Semester 2 Flashcards
High / Low Affinity Binding Curve:
What does the release of the FIRST oxygen do?
It causes a conformational change in the other 3 subunits.
It converts them from a relaxed state to a more tense state. (Back to a lower affinity!)
So we have EASIER release of the 2nd oxygen, which makes it even more tense!
And then the same process with the 3rd and 4th oxygen…
High / Low affinity binding curve:
Why is this type of curve NOT seen in Myoglobin?
Due to its structure: It only has 1 subunit and therefore NO cooperative activity.
Identify the correct characteristic of Hydroxyproline + Hydroxylysine
They are required for proper functioning of Collagen.
The protein capsid of a virus has what structure?
Primary, secondary, tertiary AND quaternary structure!
Which compound is an inhibitor of Nitric Oxide Synthase?
N-Methylarginine
Methyllysine has the following important roles…
Epigenetics + Myosin function
Food Pickling affects protein structure by disrupting…
Electrostatic Interactions
Which amino acid is commonly found in Beta Turns?
Cis- Proline
Which of the following cofactors is required for the formation of Gamma- Carboxyglutamate?
Vitamin K
The effect of pH on the binding of O2 to Haemoglobin is known as the…
Bohr Effect
The following type of Alpha-Helix is commonly found in membranes to form Pores…
Amphipathic
An elite athlete trains for 4 weeks at 4,500m. What is the efficiency of O2 transport from the lungs to the tissues?
(Graph)
37%
What molecule provides proteins with ‘Elastic’ properties?
Desmosine
What amino acid is a ‘classic’ disruptor of Alpha- Helices?
Proline
What is an INCORRECT characteristic for protein alpha- helices?
A channel is formed down the centre of the alpha helix.
Phosphoserine, phosphothreonine and phosphotyrosine are formed by…
Kinases
What methods can be used to determine the 3D structure of proteins?
X-Ray Crystallography or Nuclear Magnetic Resonance (NMR)
What roles do metals perform in Restriction Enzymes?
They help ALIGN the Scissile bond correctly in the active site and they REDUCE electrostatic repulsion.
The Aconitase enzyme converts Citrate to Isocitrate through…
Sequential processes of Dehydration/ Hydration
What roles does Mg2+ play in the functioning of Hexokinases?
It REDUCES electrostatic repulsion and correctly orientates the SUBSTRATES of the hexokinase reaction.
Why is Vitamin D currently a ‘hot topic’?
It is thought to reduce infection by the Covid-19 virus.
How can UV-visible Spectroscopy be used to detect oxygen levels in the blood?
By measuring the RATIO of the Soret band absorbance at 414nm and 429nm.
What is the biochemical role of Glutathione Peroxidase?
It converts Hydrogen Peroxide to water, utilising GSH as a reductant!
What is the biochemical / physiological function of Carbonic Anhydrase?
It is an enzyme that REVERSIBLY converts C02 to carbonic acid OR carbonic acid to C02.
What are the functions of the Cytochrome P450 enzymes?
Vitamin D Synthesis
Testosterone and Oestrogen Synthesis
Bile Salt Synthesis
Drug Metabolism
What is the function of bile salts?
They act as Biological Detergents in the small intestine and facilitate excretion of EXCESS Cholesterol.
What amino acid binds to the Iron-Sulfur centre of Aconitase?
Cysteine
An enzyme has a Km of 0.5mM while the substrate concentration is 10mM.
At what % of Vmax is the enzyme catalysing the conversion of substrate to product?
V0 = Vmax x [S] divided by KM + [S]
(Michaelis - Menten Equation)
For KM = 0.5mM
and
[S] = 10mM
( If it’s a percentage of Vmax then assume the Vmax is always 100%!)
V0 = 100% x 10 divided by (0.5 + 10)
V0 = 95% of Vmax!
An enzyme has a Km of 0.5mM, a Vmax of 100 mmoles of product formed per minute and the substrate concentration is 10mM.
Calculate V0.
V0 = Vmax x [S] divided by KM + [S]
(Michaelis - Menten Equation)
KM = 0.5 Vmax = 100mmoles product per min [S] = 10mM
V0 = 100 x 10 divided by 0.5 + 10
V0 = 95 mmoles product formed per min!
(V0 is ALWAYS IN THE SAME UNIT as Vmax!)
The reaction catalysed by Hexokinase is as follows: Glucose +ATP > Glucose-6-phosphate + ADP
What is the role of ATP in this reaction?
Provide energy to drive the reaction forward AND to donate a phosphate (Pi)
What parameters are affected by doubling enzyme concentration?
Vmax and Vi
What compound binds PERMANENTLY to a protein?
