Andreas Kukol Protein Structure Lecture 1

Learning Outcomes:
Introduction: overview of protein function
Proteins are chains of amino acids
o The building blocks: amino acids
o The peptide bond

What are the 7 FUNCTIONS OF PROTEIN?

Structure proteins provide mechanical support
Catalysis enzymes are catalysts that accelerate the rate of a chemical
reaction
Regulation transcription factors switch genes on and of
Transport proteins in cell membranes determines which substances
enter and leave the cell
Signalling receptors and other proteins take part in signalling
Movement motor proteins transport cellular cargos and organelles
Defence antibodies act against microbes

What are PROTEINS MADE UP OF?

Amino acids

How many TYPES OF AMINO ACIDS ARE THERE?

20

What is the SEQUENCE OF AMINO ACIDS IN THE PROTEIN ENCODED BY?

DNA

What are AMINO ACIDS CALLED WHICH ARE USED FOR PROTEIN
SYNTHESIS?
Proteinogenic amino acids

What are the 4 STRUCTURES THAT MAKE UP AN AMINO ACID?

Amino group
Carboxyl group
Hydrogen
Side chain variable

What are the 2 OPTICAL ISOMERS THAT AMINO ACIDS CAN OCCUR IN?
D
L

Which ISOMER REPRESENTS THE MAJORITY OF AMINO ACIDS?

L

Which ISOMER IS FOUND IN BACTERIAL CELL WALL?

D
How do AMINO ACIDS DIFFER?
Side chain

What are the 3 TYPES OF SIDE CHAINS?

Hydrophilic polar
Hydrophobic non-polar
Inbetween

What BOND LINKS AMINO ACIDS TOGETHER?

Peptide bond

What TYPE OF CHAIN IS FORMED WHEN SEVERAL AMINO ACIDS ARE

LINKED TOGETHER?
Polypeptide

Andreas Kukol Protein Structure Lecture 2

Learning Outcomes:
Primary structure
Secondary structure
o The -helix
o The -sheet
o Nonrepetitive structures (loops, turns)
o Super-secondary structure elements
Tertiary structure
Quaternary structure
Forces stabilising protein structures

What is the PRIMARY STRUCTURE?

Sequence of amino acids

What are AMINO ACIDS IN A POLYPEPTIDE CHAIN CALLED?

Amino acid residues

What is the SECONDARY STRUCTURE?

The local arrangement of the polypeptide backbone

What are the 4 TYPES OF SECONDARY STRUCTURES?

The a-helix
The B-sheet
Non-repetitive structures (loops, turns)
Super-secondary structure elements

What are the 2 TYPES OF -SHEET?

Parallel
Anti-parallel

Which TYPE OF B-SHEET IS THE MOST STABLE?

Anti-parallel

What is a SUPER-SECONDARY STRUCTURE ELEMENTS?

Combination of secondary structure elements

What are SUPER-SECONDARY STRUCTURE ELEMENTS ALSO CALLED?

Motif

What is the TERTIARY STRUCTURE?

The overall 3-dimensional arrangement of all atoms in space

What is the QUATERNARY STRUCTURE?

The spatial arrangement of the subunits in an oligomeric protein

What are the 5 TYPES OF FORCES STABILISING PROTEIN STRUCTURES?

Van der Waals interactions
Hydrophobic interactions
Ionic interactions
Hydrogen bonds
Disulphide bonds

Andreas Kukol Protein Structure Lecture 3

Learning Outcomes:
Protein domains
Structural aspects of enzymes
o The active site
Diseases related to protein structure
o Enzyme defects
o Sickle-cell anaemia

What are PROTEIN DOMAINS?

Spatially distinct units on a single polypeptide chain

What ARE PROTEIN DOMAINS LINKED BY?

Single flexible segment of the chain

What are ENZYMES?

Proteins that catalyse chemical reactions

What may ENZYMES NEED TO FUNCTION?

Cofactor

What are the 3 TYPES OF COFACTORS?

Metal ions
Coenzymes
Prosthetic groups

What is the ACTIVE SITE?

The region of the protein where the chemical reaction takes place

Where is the SHAPE OF THE ACTIVE SITE?

A cleft or groove on the protein surface

What 4 FACTORS IS THE ACTIVE SITE AND SUBSTRATE COMPLEMENTARY

IN?
Size
Shape
Charge
Hydrophobicity

What are the 2 GENERAL MODELS USED TO DESCRIBE THE BINDING OF A

SUBSTRATE TO AN ENZYME?
Lock and key
Induced fit

What are DISEASES BASED ON MALFUNCTION OF A PROTEIN CAUSED BY?

