Chapter 3: Proteins and Enzymes Flashcards
State the elements found in
a) all proteins
b) Some proteins
a) All = C, H, O, N
b) Some proteins = S
State the 3 groups found in all amino acids
- amine group
- carboxylic acid group
- residual group
Draw the structure of a generalised amino acid
State the residual groups for glycine and cysteine
Glycine = simplest amino acid as R group = H
Cysteine = R group is SH (important in forming disulfide bridges)
State the 6 main functions of proteins
Hint: think steam
Structural role e.g. keratin, collagen
Transport role i.e. Hb and Mb
Enzymes
Antibodies
Membranes i.e. intrinsic & extrinsic proteins
Hormones e.g. insulin, prolactin
Explain how to amino acids are joined together
- Condensation reaction joins two amino acids toegther
- i.e. removal of water resulting in the formation of a covalent bond
- Called peptide bond
- A series of condensation reactions are repeated to form a polypeptide chain (NB this is not an active functional protein at this stage)
Draw a diagram to show how a dipeptide is hydrolysed
Define the primary structure of a protein
Sequence of amino acids within the polypeptide chain (amino acids joined by series of condensation reactions resulting in peptide bonds)
Define the secondary structure of a protein
Folding of the polypeptide chain (ppc) to form one of 2 formations:
a) Alpha helices forms a coils
b) Beta pleated sheets forms pleated sheets
Define the tertiary structure of a protein
- Further folding of the ppc to produce complex 3-dimensional shape
- Results in globular arrangement (called G-protein)
Define the quaternary structure of a protein
Presence of 2 or more ppc joined together
OR
Presence of 1 ppc AND at least one non-protein, prosthetic group
Give 2 examples of quaternary proteins
Collagen – 3 ppc
Haemoglobin – 4 ppc and 4 haem groups
State and describe the 5 different bonds/interactions within proteins
i) Peptide: formed by condensation reaction between NH group of one AA and COOH group of adjacent AA
ii) Hydrogen: weak interactions between atoms with slight+ and slight- i.e. between dipoles
iii) Ionic: formed between R groups which have carboxyl groups (COO-) and amino groups (NH+)
iv) Disulfide: formed between the sulphur atom of R-groups of 2 cysteine amino acids
v) Hydrophobic interactions: water is repelled & excluded from hydrophobic, non-polar R-groups
Explain the principle behind how chromatography works
separates chemicals according to their solubility
State with an example the 2 different phases in chromatography
Stationary phase = paper, silica gel or column through which the solvent (mobile phase) runs
Mobile phase = liquid or gas, used to separate different chemicals
Write the formula used to calculate the Rf value
Retardation factor (Rf)
Rf = Distance travelled by the amino acid .
Distance travelled by the solvent
Explain how Rf values are used to determine the amino acids present
- Compare Rf value to Rf values of known standards
- Which have been run on chromatogram with same solvent
- At the same time i.e. same conditions
Give 2 reasons why pencil is used to draw the origin on a chromatogram
- To enable calculation of Rf
- Can’t use pen as the ink dye would also dissolve in the solvent & move up the SP
Explain how to apply a solution of amino acids to a chromatogram
- Use a narrow capillary tube
- To generate a spot with max diameter of 2-3mm
- On the, origin/starting line
- To generate/produce, a high concentrated spot (of the substance)
- Air dry between application of further spots
Explain why the chromatogram should be handled with gloves
- To avoid getting fingerprints on the stationary phase
- As the solvent may dissolve the oils in the grease
- This changes the rate the solute rises (and affects the spot formation and travel)
Explain why ninhydrin is applied to a chromatogram
To make the amino acids more visible
By forming a blue-violet compound
Explain how to confirm a spot on a chromatogram is not composed of 2 or more substances
- Run chromatogram again with different solvent
- Run chromatogram again in 2nd orientation
- i.e. 2-way chromatography
- This will increase the resolution of the spots obtained
Explain the advantage of using different solvents in chromatograms
- As different amino acids will have different solubilities in different solvents
- If only one solvent is used one (or more) amino acid may not dissolve in tit and hence give false results
- More solvent = increase probability that all amino acids present will dissolve in at least one solvent
Explain the importance of covering the chromatogram tank with a lid
- As solvent may have low heat of evaporation
- Hence could diffuse into surrounding atmosphere
- May have health risks e.g. corrosive when inhaled etc
Explain how the properties of amino acids affect the Rf value
- Amino acids with R-groups which are hydrophilic will have a higher solubility
- This means that they will have a larger Rf value e.g. serine
- Amino acids with R-groups which are hydrophobic will have a lower solubility
- This means that they will have a smaller Rf value e.g. glycine
State the two extremes of Rf values and explain their significance
Minimum = 0 and max = 1
