Tutorial - Week 12/13 - Revision Flashcards
Complete the building blocks for each molecule
Nucleic acids:
- What are the two types?
- What are they polymers of?
- How are nucleotides linked?
- Polynucleotide chains have a ________ at one end and _________ attached to…?
- Which direction are they read?
What are the differences between DNA and RNA? (list the following for both)
- 3D structure
- Sugar
- Bases
- Type
- Function
Amino acids:
- How many standard amino acids are there?
- What do all amino acids have?
- What are they called at physiological pH? What does it mean?
- They are ____________ meaning they contain properties of both _________ and ________
- Are they chiral molecules? What does this mean?
Draw a standard amino acid structure and label the parts
Polymerisation of amino acids:
- What do amino acids polymerise to form?
- What is released during the formation of a peptide bond? What are the two processes called for formation and breaking of a peptide bond?
- What kind of bonds are peptide bonds?
What is the correct nomenclature for this peptide formed at the bottom?
Dipeptide
What is the peptide bond also known as?
T/F: the bond is often written as a single bond?
How many electrons are shared and between which atoms?
What does this sharing of electrons result in?
What is peptide bond resonance?
shared electrons between C-O and C-N
Resonance effect increases stability of the C-N bond, makes it shorter, and decreases rotation around that bond
List the four levels of protein structure and describe each
List the four chemical interactions that stabilise higher levels of
protein structure
What determines the intramolecular bonds within a protein?
The sequence of amino acids (primary structure)
What are intramolecular bonds important for?
These interactions are important to fold the polypeptide chain into a 3D shape, which is essential
to obtain a functional peptide/protein
Fatty acids are…?
- Normally have an _______ number of carbons (___________)
- What kinds of bonds do they have if they are saturated?
- What kinds of bonds do they have if they are unsaturated?
- Unsaturated fatty acids have double bonds in what kind of conformation?
- Some fatty acids are ___________, but cannot be synthesised by ____________ (e.g.?)
- What are free fatty acids and are they common?
What are TAGs also known as?
What are they?
What are they used for?
What are phosphlipids?
What is their nature regarding water?
What are they and what do they do?
What are they components of?
Monosaccharides (_______ sugars)
- What are the three most common monosaccharides in the human diet?
- The common monosaccharides have what kind of structure?
- What is their basic molecular formula?
- Is there a large diversity of them? Why? Explain
- What do these variations in structure result in?
- Monosaccharides are ________ sugars
Label
How do you obtain disaccharides?
Do disaccharides have a reducing end?
Which end is non-reducing?
Describe what bioenergetics is?
How is energy stored in chemicals?
What is the principle molecule for storing and transferring energy in cells?
In Biochemical reactions:
- What is conserved and moved around the reaction?
- What are moved around to obtain different molecules? Does this change anything for the new molecule?
What is the first law of thermodynamics
Living organisms are…?
open systems constantly exchanging material and energy
Living organisms together with their surroundings constitute the _________
universe
What is the second law of thermodynamics?
Cells require sources of ___________ energy
Gibbs free
Gibbs free energy = ?
the energy available to generate work
Cells can and must use ‘____________’, G
Gibbs free energy
Cells obtain Gibbs free energy from?
nutrients (or sunlight)
Cells transform free energy into ______, or _____________
ATP
other energy-rich compounds (1st Law of thermodynamics)
Cells are __________ systems (i.e. _______________)
isothermal
temperature is constant
The Gibbs free energy function predicts the…?
direction of chemical reactions
The Gibbs free energy function predicts the direction of chemical reactions and the amount of…?
work they can perform at constant temperature
Complete - > A + B = ?
the entropy of individual reactions might not increase, but the overall entropy of the ________ increases
universe
When considering the overall system (the ________), cells release to their environment…?
universe
equal amount of energy as
heat and entropy
Reactions are thermodynamically favourable (ΔG < 0 ) if:
- they release energy in the form of heat (ΔH < 0) and/or,
- they increase the disorder of the system (ΔS >0)
What is the driving force behind biochemical reactions? What does it represent the effect of?
ΔG is the driving force in a biochemical reaction, which represents the effect of ΔH and ΔS and at a fixed temperature
Explain each component
T/F: Most reactions are reversible?
True
The direction of the reaction depends on the…? And the following three points which are?
variation of free energy content between reactant and products, ΔG:
- Concentration of each of the molecules in the reaction
- Experimental conditions (e.g. temperature)
- ΔG’0 of the reaction (this is constant to each reaction
What is the result of each of these?
Label as releases or uses energy and give example
Why is a reaction called spontatneous?