Altered amino acid residues due to mutation of genes

Andreas Kukol Chemical Kinetics Lecture 1

Learning Outcomes:
Understand the concept of a chemical reaction
Know and apply the definition of reaction rate
Be able to write down the rate law for elementary reactions
 Be able to work out the units of rate constants

What is the REACTION RATE?

The change of concentration of a chemical substance [J] per time

What is the EQUATION FOR REACTION RATE?

v = 1/vJ d[J]/dt

What does the RATE LAW SPECIFY?

The relationship between reaction rate and concentration of substances

What does the REACTION ORDER GIVEN THE SUM OF?

Exponents of the concentrations

What does a FIRST-ORDER RATE LAW DESCRIBE FOR ELEMENTARY

REACTIONS?
Uni-molecular reaction

What does a SECOND-ORDER RATE LAW DESCRIBE FOR ELEMENTARY

REACTIONS?
Bi-molecular reaction

In order TO OBTAIN THE CONCENTRATION OF SUBSTANCES OVER TIME

WHAT 2 WAYS MUST THE RATE LAW BE INTEGRATED?
Numerically
Analytically

Andreas Kukol Chemical Kinetics Lecture 2

Learning Outcomes:
Be able to write down rate laws for complex reaction mechanisms
Understand temperature dependence of rate constants and perform
relevant calculation
 Appreciate the molecular origin of rate laws

How are the RATE LAWS FOR COMPLEX REACTIONS OBTAINED?

Adding the rate laws for elementary reactions

Which REACTIONS MAY HAVE COMPLEX MECHANISMS?

Zero-order rate law

Which EQUATION DESCRIBES THE TEMPERATURE DEPENDENCE OF RATE

CONSTANTS?
Arrhenius equation

What is the ARRHENIUS EQUATION?

k = A exp(-Ea /(RT))

What happens when the TEMPERATURE IS INCREASED BY 10 K?

The reaction rate is doubled

What is the TEMPERATURE DEPENDENCE CAUSED BY?

A larger number of molecules that are able to overcome the activation
energy at higher temperature

What TYPE OF BEHAVIOUR DOES THE CHEMICAL KINETICS ON A

MOLECULAR LEVEL SHOW?
Stochastic behaviour

Andreas Kukol Enzyme Kinetics Lecture 1

Learning Outcomes:
The basics of enzyme kinetics
o The transition state
o The chemical nature of enzymes
o The mechanism of alkaline phosphate

What are ENZYMES?

Proteins with a defined 3-dimensional structure

What is the FUNCTION OF ENZYMES?

Speed up chemical reactions

What does ENZYMES NOT CHANGE?

Equilibrium constant

How does ENZYMES NOT CHANGE THE EQUILIBRIUM CONSTANT?

Stabilising the transition state

What can the COMPLEX MECHANISM ENZYME ALKALINE PHOSPHATASE BE

REDUCED TO?
Simple scheme

Andreas Kukol Enzyme Kinetics Lecture 2

Learning Outcomes:
Know the simplified reaction mechanism underlying the Michealis-
Menten equation
Understand the assumption made in deriving the Michealis-Menten
equation
 Understand the meaning of Vmax in the MM equation
Understand the meaning of Km in the MM equation
Know how enzyme activity is specified

What is the SIMPLIFIED MECHANISM THAT THE MICHEALIS-MENTEN

EQUATION IS BASED ON?
E + S ES -> P

What is the MICHEALIS-MENTEN EQUATION?

V0 = Vmax [S]/ Km + [S]

What does the MICHEALIS-MENTEN EQUATION APPLY TO?

When the substrate concentration is much higher than the enzyme
concentration

What is the STEADY ASSUMPTION EQUATION?

d[ES]/dt = 0 initially

What does the STEADY ASSUMPTION MEAN?

Reaction rate at the beginning is constant

What is VMAX?
Maximum rate at saturating substrate concentration

What is KM?
The substrate concentration at Vmax

What is KM AN APPROXIMATE MEASURE OF?

Affinity of the enzyme for its substrate

What is the TURNOVER NUMBER?

The number of reactions per active site per time

What are ENZYMES SOLD ACCORDING TO?

Catalytic activity

What is the CATALYTIC ACTIVITY OF AN ENZYME PREPARATION GIVEN IN?

International units

Andreas Kukol Enzyme Kinetics Lecture 3

Learning Outcomes:
How to perform enzyme kinetics experiment
How to analyse the data to obtain Km and Vmax
 Understand the mechanisms of reversible enzyme inhibition and how
they can be experimentally distinguished

What MUST BE ESTABLISHED FOR AN ENZYME KINETICS EXPERIMENT?

How the initial velocity depends on the substrate concentration

What are the 2 PLOTS USED TO DETERMINE VMAX AND KM?

Lineweaver-Burk plot
Hyperbolic plot

What is the LINEWEAVER-BURK PLOT ALSO CALLED?