Zero = amino acid doesn’t dissolve in the solvent/MP
One = amino acid has a high affinity for the MP So travels the same distance as the MP
Define the terms • repeatable • reproducible
If someone was to carry out the test again using the same method and got the same result, the data is said to be repeatable
If a measurement was taken using a different method and got the same result, the result is referred to as reproducible
State 7 key features/properties of enzymes
- biological catalysts i.e. speed up the rate of reaction
- lower the activation energy
- not altered or used up in the reaction
- can be reused many times
- are globular proteins
- are soluble
- have high turnover rates
Explain how enzymes lower the activation energy
- The enzyme provides an alternative pathway for the reaction
- The reactants are held in the active site by the R-groups of the amino acids
- The enzyme brings the reactants close together in the active site
- This puts strain on the reactants
- So that bonds can be made or broken more easily
- The enzyme can also transfer charges or groups from one reactant to another
Explain the difference between catabolic (C) and anabolic (A) reactions
- C: break large molecules down into smaller molecules vs A: join smaller molecules together
- C: break bonds within the initial substrate usually involve hydrolysis reactions vs A: form bonds between substrates to form larger product(s)
- C: are exergonic (give out energy) vs A: usually involve condensation reactions
State the 3 key properties of enzymes that are important in increasing the efficinecy of metabolism
Specificity
High turnover rate
Reversibility
Define the term specificity
- E only work on specific substrate(s)
- Shape of S must be complementary to the shape of the AS
Define the term reversibility
Some E catalyse reactions in either direction
Direction of reaction depends on environmental conditions
E.g. Carbonic anhydrase
Define the term high turnover rate (TOR)
- TOR = maximum number of chemical conversions of S molecules per second that a single catalytic site carries out at a given concentration of E
- E.g. catalase ~ 40million molecules of H2O2 broken down per second
Define a cofactor
additional non-protein component that is needed by the enzyme to enable it to function
Give 2 examples of cofactors
- inorganic ions (e.g. Ca2+, Zn2+)
- organic molecules (coenzymes) e.g. vitamins.
Define the term apoenzyme
An inactive enzyme which needs the presence of a co-factor to activate it
Define a holoenzyme
- A complex of an enzyme with its cofactor
- The complex is active i.e. enzyme will function
Explain how a cofactor such as chloride ions activates an aopenzyme such as salivary amylase
- Presence of Cl- ion alters shape of the enzyme
- Change in shape of the enzyme = allostery
- Causes the AS to become more complementary to the substrate
- Change in shape makes it easier for the substrate to bind to the active site
State what level of structure a holoenzyme must have to be active
Quaternary = as it must consist of at least one ppc to make the enzyme and must have a cofactor (specialised prosthetic group) to be active
State 4 factors that must be controlled when investigating the effect of enzyme concentration on the rate of reaction
- Substrate concentration
- pH
- Inhibitor concentration
- Temperature
Sketch a graph to show the effect of enzyme concentration on the rate of reaction
Sketch a graph to show the effect of substrate concentration on the rate of reaction
Sketch a graph to show the effect of pH on the rate of reaction
Sketch a graph to show the effect of temperature on the rate of reaction
Add dgm
Write the formula to calculate the pH of a solution You must be able to use this formula in exams
Add dgm
Explain the how enzymes can be permanently or temporarily denatured by changes in pH
small changes in pH can lead to temporary changes in the shape of the active site and can be reversed significant changes in pH will result in permanent denaturation as the changes are irreversible
Explain the Q10 rule
For every 1o oC rise in temperature the rate of an enzyme controlled reaction will double UP UNTIL its optimum temperature Remember: beyond the optimum temperature the RoR will decrease sharply to zero as the enzyme is denatured
Explain the difference between a collision and a successful collision
Collision: when a substrate impacts with an enzyme due to both molecules moving randomly as they possess kinetic energy Successful collision: when a substrate impacts with the active site of an enzyme in the correct orientation and with sufficient energy to form an ESC
Define an enzyme inhibitor
A small molecule that interacts with an enzyme to reduce the RoR
State the two type of inhibitor and state where they interact with the enzyme to reduce the RoR
Competitive inhibitor – interacts with the active site Non-competitive inhibitor – interacts with the allosteric binding site
Describe the relationship between a competitive inhibitor and the substrate
They are similar in shape to each other] Do NOT say they are the same
Describe the relationship between a non-competitive inhibitor and the substrate
There is no similarity between a NCI and the S The NCI is complementary to the shape to the allosteric binding site