The reaction is called spontaneous because it
can occur without the addition of energy
The reaction tends to occur until the ___________ is reached. At equilibrium, the rates of the forward and reverse reactions are equal
equilibrium
ΔG = 0, the reaction is…?
in equilibrium
Nomenclature:
ΔG = ?
is the measured free energy in the reaction. It depends on
experimental conditions
Nomenclature:
ΔG’0 = ?
Explain 4 points
ΔG, ΔG’0 and equilibrium:
- The reaction tends to occur until…?
- The concentrations of A, B, C & D at equilibrium depend on…/
- the equilibrium is reached
- the equilibrium constant of the reaction, Keq
Keq is a constant, characteristic for each reaction
Define the following from the image
ΔG’0 dependent on?
ΔG’0 is dependent on Keq
Complete where the arrows are
Bioenergetics explain…?
how a thermodynamically unfavourable reaction can be driven by coupling with favourable reactions
Complete and label as thermodynamically favourable and unfavourable
A thermodynamically unfavourable reaction can be driven by…?
coupling with favourable reactions
Reaction 1 is coupled with the hydrolysis of ATP; part of the free energy of ATP hydrolysis is used to…?
phosphorylate glucose
Energy coupling in biochemical reactions make reactions…?
thermodynamically favourable
Which reactions are thermodynamically favourable and unfavourable?
In coupled reactions, the ΔG values are ________
additive
ATP hydrolysis coupled with…?
Reactions is a central feature of metabolism
Another very important feature is…?
electron transfer in oxidation-reduction reactions (Redox reactions)
The flow of electrons in oxidation-reduction reactions is responsible, directly or indirectly, for…?
all work done by living organisms
What does electron transfer drives.
Electron transfer drives reduction potentials and supply’s free energy.
The greater the reduction potential the more __________ the free energy and more ___________ the reaction
negative
favourable
Electrons move from ________________ to _______________ (e.g. __________ )
various metabolic intermediates
specialised electron carriers
NADH, NADPH
These electron carriers provide ____________ in the cell
reducing power
ATP, adenosine triphosphate: chemical energy stored in bonds. Explain (2 points) Breakage and ADP into something…?
- breakage of a phopshoanhydre bond generates ADP + Phosphate ion (Pi), very
exergonic reaction that is normally coupled to endergonic reactions in cells - ADP can also be hydrolysed to AMP + Pi to obtain energy
NADH, nicotinamide adenine dinucleotide: reducing power, electron carrier.
Donate what…?
Donate electrons in processes that generate ATP (e.g. in respiratory chain)
NADPH, nicotinamide adenine dinucleotide phosphate: _________ power, electron carrier
Drive reductive…?
reducing
Drive reductive steps in biosynthetic (anabolic) pathways
Label as oxidation and reduction
Oxidation & reduction reactions (REDOX reactions), involve?
- The loss of electrons by one chemical species (it becomes Oxidised)
- The gain of electrons by another molecule (it becomes Reduced)
_________ is a common mnemonic to remember which is the oxidation and which is the reduction:…?
OIL RIG
Oxidation Is Loss (of electrons) and Reduction Is Gain (of electrons).
How fast is the reaction? _________ deals with the time of the reaction and it depends on…?
Kinetics
the activation energy (EA)
EA = ?
Activation energy (EA): energy input to start a reaction
For chemical bonds (in A & B) to break and allow new ones
to form (in C & D) the molecule goes into a…?
transition state (higher energy), which is unstable
The EA of a reaction determines the rate at which the reaction proceeds:
- The higher the EA…
- The lower the EA…
- The higher the EA, the slower the chemical reaction
- The lower the EA, the faster the chemical reaction
What are enzymes?
Enzymes are proteins that catalyse biochemical reactions by lowering their activation energy
What are enzymes? (4 points)
Enzymes affect the…?
rate of the reaction, not the equilibrium
The reaction equilibrium is dependent on…?
the thermodynamics of the
reaction (remember ΔG’0 = −RT ln Keq)
Complete
What happens in a biological system?
Enzymes, pathways, catabolic pathways, anabolic pathways, metabolism
Enzymes are classified according to…?
the type of reaction they catalyse
Enzymes have an ________ site:
- It provides a…?
- It binds and…?
Enzymes have an active site:
1. It provides a specific environment that helps accelerate the reaction
2. It binds and recognises a specific substrate(s)
Complete
How enzymes work?
Many enzymes require…?
Cofactor = ?
Coenzyme = ?
Prosthetic group = ?
Apoenzyme = ?
Holoenzyme = ?
Many enzymes require non-protein cofactors for their catalytic function
What are the features that make a protein an enzyme?
