1: Amino acids and peptides

What is reaction thermodynamics?

Describes the energetic of chemical reactions

What is Gibbs free energy?

Energy of the reaction available to do work, also called ‘available energy’

How is ΔG calculated?

G_(products) - G_(reactants)

What is the difference between enthalpy and entropy?

enthalpy = heat

entropy = disorder

How is ΔG calculated?

ΔG = ΔH - TΔS

change in Gibbs free energy = change in enthalpy - T x change in entropy

Is ΔG positive or negative for spontaneous reactions?

negative

Describe an exergonic reaction

ΔG = -ve

free energy released

favourable, spontaneous

Describe an endergonic reaction

ΔG = +ve

free energy absorbed

unfavourable, not spontaneous

What is the difference between exergonic and endergonic reactions?

exergonic is spontaneous and free energy is -ve and released. endergonic is unfavourable and free energy is +ve and absorbed

What is the difference between exothermic and exergonic?

exothermic = heat released

exergonic = free energy released

What does +ΔS mean?

more disorder

What does -ΔS mean?

less disorder

What is K_eqm?

equilibrium constant, describes the relative concentration of each components when reaction is at equilibrium

What is the expression for K?

What is ΔGº?

the standard free energy change, a constant for the particular reaction which is measured upon standard conditions, measures how much work the reaction can do

How do ΔG and ΔGº differ?

ΔG is variable, ΔGº is a constant

How is ΔG calculated?

i for initial conditions

What is R?

universal gas constant

Why are standard conditions used?

to compare changed (like in free energy or pressure) easily

What is ΔG’º?

biochemistry standard conditions

• 298K (25ºC)

• gases at partial pressure of 101.3 kPa (1 atm)

• reactants and products at 1M

  • [H⁺] = 10^-7

  • Mg²⁺ = 1mM

Why does ΔGº and ΔG’º differ?

ΔGº = standard conditions for chemists/physicists

• use conditions that are suitable for chem/phys

ΔG’º = standard conditions for biochemists

• use well buffered aqueous solutions at pH 7, like the body

When does ΔG = ΔGº?

when the concentration for products/reactants = 1

What is ΔG at eqm?

ΔG = 0

What are the three main equations for free energy?

What term is most important to predict if a reactions is spontaneous?

ΔG

What is a kinetically driven reaction?

• reaction where one or more of the products are being removed at a rate much faster than it is being produced OR

• reaction where one or more reactants are being replenished at a faster rate than it is removed

How can you make an unfavourable reaction go?

• replenish reactants (kinetic)

• remove products (kinetic)

• couple the unfavourable reaction with a highly favourable one (thermodynamic)

What do you need to keep in mind about coupling reactions together?

they are done under standard conditions, need to consider actual free energy/conditions in the cell

Does a positive change or a negative change in free energy indicate a favourable reaction?

negative

How is the free energy change of the reverse reaction related to that of the forward reaction?

If some spontaneous event is endothermic, what must have been the “driving force” behind that event, enthalpy or entropy?

enthalpy as thermic = heat, entropy = free energy

If a reaction has a positive DG′⁰ it is often described as ‘unfavourable’. What is wrong with this statement? 

It can still occur, it just need extra energy added for it to occur

Explain why energy is released when ATP is hydrolysed and why energy is absorbed when ATP is formed from ADP and Pi.

What is a nucleotide?

base + sugar + phosphate

What is a nucleoside?

base + sugar like ADP

What is the difference between a nucleotide and nucleoside?

nucleoside is just base + sugar like ADP

nucleotide is base + sugar + phosphate like ATP

What is ATP?

adenosine triphosphate

a nucleotide (adenine + ribose + three phosphate)

Where bond released energy in ATP when broken?

phosphoanhydride bonds

Is energy required or released when bonds are broken and repaired?

breaking bonds = energy absorbed

forming bonds = energy released

What is the ATP → ADP reaction?

Is ATP → ADP exergonic or endogonic?

exergonic (release free energy)

Why is ATP → ADP exergonic?