Explain how a CI reduces the rate of reaction
CI temporarily forms an association with active site but does not bind with it i.e. occupies some/all of the active site and forms an enzyme-inhibitor complex (EIC) Prevents access of the true substrate and so no ESCs can occur Hence no reaction can occur and no product is formed
Describe the relationship between the concentration of CI and the rate of reaction
The degree of inhibition is determined by the relative concentration of substrate and inhibitor The higher the concentration of inhibitor the more likely it is that an EIC forms rather than an ESC and hence the degree of inhibition increases
Give a named example of a CI
Digitalis – affects ATPase contraction of cardiac muscle
Explain how a NCI reduces the rate of reaction
NCI does not attach to the active site but attaches at another binding site on the surface of the enzyme called the allosteric binding site at a location away from the active site This distorts the tertiary structure of the enzyme i.e. it disrupts hydrogen bonds & hydrophobic interactions holding enzyme in the 3D shape (i.e. 3o structure) The effect of the disruption ripples across the enzyme and alters the shape of the active site preventing the actual substrate from binding; this prevents the formation of ESCs. The change in shape of the enzyme is called an allosteric effect (allostery means ‘change in shape’)
Describe the relationship between the concentration of NCI and the rate of reaction
The degree of inhibition is NOT determined by relative concentration of the S and the I When the inhibitor concentration is at its maximum then the Rate of Reaction = 0 Changing the substrate concentration will not alter the RoR as all the active sites are involved in EICs
Give a named example of a NCI
Antibiotic (penicillin) – permanently occupies the AS essential for synthesis of bacterial cell wall
Make sure you can sketch and label a RoR graph showing the trends for a) just the E b) E in presence of a CI c) E in the presence of a NCI
Add dgm
Define the term ‘active site’
small indentation on the surface of the enzyme made from only 3-12 R-groups; the rest of the ppc is important in holding those R-groups in the correct orientation to form the active site
State the 3 conditions that must be present for a successful collision to occur
the substrate must collide with the active site in the correct orientation with sufficient energy to overcome the activation energy
State 4 reasons coagulation of blood is may be necessary
Prevent entry of pathogens by forming physical barrier to seal the opening/wound Prevent excessive blood loss i.e. ensures hemostasis (stops blood flow)
State 2 important roles of hemostasis
Reduces the risk of hypovolemic shock Aids the maintenance of blood volume
Compare the process of controlled blood clotting with uncontrolled blood clotting
Controlled blood clotting: • Clot forms from platelets & proteins in blood plasma • Seals wound • Clot prevents bleeding • After wound has healed the clot dissolves naturally Uncontrolled blood clotting • Occurs when a clot fails to dissolve naturally • Or a clot can form inside a blood vessel when no injury has occurred • If the clot forms in a major vein it can result in less blood being returned to the heart Blood can accumulate behind the clot leading to swelling & pain
State the 2 main risks of DVT
If the clot then dislodges it can travel to the o heart where it can cause a pulmonary embolism brain where it can cause a stroke
State 3 stimuli for blood clotting
when there is damage to: a) the walls of a blood vessel(s) i.e. exposes collagen fibres in the vessel wall and connective tissue b) other tissues around the blood vessel c) platelets
Describe the process of blood clotting
• Damage occurs to the blood vessel(s) which exposes collagen fibres • This activates platelets which adhere to each other and onto the surfaces of the damaged blood vessel(s) and fibrin fibres to form a ‘plug’ • Leucocytes collect at the site of damage. • The tissue just beneath the endothelium release the enzyme thromboplastin • The activated platelets also release thromboplastin • In the presence of Ca2+ ions thromboplastin converts the inactive plasma protein prothrombin into active thrombin (an enzyme) • Thrombin in the presence of Ca2+ ions hydrolyses 4 small peptides from each soluble fibrinogen molecule (large, soluble globular plasma protein) to convert fibrinogen into insoluble fibrin (fibrous protein) i.e. thrombin is a proteolytic enzyme • Fibrin molecules then link together to form a fibrous mesh over the wound • Erythrocytes and platelets are trapped in the mesh and adhere to the mesh to form a clot • The initial clot is a gel but fluid (serum) from the clot is squeezed out onto the surface of the skin. • The clot dries when exposed to the air and shrinks. • This pulls the fibrin threads closer as the sides of the clot retract. • The dried, shrunken clot is called a scab. • Under the scab cells at the edge of the wound divide by mitosis over and over again • New tissue develops over time and heals wound. Scab falls away once new wound is healed or is dissolved by the enzyme plasmin.
