changes
.
Fibrous proteins usually have a structural function. Suggest why.
long unbranched chains give strength
Globular proteins can be used as recognition molecules on cell surfaces. Explain why.
Specific 3D shapes makes the protein distinctive for recognition
Explain how a change of one amino acid can lead to a change in the structure and properties of the haemoglobin protein.
- primary structure is the sequence of amino acids in a polypeptide chain.
- 20 naturally occurring amino acids and they all have different chemical groups making them be unique
- as well as leading to different bonds such as ionic, hydrogen and disulphide bonds.
- change of one amino acid ultimately led for the properties of the haemoglobin to change such as the solubility, flexibility.
Give three differences between fibrous and globular proteins.
- Globular proteins are soluble in water.
- Globular proteins were hydrophilic on the outside.
- Globular proteins typically have metabolic roles while fibrous proteins
The skin contains a fibrous protein. This protein forms a barrier to the entry of microorganisms, name the protien
keratin
Describe the structure and properties of fibrous proteins.
- little amount of tertiary and quaternary structure
- made up of long polypeptides
- polypeptides can link through different bonds
- both insoluble and tough.
Describe the three-dimensional (tertiary) structure of an enzyme
- globular proteins
- active catalysts
- Active sites are folds in the tertiary structure.
- Molecules of the right arrangment of attractive groups can fit into active sites.
What is the best description of denaturation of proteins?
The unfolding of the protein into a random, less useful shape
Collagen is an example of which type of protein?
structural protein
Explain the strength of collagen fibres?
Bonds occur between amino acids of adjacent polypeptide chains
Which best describes the quaternary structure of collagen?
Three polypeptide chains wound together with bonds between amino acids of adjacent chains
define complementary
similar shaped molecules which can fit together
define enzymes
- biological catalysts + proteins
- speed up the rate of chemical reactions without being used up
- lowers activation energy
- can be reused and are effective in small amounts
Describe how an enzyme such as pepsin breaks down a substrate
- substrate will fit pepsin’s active site
because it is complementary to the enzyme’s active site shape - the active site shape will then slightly alter = conformational changes
- this is the induced fit hypothesis
- an enzyme substrate complex is formed
- bonds in the substrate get destabilised
forming an enzyme product complex - products leave the active site
in this case the products are amino acids
describe impact of changing pH on enzyme activity?
- as pH increases enzyme activity increases
- until certain point wher as pH increases rate of enzyme activit drops sharply and decreases
- at extreme pH
hydrogen and ionic bonds that hold tertiary structure together are broken due to excess H+ and OH- ions leading to desaturations - enzyme substrate complex forms less easily due to active site being altered
describe the graph for substrate conc
- there is a linear increase in reaction rate as substrate is added
- which then plateaus when all active sites become occupied
how can end product inhibiton be used?
- enzyme converts substrate to product
- process is itself slowed down as the end-product of the reaction chain binds to an alternative site on the original enzyme
- changes the shape of the active site and preventing the formation of further enzyme-substrate complexes
- end-product can then detach from the enzyme and be used elsewhere
allows the active site to reform and the enzyme to return to an active state
as product levels fall, the enzyme begins catalysing the reaction once again, in a continuous feedback loop
how can pH affect the tertiary structure of a protein?
- causes bonds which hold the tertiary structure to break
- shape no longer maintained
how does the enzyme active site chanaging shape as a result of change to tertiary structure relate to structure?
- substrate will no longer fit into active site
- enzyme substrate complex cannot be formed
- enzyme can no longer carry out its function
how does the enzyme active site shape relate to structure?
- it is determined by the enzyme’s tertiary structure
- in turn is determined by the primary structure
how does the enzyme being specific relate to structure?
only one complementary substrate will fit into the active site
how does the primary structure of a protein relate to structure?
- determined by a a gene
- if mutation occurs in the gene then it could change primary and tertiary structure of enzyme produced
- enzyme active site shape changes
In humans the enzyme maltase breaks down maltose to glucose. This takes part at normal body temperature.
Explain why maltase:
- only breaks down maltose
- allows this reaction to take place at normal body temperature
- tertiary structure of enzyme
active site shape is complementary to maltose - the shape of active site changes as substrate binds to it + complimentary to substrate form E-S complex
- enzyme is a catalyst lowers activation energy to body temperature
what happens to counteract the increase in competetive inhibitor conc?
- increasing the substrate concentration can increase the rate of reaction once more
- more substrate molecules mean they are more likely to collide with enzymes and form enzyme-substrate complexes
what are non competetive inhibitors?