Catalytic Power: enzymes accelerate the…?
rate of a reaction
What is the transition state?
highest energy
arrangement of atoms during a reaction
What is the ΔG‡ free energy of activation
Activation energy (Ea): energy
difference between the substrate and
the transition state.
Determines the rate of the reaction
What is the ΔG‡ free energy of activation (Ea)
catalysed:
when the enzyme is
complementary to the transition state, it helps destabilise the
substrate (bend stick), reduces the Ea and accelerates the reaction.
Enzymes catalyse reactions: How?
substrates bind to the active site of the enzyme, which accelerates the chemical reaction, products are formed, and then allow products to dissociate.
What is the function of enzymes?
To lower the activation energy (Ea) to accelerate the reaction.
What does enzyme specificity mean?
Specificity: enzymes recognise a specific substrate
Describe enzyme specificity (7 points)
T/F: Enzymes act as a template for the reaction to occur, they bind to specific substrate (s), stabilise the transition state, lower the activation energy and accelerate the reaction
True
What are the two models of enzyme specificity? Describe both (3 points for first and 4 points for second)
enzyme kinetic activity is regulated by what?
activators or inhibitors
List and describe the types of enzyme inhibitors
What is Allosteric regulation?
regulation at a different site
Label the type of allosteric regulation for each
What does an allosteric inhibitor do?
What does an allosteric activator do?
Most enzymes have certain kinetic properties in common: what are they?
Substrate concentration, [S], affects the rate of the reaction
The rate of an enzymatic reaction depends on…?
the formation of enzyme-substrate complex (ES), which depends on the concentration of substrate, until all the enzyme binding sites are occupied with substrate.
The rate of an enzymatic reaction depends on what?
the substrate concentration;
When is a reaction faster?
The reaction is faster at the beginning when there is
more substrate (initial rate, Vo)
What happens as the reaction proceeds and substrate(s) is(are) consumed
the rate slows down
The rate of an enzymatic reaction can be determined by…?
the variation of product produced over time
The initial rate of an enzymatic reaction, V0, can be determined by…?
the variation of product produced over time, at the beginning of reaction (as shown in the figure, is the tangent at the beginning of the reaction/linear part of the curve)
What do the arrows means?
What does the Michaelis-Menten enzymatic reaction predict?
a model that describes the kinetics of many enzymatic reactions
What is the Michaelis—Menten equation? What do the parts mean?
Complete the sentence
are used to compare enzyme kinetics
A traditional approach to determine these parameters is by using the ____________________ to __________ the Michaelis-
Menten plot, an approach that takes the _________ of both sides of the Michaelis-Menten equation
Lineweaver-Burk plot
linearise
reciprocal
Competitive inhibitor: Describe what it does
competes with the substrate for the active site. If the inhibitor occupies the
active site, the substrate cannot bind
Understand how to use a Lineweaver-Burk plot to determine the type of inhibitor
What is an Uncompetitive inhibitor?
Binds to a site different from active site, but binds only to the ES complex
What is a Non-competitive (or mixed) inhibitor…?
Binds to a site different from Binds to a site different from
active site , but binds to E or to the ES complex
General acid & base catalysis: involves…?
Covalent catalysis: involves…?
nucleophilic attachment (electron donation), results in a transient covalent bond.
Several amino acid side chains, and the functional groups of some cofactors can serve as nucleophiles in the formation
of covalent bonds with substrates. These covalent complexes always undergo further reaction to regenerate the free
enzyme.
Metal ion catalysis: Explain
Ions in the active site introduce ionic interactions, which assist with the orientation of the
substrate, or stabilise charges during transition states.
What are pathways?
Pathways: consecutive reactions catalysed by enzymes
The products of one reaction become the reactants of
the next one
What are catabolic and anabolic pathways?
What are pathways catalysed by?
Pathways are catalysed and regulated by enzymes
Describe the Basic strategies of metabolic pathways:
- Pathways.
- Metabolism
- Catabolic pathways
- Anabolic pathways
- ATP
Metabolic pathways maintain the levels of key _________, such as ____ and ______ in cells and glucose in the blood.
metabolites
ATP
NADH
The rate of metabolic pathways is regulated by ____________, which can be regulated in different ways:
What are those different ways?
enzyme activity
Regulation of the amount or the activity of an enzyme:
Explain course control:
- long term control of enzymes, it can take hours, or days
- it normally relates to changing the amount of enzyme
available
Regulation of the amount or the activity of an enzyme:
Define fine control
- short term control, it can take milliseconds up to min
- it normally relates to a direct effect on the catalytic
activity of existing enzyme
Breaking down of sugars in aerobic conditions: catabolic
process:
What are the three pathways this is subdivided into?