Double reciprocal plot

What is the HYPERBOLIC PLOT ALSO CALLED?

Saturation plot

What is on the X AXIS ON THE LINEWEAVER-BURK PLOT?

1/[S]

What is on the Y AXIS ON THE LINEWEAVER-BURK PLOT?

1/Vo

What is the UNIT FOR 1/[S]?

mM-1

What is the UNIT FOR 1/VO?

s

What is the EQUATION TO WORK OUT VMAX FROM THE LINEWEAVER-BURK

PLOT?
1/y-intercept

What is the EQUATION TO WORK OUT KM FROM THE LINEWEAVER-BURK

PLOT?
Slope/y-intercept

What is ONE DISADVANTAGE OF THE LINEWEAVER-BURK PLOT?

Most of the data points are crowded in a small part of the plot

What is on the X AXIS ON THE HYPERBOLIC PLOT?

[S]

What is on the Y AXIS ON THE HYPERBOLIC PLOT?

Vo
What is the UNIT FOR [S]?
mM

What is the UNIT FOR VO?

s-1
How is VMAX CALCULATED USING THE HYPERBOLIC PLOT?
Extend the curve
Draw a line from the highest point of the curve to the y axis

How is KM CALCULATED USING THE HYPERBOLIC PLOT?

Determine Vmax
Draw a line from Vmax to the curve and down towards the x axis

What is the BEST METHOD TO OBTAIN KM AND VMAX?

Non-linear curve fitting

What are the 3 TYPES OF INHIBITION?

Competitive
Un-competitive
Mixed

What is COMPETITIVE INHIBITION?

Inhibitor competes with substrate for binding to the active site

What is UNCOMPETITIVE INHIBITION?

Inhibitor binds to the ES complex

What is MIXED INHIBITION?

Inhibitor binds to both the free enzyme and ES complex

What TERM IS GIVEN TO EXPLAIN COMPETITIVE INHIBITION?

Isosteric

What TERM IS GIVEN TO EXPLAIN MIXED INHIBITION?

Allosteric

What is the LINEWEAVER-BURK PLOT USEFUL IN DISTINGUISHING

BETWEEN?
Types of inhibition

Steve Hall Thermodynamics Lecture 1

What is the FIRST LAW OF THERMODYNAMICS?

Energy cannot be created or destroyed, but only converted from form into
another
What are the 3 TYPES OF ENERGY?
Kinetic
Potential
Chemical

What is CHEMICAL ENERGY?

Energy stored in molecules that have bonds

What is BOND ENERGY?

Amount of energy stored in a bond between 2 atoms

What 2 MEASURES DOES THE ACTUAL BOND ENERGY DEPEND ON?

Identity
Environment

What TERM IS GIVEN WHEN ENERGY IS GENERATED?

Bond formation

What TERM IS GIVEN WHEN ENERGY IS CONSUMED?

Bond breaking

What 2 OBJECTS IS ENERGY TRANSFERRED BETWEEN?

System
Surroundings

What are the 3 TYPES OF SYSTEMS?

Open
Closed
Isolated

What is an OPEN SYSTEM?

Both matter and energy can be transferred between system and
surroundings

What is a CLOSED SYSTEM?

Only energy can be transferred between system and surroundings

What is an ISOLATED SYSTEM?

Neither matter or energy can be transferred between system and
surroundings

What is the OVERALL ENERGY CHANGE CALLED?

Enthalpy of reaction
What SYMBOL IS USED TO REPRESENT ENTHALPY CHANGE?
H

What are the UNITS FOR THE ENTHALPY OF REACTION?

kJ mol-1
What happens during an EXOTHERMIC REACTION?
Releases energy from system to surrounding

What happens during an ENDOTHERMIC REACTION?

Absorbs energy from surrounding into the system

What is the ENTHALPY FOR AN EXOTHERMIC REACTION?

Negative

What is the ENTHALPY FOR AN ENDOTHERMIC REACTION?

Positive

What is E?
Sum of the bond energies

What is the ENTHALPY IF E (REACTANTS) > E (PRODUCTS)?

Positive

What is the ENTHALPY IF E (PRODUCTS) > E (REACTANTS)?

Negative

What does the SYSTEM BECOME WHEN IT LOSES ENERGY DURING AN

EXOTHERMIC REACTION?
More Stable

Are the PRODUCTS MORE STABLE THAN REACTANTS IN AN EXOTHERMIC

REACTION?
Yes

What does the SYSTEM BECOME WHEN IT GAINS ENERGY DURING AN

ENDOTHERMIC REACTION?
Less stable

Are the PRODUCTS LESS STABLE THAN REACTANTS IN AN ENDOTHERMIC

REACTION?
Yes

What TYPE OF REACTION HAS NEGATIVE ENTHALPY?