Explain why the process of blood clotting is described as an example of positive feedback
It is a cascade reaction the effect of stage 1 means that the effect at stage 2 is increased and so on
Explain how hypovolemic shock can result in organ failure
• Insufficient blood is pumped around the body • Hence reduced delivery of nutrients and reduced removal of (toxic) waste Resulting in cell & tissue death
State 4 possible causes of hypovolemic shock
• Ruptured spleen • Severe burns • Diarrhoea • Excessive, perspiration / sweating Excessive vomiting
Explain the difference between a diagnostic enzyme and an enzyme used in treatments
Diagnostics – enzymes used directly or as a component of an assay Treatment – enzymes used to treat a specific disease
Describe the role of antithrombin
prevent thrombin from working continuously after clot is formed after ~20 minutes usually no more thrombin is made
Explain how antithrombin is used in medicine to treat a patient
• Circulates at a high concentration • Only becomes capable of efficient thrombin inhibition on interaction with heparin (which acts as a cofactor) • Natural, reversible competitive inhibitor • Combines with active site of thrombin for ~20 min • Partially blocks the active site • Hence fibrinogen can’t bind to the active site Hence no fibrin is formed
Explain how serum amylase can be used as a diagnostic enzyme
• Enzyme hydrolyses polysaccharides (hydrolyses glycosidic bonds) • If the pancreas is inflamed, necrotic or diseased amylase is released into the blood plasma Hence presence of amylase in the plasma can be used to diagnose pancreatic disorders e.g. alcoholism, gall stones, pancreatitis
Name 3 disorders that can be diagnosed by the presence of serum amylase
• alcoholism • gall stones pancreatitis
State 4 disorders that could be present if the presence of LDH is detected
haemolysis, myocardial infarction muscle trauma bone fractures anaemia pre-eclampsia hypothyroidis certain infections e.g. bacterial meningitis, HIV
Describe 2 situations where LDH can be used to monitor certain diseases
Effectiveness of chemotherapy for lymphoma Progression of certain conditions e.g. Muscular dystrophy
Define an isoenzyme
enzymes that differ in amino acid sequence but catalyse the same chemical reaction
State and explain the level of protein structure for LDH
Quaternary structure Because LDH has 4 ppc subunits: 2 M chains and 2 H chains
How many genes are involved in the production of LDH
2 different chains coded for by 2 different genes
State the 5 different isoenzyme structures of LDH and state where they are found
Insert image of table
State the function of cyclo-oxygenase (COX)
catalyses the formation of prostaglandins
What are prostaglandins
group of chemicals synthesised from a fatty acid called arachidonate
State the 2 main functions of aspirin
Anti-prostaglandin agent Anti-platelet agent
Explain how aspirin acts as an anti-prostaglandin agent
• Aspirin adds an acetyl group to an amino acid, serine, close to the active site of COX • Prevents the fatty acid being made stops the prostaglandins being produced i.e. aspirin acts as a non-competitive inhibitor
Explain how aspirin acts as an anti-platelet agent
• COX also stops bleeding by preventing the production of another enzyme thromboxane (hormone released by platelets that catalyses aggregation of platelets adhere) Hence no platelet plug is formed over the wound.