• ATP (-4) less stable because it has higher negative charge density than ADP (-3)

• P_i is very stable; multiple resonance stated exist

• ATP phosphoanhydride bonds are very weak

• ADP phosphoanhydride and P_i bonds are very strong

What are proteins and what are they used for?

main agents of biological function

used in:

• catalysis

• transport

• structure

• motion

• signalling (transduction)

What are proteins made of?

linear heteropolymers of α-amino acids

What are functions of amino acids?

• capacity to polymerise

• useful acid-case properties

• varied physical propertirtes

• varied chemical functionality

What is the structure of amino acids?

tetrahedral (Sp3 central carbon)

• central carbon

• acidic carboxyl group (COO^-)

• basic amino group (NH₃⁺)

• hydrogen

• R group (unique)

Are amino acids chiral?

Yes! Because they are tetrahedral and have different substituents bonded.

Are naturally occurring proteins L- or D- amino acids?

L

What are D- and L- amino acids?

• stereoisomers, optical isomers

• D = dextrorotatory (+), right, clockwise

• L = levorotatory (-), left, anticlockwise

How to determine chirality rotation?

place H to the back, if CORN can be read clockwise = L

How can amino acids be categorised?

• polar/non-polar

• aliphatic/aromatic

• charged/uncharged/negative/positive

What is pK_a?

pH when an ionisable group is 50% protonated, 50% de-protonates

How are the side chain atoms lettered?

greek alphabet

backbone = alpha

beta

gamma

delta

epsilon

zeta

eta

what is a guanidino group?

trigonal planar of central C and three Ns surrounding it

What is the Beer-Lambert law?

A = εcl

absorbance = extinction coefficient/molar coefficient x concentration x path length

What are aromatic side chains responsible for?

most ultraviolet absorbance and fluorescence properties of proteins

What does aliphatic mean?

relating to oils and fats, alkanes, almost exclusively hydrogen and carbon

What is lysozyme and what does it do?

a protein/enzyme which cleaves the polysaccharide chains in the cell walls of bacteria

What is the native conformation of a protein?

fold with the lowest free energy, therefore it is favoured over mis-folded/semi-folded states.

How are protein structures represented?

worm/tube - backbone - trace only

ribbon - backbone - secondary structure

space-filling - heavy atoms - molecular surface

line - all atoms

How are peptide bonds formed?

carboxylic acid group of one amino acid reacts with the amino group of the next one to form a peptide bond through a dehydration reaction

What is the N- and C-terminus and how are they formed?

N- = +ve Nitrogen terminus

C- = -ve Carbon terminus

the order and structure of amino acids is fixed, so when they form a polypeptide chain, there will always be a positive and negative terminal

How do bonds affect rotation?

• single bonds allow free rotation

• multiple bonds are planar with very limited movement

What is the peptide bond geometry? Where are the peptide bonds?

(-N-Cα-C)peptide(-N-Cα-C-)…

Can peptide bonds have isomers?

Yes! Due to partial double bonds, can have cis and trans isomers

Are cis or trans conformations favoured in peptide bonds?

Trans due to steric hinderance of the CO - Cα on opposing amino acids - EXCEPT for proline where cis is favoured

What order are amino acids in a polypeptide labeled?

N → C terminus

i-2, i-2, i, i+1, i+2

True or False: peptides bonds are flat and planar

true

trans omega (ω) bonds

ω = -180º

cis (ω) bond

ω = 0º

How do proteins fold if there is limited movement in the CO - NH backbone peptide bond?

via. the N - Cα - C single bonds within an amino acid = dihedral angles

What are dihedral angles?

the N - Cα - C single bonds within an amino acid

N - Cα = φ angle (phi)

Cα - C = Ψ angle (psi)

What is the φ angle (phi)?

N - Cα, comparing the C(O)s

What is the Ψ angle (psi)?

Cα - C, comparing the Ns

Why are φ and Ψ so important?

because, if assuming all the peptide bonds are trans, the only conformational freedom is between these dihedral bonds, everything else is fixed

What are side chain dihedral angles called?

χ (chi)

• χ₁ between Cα and Cbeta

• χ₂ between Cbeta and Cgamma

• χ₃ between Cgamma and Cdelta