Prosthetic Group
What molecule is NOT an enzyme cofactor?
Glutamate
Enzymes are biological catalysts that…
INCREASE the rate of reaction by REDUCING the Transition State Energy Barrier
The affinity of an enzyme for a substrate is indicated by the…
Km
The Km of a reaction is 5mM, Vmax is 20nmoles / minute and substrate concentration is 5nM.
What is the rate of reaction Vi? (Interchangeable with V0)
V0 = vmax x [S] divided by km + [S]
V0 = 20 x 5 divided by 5 + 5
V0 = 10 nmoles / min (SAME UNITS AS VMAX!)
What mechanims of Rate Enhancement are used by Chymotrypsin?
Acid base catalysis
Covalent catalysis
Electrostatic catalysis / environment
Proximity + orientation effects
B with a lone pair of electrons in covalent and base catalysis is a…
Base Catalyst
NADPH donates … electrons to Cytochrome P450 Reductase, which donates… electrons to Cytochrome P450
2
1
In the catalytic mechanism of Chymotrypsin, His 57 acts as a…
BOTH base and acid catalyst
What rate enhancement mechanism is NOT used by Chymotrypsin?
Metal Ion Catalysis
Base Catalysis is defined as…
Temporary proton abstraction
In Elastase, the catalytic triad consists of…
Asp-102, Ser-195 and His-57
The substrate specificity of Trypsin is defined by a binding pocket that contains…
A negatively charged Aspartate residue
The catalytic mechanism of chymotrypsin, trysin and elastase is a…
2 substrate ping pong mechanism
What is INCORRECT regarding covalent catalysis?
Cannot take place with hydroxyl groups
The first step in catalysis by Chymotrypsin is…
Substrate binding
Rate Enhancement strain and distortion takes place in…
Lysozyme and Endonucleases
If you add 200ul of your 6M ethanol to the reaction, what is the FINAL concentration in the cuvette during the reaction? Final volume = 2.4 ml.
Vi x Ci = Vf x Cf
Vi = 200ul Vf = 2400ul (CONVERT UNITS) Ci = 6000mM (as answer was in mM, if theres a M and an mM value, convert to mM!)
Cf = 200 x 6000 / 2400
= 500mM
In the alcohol dehydrogenase practical (ADH), you measured the initial rates (Vi) of the following reaction:
C2H5OH + NAD+ > CH3CHO + NADH + H+
Which component is DIRECTLY measured?
NADH increase (you are measuring the change in absorbance at 340nm ie. the conversion of NAD+ to NADH)
In the ADH practical you measured the initial rate over … seconds
30
You are using a P200 pipette set at 050. What volume will this measure?
50 ul
In order to measure the REDUCTION of NAD+ to NADH your spectrophotometer wavelength will be set to…
340 nm
In the ADH practical, the spectrophotometer should be ‘blanked’ by…
Checking the correct wavelength has been set, inserting a cuvette containing 2.5ml water OR buffer, then pressing ‘measure blank’
In order to measure the OXIDATION of NADH to NAD+ your spectrophotometer wavelength will be set to…
340nm
You have measured the absorbance of 1nM solution of pure compound Y at 340nm.
The pathlength of the cuvette is 1cm. If the measured absorbance is 0.05, what is the extinction coefficient of compound Y?
Beere-Lambert equation: Abs =ecl
E = Abs/ cl
= 0.05 / (1mM x1cm )
= 50 mM -1 cm -1
Which component of the enzyme reaction is added immediately before oressing ‘measure sample’ on spectrophotometer?
Enzyme
What is NOT a common function of carbohydrates?
Catalysing reactions in cells
Which carbon atom in a glucose ring can have a hydroxyl group bound in an ‘Up’ or ‘Down’ orientation?
Anomeric carbon
Which bond links glucose monomers in Maltose?
Alpha 1-4 glycosidic bonds
Which is NOT a storage carbohydrate in plants?
Glycogen
What is FALSE about cellulose?
Coils are stabilised by hydrogen bonds
Mushroom cell walls are made from…
Chitin
Which enzyme is most likely to hydrolyse a Beta 1-4 glycosidic bond?
Endochitinase
What property of cellulose makes it HARD for most mammals to digest?
The anomeric state of its monomers!
What is the name of the monomers that make up Chitin?
N - acetylglucosamine
When Chitin is converted to Chitosan, which group is LOST from its structure?
Acetyl
The shells of molluscs are made from chitin.
True or false?
FALSE
Shells are made from calcium carbonate, beaks and teeth are made from chitin
What is NOT a common function of carbohydrates?