Explain why it is inaccurate to refer to COX as a blood thinner
inaccurate as it does not alter the viscosity of the blood
Explain why it is technically inaccurate to refer to COX as a anti-platelet agent
it does not ¬reduce the number of platelets. One side effect of taking aspirin is bleeding but it is successfully prescribed to prevent strokes and heart attack
Explain how Warfarin inhibits the production of clotting factors
• Inhibiting the enzyme epoxide reductase • This reduces the amount of vitamin K available • Also reduces the amount of vitamin K hydroquinone in the tissues • This inhibits the carboxylation activity of glutamyl carboxylase. Which in turn prevents the formation of prothrombin in liver cells
State the 2 main reasons for prescribing Warfarin
Prevent formation of blood clots & prevents increase in size of blood clots
State 5 medical conditions that may be treated by prescribing Warfarin
irregular heart rate prosthetic heart valves heart attacks venous thrombosis pulmonary embolism
State 2 possible side effects of taking Warfarin
rapid bruising after minimal trauma unnoticed bruising after minimal trauma
How does thrombolytic therapy work?
dissolves blood clots
State and explain the role of tissue plasminogen activator
serine protease found on endothelial cells that line the blood vessels catalyses the conversion of plasminogen to plasmin
What is streptokinase?
Enzyme secreted as a toxin by many different species of Streptococcus bacteria
Explain why streptokinase can only be used successfully to treat a patient who is experiencing their first heart attack
as it is a bacterial enzyme the human immune system recognises the enzyme as foreign Can result in the patient building up immunity to the drug
If a patient experiences a 2nd heart attack describe how they may be treated
genetically engineered drugs can be used (but are more expensive)
State the 3 antigens found on erythrocytes
• Antigen A • Antigen B Rhesus antigen (D)
List the 8 types of blood group that can exist
A Rh+ A Rh- B Rh+ B Rh- AB Rh+ AB Rh- O Rh+ O Rh-
State which blood groups have antibodies present in their serum. In each case state the blood group and the antibodies present.
Blood group A = has anti-B antibodies Blood group B = has anti-A antibodies Blood group O = has anti-A and anti-B antibodies
For each blood group state which antigens are present on the erythrocytes
Blood group A = antigen A present on erythrocytes Blood group B = antigen B present on erythrocytes Blood group AB = antigen A and B present on erythrocytes Blood group O = no antigens resent on erythrocytes
State and explain which blood group is the universal donor
Blood group O As there are no antigens on the surface of the erythrocytes
State and explain which blood group is the universal recipient
Blood group AB As there are no antibodies in the plasma
Explain the term agglutination (in the context of a miss-matched blood donation)
Clumping of erythrocytes occurs the process that occurs if an antigen is mixed with its corresponding antibody
When evaluating the compatibility of donated blood what are the 2 aspects you should consider
The antigens on the surface of the donor blood erythrocytes The antibodies present in the recipients plasma
What is the legal age to donate blood
17-66years
How frequently can a person donate blood
Males – every 12 weeks Females – every 16 weeks
State some reasons why a person may not be able to donate blood
5 from Anaemic Had infection in last 2 weeks Have any of following symptoms: cough, cold sore, sore throat Have had jaundice or hepatitis in the last year Have had tattoo or semi-permanent make up or piercing in last 4 months Had acupuncture in last 4 months outside of the NHS Received blood since 1st January 1980 Ever injected blood Are male and had sexual intercourse with another man in last year Are female and had sexual intercourse with man in the last year who has had sexual intercourse with another man
What are the 5 key stages to making a blood donation
- Preparation before the actual donation 2. Arrival, welcome and registration 3. Health screening 4. Donation After-care
How should a donor prepare for donating blood on the donation day
• Donor should eat regular meals & drink plenty of non-alcoholic fluids before donating Donor should avoid vigorous exercise before donating
Describe what happens during the health screening process during a blood donation
• Private health screening form is completed • Confirms donor’s identity • Questions are confidential and look at donor’s recent medical and travel history Pin-prick anaemia test is carried out (drop of blood times as it falls through copper sulphate)
