Amino acids & peptides Flashcards
(38 cards)
Know the expression relating change in Gibbs free energy, change in
enthalpy and change in entropy; and know what each term represents
- Gibbs free energy = the energy of the reaction available to do work (called available energy)
- it takes into account enthalpy (heat) and entropy (disorder)
(change(G)=change(H)-Txchange(S) where temp is in Kelvin) - negative gibbs energy can be given by: negative enthalpy or positive entropy or any combo making changeG negative
Define exergonic, endergonic, exothermic, endothermic, positve/negative entropy values
- Exergonic = G is neg, free energy released, favourable, spontaneous
- Endergonic = G is pos, free energy is absorbed, unfavourable, non-spontaneous
- Exothermic = H is neg, heat is released
- Endothermic = H is pos, heat is absorbed
- Entropy is neg = less disorder
- Entropy is pos = more disorder
> Exergonic / Endergonic describe the spontaneity of a reaction.
They are based on the Gibbs free energy change (ΔG).
Exothermic/Endothermic describe energy changes in the form of heat during a reaction, and are based on the enthalpy change (ΔH).
🔥 Heat = random energy transfer
- It’s energy in transit from hot to cold.
- It increases the disorder/random motion of particles.
- You can’t always use it to do useful work (some of it is “lost”).
⚙️ Free energy = usable energy
- It’s the portion of energy that can actually do work (like making ATP).
- Includes contributions from both:
- Heat (ΔH)
- Entropy (ΔS)
🧪The eqn:
At higher temperatures, particles are more energetic → disorder matters more
- So T×ΔS tells you how much of the energy is “used up” just increasing randomness
🔹 ΔH gives you how much energy is available in form of heat
🔹 TΔS tells you how much is “lost” to entropy
🔹 So ΔG = energy you can actually use to do work
–> Summary: Gibbs free energy tells you how much of the heat energy is actually usable, after subtracting the energy lost to randomness (entropy).
🔥 Why does Gibbs free energy only use heat energy?
Because it’s made for reactions happening in everyday conditions — like in your body or in a lab — where:
- Pressure and temperature stay constant
–> (Pressure is how much force is applied over a certain area.) - The main energy being exchanged is heat
Heat vs temp:
Heat Temperature
🔥 Energy in transit 🌡️ Measure of average
kinetic energy
Is a form of energy Is a property of matter
Flows from hot to cold Doesn’t flow — it’s just a measurement
Depends on mass +
type of substance + temp
Depends only on how fast
particles move
Be able to interpret a Gibbs free energy plot
Predict from ∆G whether a reaction is spontaneous or not.
A spontaneous reaction:
- has negative AG
Does breaking bonds release or require energy??
✅ Truth:
Breaking bonds always requires energy.
Energy is released when new, stronger bonds form.
In cell respiration process:
Bonds in glucose and oxygen are broken 🧨 (costs energy)
New bonds in CO₂ and H₂O are formed 🔥 (extra energy used to maintain higher energy/unstable reactants is released)
🔥 Net result:
The bonds formed (in CO₂ and H₂O) are stronger and lower-energy than the ones broken — so more energy is released than required overall
So when you hear “glucose has stored energy,” that’s shorthand for:
It has bonds that, when broken and replaced with more stable bonds, result in net energy release that can be used to make ATP (an energy storage molecule)
✅ Yes — in exergonic (energy-releasing) reactions, the products are generally more stable than the reactants. That’s why energy is released!
How is hydrogen bonding done?
A hydrogen atom is covalently bonded to a highly electronegative atom:
N, O, or F
That hydrogen interacts with a lone pair on another N, O, or F atom
^can be inter or intra molecular
Role Examples
Donor (has H attached) –OH, –NH, –NH₂
Acceptor (has lone pair) :O:, :N:
Explain how ∆G is different from ∆G’°.
- ΔG=ΔH−TΔS is about why a reaction is spontaneous (underlying physics).
- This is a fundamental thermodynamic relationship.
- It links energy changes (enthalpy) and (entropy) to tell you whether a process is spontaneous.
- It applies to any kind of process — chemical, physical, even phase changes like melting or evaporation.
- It doesn’t consider concentration because it’s about the energy difference between two defined states.
🧠 Think of this as the definition of Gibbs free energy.
- ΔG=ΔG∘+RTlnQ is about whether the reaction is
spontaneous under current conditions.
- This is used specifically for chemical reactions.
- It tells you the actual free energy change based on how far you are from equilibrium.
- It does depend on concentrations (via Q) because that tells us how the reaction is actually behaving right now.
- It lets you adjust the standard value (Δ𝐺∘) based on real-world conditions.
🧠 Think of this as a correction formula: “How does the free energy change under real, non-standard conditions?”
⚖️ Logic behind the whole equation:
Δ𝐺∘: tells you what the reaction wants to do under perfect conditions.
RTlnQ: tells you what the current concentrations are doing to help or oppose that tendency
If 𝑄<1
Q<1: reactants dominate → reaction tends to go forward
If 𝑄>1
Q>1: products dominate → reaction tends to go backward
If 𝑄=𝐾
system is at equilibrium →
Δ𝐺=0
🔑 Final clarity:Δ𝐺∘
: “How much energy would be released/required if everything was 1 M”
RTlnQ: “How far are we from that situation?”
ΔG: “Given where we actually are, how much energy will be released/required now?”
🔍 So why does concentration affect free energy?