- molecules that bind to the enzyme at an alternative site (called allosteric site)
- alters tertiary structure
changes shape of the active site - prevents the substrate from binding to it
- do not compete with substrate molecule bc they are diff shape
what are the enzyme properties?
- very specific - only catalyse one reaction
active site shape - primary structure of a protein
- if tertiary structure is altered shape of active site with change
what are the factors affecting enzyme action?
- temperature
- pH
- enzyme concentration
- substrate concentration
- concentation of competetive inhibitors
- concentration of non competetive inhibitors
what are the two types of enzymes and where can they act?
- intracellular (enzyme that acts within a cell/at a cellular level)
- extracellular (secreted by cells + acts outside the cell they are made from)
what happens to counteract increase in conc of non comp inhib?
- increasing the substrate concentration cannot increase the rate of reaction once more
- as the shape of the active site of the enzyme remains changed and enzyme-substrate complexes are still unable to form
what happens to the enzyme when pH changes?
- changes the number of hydroxide ions and hydrogen ions (OH− and H+) surrounding the enzyme
- interact with the charges on the enzyme’s amino acids, affecting hydrogen bonding and ionic bonding
- so resulting in changes to the tertiary structure.
what happens if you increase conc of inhibitor on rate of reaction?
reduces the rate of reaction and eventually, if inhibitor concentration continues to be increased, the reaction will stop completely
what is a catabolic reaction?
- breaking down of complex molecule into simpler products
- single substrate drawn into active site => broken apart into two or more products
- fit into active site -> strain on bonds in substrate -> substrate molecule breaks up more easily
what is a competitive inhibitor?
- have similar shape to that of the substrate molecules
- compete with the substrate for the active site
- rate of reaction decreases or wont occur
- block active site so that no substrate can fit + bind
what is an anabolic reaction?
- reaction that joins molecules
- draw two or more substrates into active site => form bond => release single product
- being attached to an enzyme hold them
close together => reduces repulsion between molecules => bond easily
what is an example of each enzyme?
- catalase (intra)
- amylase (extra)
what is an inhibitor?
- stops or reduced enzyme activity
- act as regulators in metabolic pathways
two types:
- competetive
- non competetive
what is induced fit hypothsis?
- enzyme active site shape is complementary to the substrate
- will bind and form enzyme substrate complex
- enzyme and its active site (and sometimes the substrate) can change shape slightly as the substrate molecule enters + binds to enzyme
- changes in shape are known as conformational changes
- deal binding arrangement between the enzyme and substrate is achieved
- This maximises the ability of the enzyme to catalyse the reaction
what is the end product inhibition?
- Metabolic reactions controlled
- using the end-product of a particular sequence of metabolic reactions as a non-competitive, reversible inhibitor
what is the imact of temp?
- low temperatures slow down reactions
= molecules move realtively slow so there are less frequesnt and successful collisions between substrate molecules and enzyme active site
= less frequent enzyme substrate complexes formed and enzymes collide with less energy
= less likely for bonds to form/break - high temperatures speed up reactions
molecules move quicker
= highly frequent and successful collisons between enzyme active site and substrate
= substrate and enzyme collide with more energy
= more likely to break/form bonds - temp continues to increase
= bonds holding enzyme molecule in its shape begin to break
= teritiary structureof enzyme changes
= permanently damges active site, prevents substrate from binding
= denatured - specific optimum temperature
catalyse reaction at maximum rate
what is the impact of enzyme concentration?
- as enzyme concentration incrases, rate of reaction increases
= more enzyme substrate complexes can be made to create products - as enzyme conc increases where there is a fixed amount of substrate, rate of reaction remains the same
= substrate is the limiting factor
= no further substrates to form enzyme substrate complexes with other enzymes
what is the impact of substrate conc
- Greater substrate concentration = higher rate of reation
= more enzyme substrate complexes can be made to create products - If the enzyme concentration remains fixed but the amount of substrate is increased past a certain point = rate of reaction stays the same
= available enzyme’s active site are all occupied/become saturated
= substrate molecules that are added have nowhere to bind in order to form an enzyme-substrate complex
what is the lock and key hypothesis?
- shape (as well as the shape of the active site of an enzyme) is determined by the complex tertiary structure of the protein that makes up the enzyme
- enzymes are highly specific
- enzymes and substrates were rigid structures that locked into each other very precisely, much like a key going into a lock
active site shape is complementary to substrate
= substrate fits into active site like key into lock
what is the structure of an enzyme?
- tertiary
- globular
- functional part: active site (where substrate binds)
what is Vmax
- maximum initial rate of reaction
- v = velocity/speed of reaction and max rate
why are these models
they are the best accepted theories based on the evidence we have
why is the induced fit model accepted?
better able to explain how catalysis actually occurs