Catalysing reactions in cells
Which carbon atom in the pyranose form of glucose can have a hydroxyl group bound in an ‘UP’ or ‘down’ orientation?
Anomeric carbon
What type of bond links glucose monomers in a molecule of maltose?
Alpha 1-4 glycosidic bond
What is a branched homopolysaccaride?
Glycogen
Which polysaccharide has alpha 1-6 glycosidic bonds every 24-30 residues?
Amylopectin
What polysaccharide does NOT contain an N- acetyl group?
Heparin
What is the best description of a proteoglycan?
A Core protein with an attached glycosaminoglycan.
What is NOT a major component of the Extracellular Matrix?
Actin filaments
Are GAGs heteropolysaccharides or homopolysaccharides?
heteropolysaccharides
Which GAG has the longest chain length?
Hyaluronan
Which GAG forms ‘dead horny’ structures?
Keratan sulfate
One monomer in the repeated disaccharide that makes up a GAG is ALWAYS…
N-acetylglucosamine OR N-acetylgalactosamine
Which GAG is NOT most commonly found bound to proteins?
Hyaluronan
What is
According to a recent paper, which type of molecule helps coronavirus bind to cells?
Heparan sulfate proteoglycan
Which molecules determine human blood types?
Glycolipids
N-linked glycoproteins have carbohydrates attached to which amino acid?
Asparagine
What is the best description of a proteoglycan?
Core protein with attached GAG
Which atom is NOT involved in linking oligosaccharides to glycoproteins?
Oxygen in the R group of asparagine
What best describes a glycoprotein?
Large protein with small CHOs attached
The time course of the alcohol dehydrogenase graph shows different final absorbances depending on the ethanol concentration.
This is due to…
The reactions reaching an equilibrium (reaction is reversible)
The absorbance for alcohol dehydrogenase was measured at 340nm because…
NAD+ was being reduced to NADH
What would the x axis label be for the Michaelis Menten alcohol dehydrogenase plot?
Ethanol concentration - mM
What would the y axis label be for the Michaelis Menten alcohol dehydrogenase plot?
Initial velocity - Change in Abs at 340nm min-1
What is the best definition of vmax?
Vmax is the maximum rate of reaction under specific conditions used
How can you use Michaelis Menten plot to estimate vmax?
Find the y axis value where the plot plateaus off at an infinite substrate concentration
What is the best definition of Km?
Km is the Michaelis constant, a measure of enzyme- substrate affinity
How can you use Michaelis Menten plot to estimate Km?
Find the x axis value where rate = 1/2 of vmax
What is the shortest length of hydrocarbons in a fatty acid?
4
because subunit that produces fatty acids can only add 2 carbons at a time
What is the longest length of hydrocarbons in a fatty acid chain?
36
What do triglycerides include?
3 fatty acids, 3 ester bonds and 1 glycerol
How many calories per gram of fat?
9
Sphingolipids can be classed as?
Phospholipid and a glycolipid
How many non- polar tails do sphingolipids, finger lipids and galactolipids have?
2
A lipid wrapped in a cell membrane contains cholesterol and…
Sphingolipids
Eicosanoids are derived from…
Arachidonic acid
What cannot passively cross the cell membrane?
Cholesterol
Which vitamin is NOT found in eggs?
Vitamin C
What levels of protein structure only apply to 1 polypeptide chain?
Secondary structure
Tertiary structure
Primary structure
What are the control points of glycolysis?
Pyruvate kinase
Hexokinase
Phosphofructokinase
Stage 1 of respiration takes place in the…
Cytosol
Where does glycolysis take place in the cell?
Cytosol
What is the benefit of lactate fermentation in humans?
Continued supply of NAD+
What enzymes are found in the mitochondrial matrix?
Malate dehydrogenase
Fumarase
Succinyl CoA synthetase
The end product of glycolysis is…
Pyruvate
What inhibits the formation of Acetyl CoA from pyruvate?
Acetyl CoA
The role of ATP in the reaction catalysed by Hexokinase is to…
Provide energy to drive reaction forward
Donate a phosphate
In glycolysis, ATP is utilised by the following enzymes…
Phosphofructokinase-1
Hexokinase
Phosphofructokinase-2
Fructose 1-6 bisphosphate is formed during glycolysis because…
It can be broken down into 2,3 carbon sugar phosphates
It is symmetrical
Glucose 6 phosphate is produced during the first reaction in glycolysis. Why?
Because glucose 6 phosphate does NOT affect concentration gradient of glucose, allowing continued glucose uptake
Because glucose 6 phosphate is NOT a ligand for glucose transporters
What intermediate is unique to glycolysis in Erthrocytes?