Spontaneous

What TYPE OF REACTION HAS POSITIVE ENTHALPY?

Non-spontaneous

What is ENTROPY?
A measure of the spread of energy through system/surroundings

What can ENTROPY BE A MEASURE OF ALSO?

Energetic disorder
What is the SECOND LAW OF THERMODYNAMICS?
A process can occur spontaneously if the sum of the change of entropies
of system and surroundings increases

What SYMBOL IS USED TO REPRESENT ENTROPY CHANGE?

S

What TYPE OF REACTION HAS NEGATIVE ENTROPY?

Non-spontaneous

What TYPE OF REACTION HAS POSITIVE ENTROPY?

Spontaneous

What SYMBOL IS USED TO REPRESENT FREE ENERGY CHANGE?

G

What TYPE OF REACTION HAS NEGATIVE FREE ENERGY?

Spontaneous - exergonic

What TYPE OF REACTION HAS POSITIVE FREE ENERGY?

Non-spontaneous endergonic

What are 2 STANDARD CONDITIONS?

298 K temperature
1 bar (105 Pa) pressure

What do the SYMBOLS H AND G BECOME DURING STANDARD

CONDITIONS?
HO
GO

What is ATP?
Energy currency of a cell

What TYPE OF REACTION HAVE A LARGE NEGATIVE GO?

Catabolic

What TYPE OF REACTION HAVE A LARGE POSITIVE GO?

Anabolic

What is EO?
Redox potential of a half-reaction
Steve Hall Radioactivity Lecture 1

What are RADIOISOTOPES?

Isotopes that readily lose mass/energy to reach a more stable state

What are RADIOISOTOPES ALSO CALLED?

Radionuclides

What is RADIOACTIVE DECAY?

Loss of mass/energy

What are the 5 TYPES OF RADIOACTIVE DECAY?

Loss of an a particle
Loss of a b particle
Emits y radiation
Positron product
Electron capture

How does NUCLEAR FISSION DIFFER FROM RADIOACTIVE DECAY?

The fissile element fragments into 2 elements of similar size

What ORDER DOES RADIOACTIVE DECAY FOLLOW IN KINETICS?

1st order

What is DECAY CONSIDERED IN TERMS OF?

Number of nuclei present at a given time

What is the KINETICS OF DECAY EQUATION?

lnN = lnNo kt

What TYPE OF PLOT IS LNN AGAINST T?

Linear

What is HALF-LIFE?
The time taken for half the parent to decay to the daughter nuclide

What is the HALF-LIFE FOR 1ST ORDER KINETICS?

Constant

What 2 MEASURES CAN BE FOUND FROM THE LINEAR PLOT?

Rate constant, k
Half-life

What TYPE OF ISOTOPES DOES RADON GAS NOT HAVE?

Stable isotopes

What TYPE OF GAS IS RADON?

Noble gas

What are the SI UNITS OF RADIOACTIVITY?

Becquerel Bq

What is the OLDER UNIT OF RADIOACTIVITY?

Curie Ci
What is the SI UNIT OF ABSORBED DOSE?
Gray G

What is the OLDER UNIT OF ABSORBED DOSE?

Radiation absorbed dose rad

What 3 INSTRUMENTS ARE USED TO MEASURE RADIATION LEVELS?

Dosimeter
Geiger counter
Scintillation counter

Jennifer Young Overview of Metabolism Lecture 1 and 2

Learning Outcomes:
Understand the importance of metabolism to the maintenance of life
Describe the key catabolic and anabolic pathways
Describe the basis of substrate level and oxidative phosphorylation
Appreciate the relationship of metabolic pathways to health and
disease

What is METABOLISM?
The sum of all chemical reactions that takes place in a living organism

What are the 4 PURPOSES OF METABOLISM?

Mechanical work
Active transport
Synthesis
Nervous transmission

What are the 2 SUBDIVISIONS OF METABOLISM?

Catabolism
Anabolism

What is CATABOLISM?
Breakdown of complex molecules to simple molecules

What is ANABOLISM?
Synthesis of complex molecules

What HAPPENS DURING CATABOLIC REACTIONS?

Energy is released

What HAPPENS DURING ANABOLIC REACTIONS?

Energy is consumed

What are COUPLED REACTIONS?

Energy released from one reaction drives another reaction

What is the ENERGY CURRENCY OF A CELL?

ATP

What are the 3 SOURCES OF ATP?

Carbohydrates
Fats
Proteins

What PROCESS PRODUCES ATP DIRECTLY?

Substrate phosphorylation

What PROCESS PRODUCES ATP INDIRECTLY?

Oxidative phosphorylation

What 2 INTERMEDIATES ARE INVOLVED IN OXIDATIVE PHOSPHORYLATION?

NAD+
FAD