Glycolysis is how many enzymatic reactions
10
IMPORTANT:
_______________ is degraded in a series of _______________ to yield _________________
1 molecule of glucose
10 enzyme-catalysed
reactions
2 molecules of pyruvate.
In the sequential reactions of glycolysis, three types of chemical transformations are particularly relevant:
What are they?
There are three regulatory enzymes, which catalyse irreversible reactions: Which are?
- Hexokinase (reaction 1): inhibited by the products
- Phosphofructokinase-1 (PFK-1; reaction 3)
- Pyruvate kinase (reaction 10, last step): inhibited by ATP & acetyl-CoA
What is the key enzyme in the control of glycolysis
(it catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate)
Phosphofructokinase-1
High ATP allosterically inhibits…?
High AMP allosterically activates?
High ATP/AMP decreases…?
Low ATP/AMP increases…?
Describe Reciprocal regulation of glycolysis and glucogenesis:
one pathway is
relatively inactive, while the other is highly active
What are the Molecules that induce reciprocal regulation by allosteric control on the enzymes that differ in
the two pathways:
- Glucose-6-phosphate
- inhibits Hexokine (glycolysis)
- activates Glucose-6-phosphatase (glucogenesis) - Fructose 2,6-biphosphate (is a REGULATOR, not part of the pathways), AMP
- activates Phosphofructokinase-1
- inhibits Fructose 1,6 biphosphatase-1 - Acetyl-CoA
- inhibits Pyruvate kinase
- activates Pyruvate carboxylase
Synthesis of acetyl-CoA and regulation of pyruvate dehydrogenase:
What is the reaction catalysed by?
Activity of pyruvate dehydrogenase is tightly regulated:
what is it activated and inhibited by?
Glycolysis (How many enzymatic reactions?)
- Where does it occur?
- How many molecules of glucose degraded into how many molecules of pyruvate?
- It generates ____ ATP molecules and ____ molecules of ______
Conversion of pyruvate to acetyl-CoA (catalysed by Pyruvate dehydrogenase):
- Where does it occur?
- ______ is converted into ________
Tricarboxylic acid cycle (____ enzymatic reactions):
- where does it occur?
- ______ is converted into _______
- oxidative reactions to transfer…?
Oxidative phosphorylation (membrane-bound electron transport chain and ATP synthetase):
- occurs where?
- electrons from ______ and _______ are transferred…?
- Energy from ________ is used to synthesise…?
Complete oxidation of ________ of glucose to ____ yields ________ molecules
1 molecule
CO2
30 or 32 ATP
The use of FA as fuel requires 3 stages of processing: what are they?
Fatty acid catabolism: degradation (β-oxidation):
What are the three steps of degradation?
FAs β-oxidation repeats a sequence of 4 reactions:
What are they?
Each round of the 4 reactions shortens the acyl chain by 2 carbons, and generates:
1 acetyl-CoA, 1 NADH and 1FADH2
Degradation of fatty acids (β-oxidation), an overview:
Each round of the 4 reactions shortens the acyl chain by ______, and generates?
2 carbons
1 acetyl-CoA (2C), 1 NADH and 1 FADH2
FA β-oxidation is repeated until…?
the acyl chain is all converted into acetyl-CoA
molecules
For example: Palmitoyl-CoA with 16 carbons, needs…?
7 rounds of β-oxidation to
obtain 8 Acetyl-CoA, 7 NADH and 7 FADH2
T/F: Acetyl-CoA can be further oxidised in the TCA cycle
True
- The acetyl-CoA produced from?
- One molecule of Palmitoyl-CoA (C16) when fully oxidised to CO2 generates…?
- Activation of Palmitoyl to Palmitoyl-CoA is equivalent to…?
- The net ATP yield is?
Biosynthesis of fatty acids, overview:
- Where does it occur?
- It is initiated by?
- The malonyl group is covanlently linked to the _____
- FA synthesis occurs through the condensation of….?
- These reactions occur in the…?
- Each round of the 4 reactions increases the acyl chain by…?
Biosynthesis of fatty acids is tightly regulated by…?
the activity of acetyl-CoA carboxylase
Biosynthesis of fatty acids, overview:
- Each round of the 4 reactions increases the?
- To generate 1 palmitate fatty acid (C16:0), it requires…?
Compare and contrast β-oxidation versus biosynthesis of fatty acids
Regulation of metabolism: tissues & hormones:
Each tissue/organ has a unique metabolic profile:
Describe the following
- Brain
- Liver
- Adipose tissue
- Skeletal muscle
- Heart muscle
What is the major anabolic endocrine hormone? Explain 6 points
What are the major catabolic endocrine hormones? Explain 5 points
How to prepare for the final?