Describe the events during an actual donation i.e. when the person actually gives blood
• Donor sits in specialised chair • Sphygmomanometer used to apply pressure to arm used for donating (non-dominant arm) • Carer sterilises arm using alcohol (antiseptic) sponge for 30 seconds • Carer locates suitable vein • Carer inserts sterile needle into vein • During donation donor should keep moving feet to reduce blood pooling & maintain circulation (reduce risk of fainting at end of session when donor stands) • Donor should also carry out muscle tension to maintain blood pressure in donation arm Donation takes ~7minutes (according to flow speed)
Describe the events that occur after immediately after a person has donated blood
• Needle is removed by carer • Donor is returned to upright sitting position for 2 minutes • Sterile gauze is applied to wound & donor applies pressure to sterile roll for ~1minute • As long as no bleeding continues sterile dressing is applied along with pressure roll Donor is then instructed to sit for 2 small drinks & small snack (crisps, biscuits) for 15min within the donor centre
State what whole blood is, how it can be used and how long it can be stored for
Contents Plasma, leucocytes, erythrocytes, platelets & clotting factors Use • Very rarely used nowadays • Only used in severe blood loss Shelf-life ~24h
State what leuco-depleted blood is, how it can be used and how long it can be stored for
Contents Plasma, erythrocytes, platelets & clotting factors Use For patients who receive regular transfusions Shelf-life Up to 42 days
State what packed red blood cells are, how they can be used and how long they can be stored for
Contents Only erythrocytes – these are diluted with SAGM S – sodium chloride A – adenine G – glucose M – mannitol No leucocytes or platelets Use • To treat severe anaemia • Replace blood loss after childbirth • Replace blood loss after surgery • After major blood loss e.g. trauma Shelf-life Up to 35 days
State how platelets can be used and how long they can be stored for
Contents Only platelets Use • To treat bone marrow failure patients • Following transplant • Following chemotherapy • Following leukaemia treatment • Liver cirrhosis Shelf-life Up to 7 days
State how clotting factors can be used ad how long they can be stored for
Contents Only clotting factors Use • Various CF disorders • E.g. Factor V: Leiden thrombophilia • To produce immunisations e.g. tetanus Shelf-life Varies according to which specific clotting factor it is
State how plasma can be used and how long it can be stored for
Contents All cells & platelets removed (but still contains CF) by centrifuging within 2h of donation Use • Cardiac surgery to reverse anti-coagulation treatment • Excessive blood loss during child birth • Replace CF after major transfusions • Liver disease Shelf-life 1 year
State what serum is and how it can be used
Contents Plasma with clotting factors removed Use • Snake bites (only need antibodies and antitoxins) Source of antibodies
Explain why SAGM is added to packed red blood cells for their storage
Sodium chloride: reduces viscosity to allow RBC to flow easier reduces damage to csm of RBC Adenine: prevents clotting Glucose: provides respiratory substrate from RBC to carry out glycolysis & produce ATP Mannitol: free-radical scavenger to stabilise the csm of the RBC
Describe the optimal conditions for storing whole blood
4oC In the presence of a buffer In the presence of a chelating agent In the presence of an anticoagulant In sterile conditions In a gas permeable bag
Explain why whole blood must be stored at 4oC
• Prevents ice crystals forming • Prevents damage to CSM • Prevents proteins & enzymes denaturing • Slows (not stops!) enzyme controlled reactions Slows microbial growth
Explain why whole blood must be stored in a buffer solution
To prevent proteins and enzymes denaturing
Explain why whole blood must be stored in the presence of a chelating agent
• To remove calcium ions • To prevent the blood clotting E.g. citrate
Explain why whole blood must be stored in an anticoagulant and give a named example of an anticoagulant
• To prevent the blood clotting E.g. Heparin
Explain why whole blood must be stored in a a gas permeable bag
• To allow gas exchange • i.e. oxygen to diffuse into the contents of the bag and carbon dioxide to diffuse out of the bag
State 5 different diseases that donated blood is routinely screened for
• Syphilis • Hepatitis virus HIV
State 3 other diseases that donated blood can be screened for depending on the medical and travel history of the donor
• Western Nile virus • Malaria T-Cruzi Jacob’s