2,3-bisphosphoglycerate
In the FULL oxidation of a 16-carbon fatty acid during respiration, the NET yield of ATP per fatty acid is approx…
108 ATP
Is you were asked to measure a volume of 15ul what pipettes should you use?
P20
What is the main energy source of Erythrocytes?
Glucose
In the alcohol dehydrogenase practical, you calculated the extinction coefficient for NADH.
You calculated value was lower than the expected value, why?
The assumption that ALL NAD+ is converted to NADH is incorrect.
It is a reversible reaction, thus equilibrium has been reached!
Synthesis of FAs by fatty acid synthase:
Most 2 carbon units are provided by the substrate…
Malonyl CoA
Acetyl CoA is only for the very first 2C units
Identify the component that does NOT form part of glycerophospholipids
Sphingomyelin
Mammals can’t introduce double bonds to FA chains between which carbon and terminal end?
C10
Can readily introduce at C9
The reaction catalysed by which enzyme is the rate limiting step of FA biosynthesis?
Acetyl- CoA carboxylase
Production of manyl CoA from Acetyl CoA
Where does FA synthesis take place?
Cytosol
In TOTAL one 16 carbon fatty acid can produce how many molecules of ATP?
108 ATP
Which enzyme is the rate limiting step for B oxidation?
Carnitine acyl- transferase 1
What following compounds are classified as hydrophobic vitamins…
Vitamins A, D, E and K
What molecule triggers the release of fatty acids from adipocytes?
Glucagon
Which additional enzyme is required for B oxidation when catabolising an UNsaturated FA?
Enoyl-CoA isomerase (making an isomer, cis-trans)
The utilisation of a proton gradient to generate heat rather than ATP is due to the presence of… in the inner mitochondrial membrane
Uncoupling Protein 1
What metabolite is NOT an intermediate of the Citric Acid Cycle?
Acetyl-CoA
In the reaction of Succinyl CoA to Succinate, the conversion of GDP + Pi > GTP is an example of…
Substrate level phosphorylation
The transport of ADP into the mitochondrial matrix requires…
Adenine Nucleotide Translocase (antiporter)
In the electron transport chain ETC, FADH2 donates electrons directly to…
Complex 2
The transportation of hydrogen ions by the ETC generates which force?
Proton motive force
During oxidative phosphorylation, how many protons are required for the generation of 1 ATP from ADP + Pi?
4
Entry of Acetyl-CoA into the citric acid cycle is DECREASED when…
The ratio of [ATP] to [ADP] is HIGH
In the mitochondrial ATP synthase complex, the following functional unit is integrated into the inner mitochondrial membrane…
F0
In mitochondria, the following compartment has a Low pH…
Inter-membrane space
Compound X is a competitive inhibitor of succinate dehydrogenase enzyme of the citric acid cycle.
What compound would you expect to DECREASE in concentration?
Fumarate
In the mitochondria, succinate dehydrogenase has the following functions…
Producing fumarate
Donating electrons to complex 2 of the electron transport chain
The proton motive force links electron transport across mitochondrial inner membrane and creates an electrochemical proton gradient. The proton gradient is formed by…
Proteins actively transporting protons across inner mitochondrial membrane to the inter membrane space
Transfer of protons from mitochondrial matrix to inter-membrane space
Releasing protons from inter-membrane space into mitochondrial matrix
In the mitochondrial ETC the transfer to electrons to Cytochrome C is via…
Complex 3
Allosteric Regulators of the citric acid cycle include…
ATP ADP NAD+ NADH Ca2+ Succinyl CoA
The mitochondrial ETC does NOT contain…
ATP Synthase
What is true about the Xylose extracted from wood?
Always a D enantiomer
What type of sugar is xylose?
Aldopentose
What makes a carbon chiral?
It has 4 different groups attached
How do we know something is a D enantiomer?
Almost ALL sugars commonly found in nature are D enantiomers
What is meant by the term an anomer?
Either the a or B form produced when the sugar forms a ring
What are the rules for numbering the carbon in glucose?
Clockwise from the oxygen in the ring
What is the anomeric carbon in glucose?
Carbon 1
What best describes the structure of glycogen?
A branched homopolysaccharide
Why is cellulose difficult for many organisms to digest?
It contains B 1-4 glycosidic bonds
True or false:
Heteropolysaccharides usually store energy
FALSE
Which chemical group is NOT commonly found in glycosaminoglycans?
NH3+ (amino)
What best describes a glycoprotein?
A relatively large protein with small carbohydrates attached
Which atom is NOT involved in linking an oligosaccharide to a glycoprotein?
The O in the R group of asparagine
How many chiral carbons does xylose have?
3