Because concentrations determine how far a system is from equilibrium — and that’s what gives it the potential to do work.
🔁 At equilibrium:
The system has no drive to move forward or backward.
Therefore, ΔG = 0
⚠️ No work can be extracted — the system is at “dead energy” for that reaction.
🧠 Analogy: Water flow
Think of ΔG like water pressure in a pipe:
High reactants, low products = full tank at the top of a hill → lots of pressure to flow downhill (negative ΔG)
Equal reactants and products = tank is flat → no pressure (ΔG = 0)
High products, low reactants = water wants to flow the wrong way → you have to do work to make it go (positive ΔG)
✅ So the punchline:
🧠 Free energy depends on concentrations because the system’s ability to do work is directly tied to how far it is from equilibrium.
The more unbalanced the concentrations, the more “push” the reaction has — and that push is the free energy.
Demonstrate how imposing equilibrium conditions allows the
relationship between standard free energy change and equilibrium
constant to be derived
Describe how understanding free energy changes allows the prediction
of features of a reaction.
Describe three (3) ways an ‘unfavorable’ reaction can be made
favorable.
1) Remove one or more of products at a rate much faster than it is produced; the reaction is now “kinetically” driven
2) Replenish one or more of the reactions at a rate much faster than it is removed
3) Couple the “unfavourable” reaction with a highly “favourable” reaction (in the active site of an enzyme)
> This describes favourability under standard conditions, must always consider how actual conditions affect free energy change
(By the end of semester) explain why certain ‘unfavorable’ metabolic
reactions are favorable in the cell.
YES
Explain why ATP is considered an “energy rich” molecule.
Draw or identify D and L amino acids
Use CORN
- H @ front & clockwise = L
- H @ back & anticlockwise = D
- H @ front & anticlockwise = D
- H @ back & clockwise = D
Name/draw/identify each of the 20 naturally occurring amino acids
- Non-polar (hydrophobic)
- Glycine
- Alanine
- Proline
- Valine
–> Leucine
–> isoleucine
–> methionine
–> phenylalanine
–> tryptophan - Aliphatic R groups
- Leucine
- Isoleucine
- Methionine
–> alanine
–> valine
–> proline - Positively charged groups (Basic)
- Lysine
- Arginine
- Histidine - Aromatic R groups
- Phenylalanine
- Tyrosine
- Tryptophan - Negatively charged groups (Acidic)
> 🔹 Why do acidic amino acids have a negative charge?
Because they donate a proton (H⁺) from their side chain, and when a molecule loses a proton, it becomes negatively charged.
- Aspartate
- Glutamate - Polar uncharged groups (amides)
💡 Why are amides uncharged?
The amide group (–CONH₂) does not lose or gain protons under biological conditions.
It’s polar (can form hydrogen bonds), but it’s electrically neutral.
- serine
- threonine
- asparagine
- glutamine
❌ Cysteine is not an amide although IT IS polar and uncharged
✅ Cysteine is only one with a REACTIVE sulpfur containing side-chain - can form disulphide bonds
Explain uncharged polar amino acid structures in detail
- asparagine & glutamine
- not chemically reactive
- polar
- H-bond acceptor and donor
- deaminate (remove NH2 group) to aspartate and glutamate at high and low pH - Serine and threonine
Not very chemically reactive
→ Their –OH (hydroxyl) group isn’t super reactive on its own, but it can be modified (like in phosphorylation).
Polar
→ The –OH group makes them hydrophilic (water-attracting), so they’re found on the outside of proteins.
Hydrogen bond donor and acceptor
→ The –OH group can donate or accept hydrogen bonds, helping with protein structure and interactions.
Threonine has an extra chiral center
→ It has two carbon atoms with 4 different groups, making it more complex in shape than serine.
Methyl group on Threonine
→ Threonine has a –CH₃ (methyl) group, which makes it slightly more bulky and gives it a bit of non-polar character.
Both polar and slightly non-polar
→ Threonine’s side chain is polar because of the –OH but has a non-polar part (methyl group) too.
Explain non-polar amino acid structures in detail
- Alanine and valine
- no reactive groups
- non-polar and hydrophobic - Leucine and Isoleucine
- no reactive groups
- non-polar and hydrophobic
- isoleucine has extra chiral centre and is a structural isomer of leucine - Proline
- no reactive groups
- non-polar and hydrophobic
- cyclic 5-membered ring
- covalent bond between N to delta-CH2
- no NH group - imino acid
- cant act as a backbone H-bond donor
- restricted phi angle - Glycine
- side chain hydrogen
- no reactive groups
- non-polar and hydrophobic
- not chiral - no D or L isomers
- less steric clashes
- can form:
> left handed turns
> right handed turns
Explain Sulfur containing amino acid structures in detail
- Cysteine
- thiol polar
- partially deprotonated
- very reactive
- nonpolar upon oxidation - Methionine
- thioesther
- nonpolar
not particularly reactive
- can be air oxidised to sulfoxide
- thiolate
- most reactive side chain used in enzyme active sites
- disulfide bonds can form between two cysteine side chains
- cysteine can form interchain and intrachain disulfide bonds
- disulfide bonds also absorb UV weakly
- reductants = B-mercaptoethanol, Dithiothrietol, glutathione
Disulfide bond example - insulin
- Two polypeptide chains
–> A (white) and B (yellow) chain linked by inter-chain disulfides (intra-chain disulfide in A)
Disulfide bond example - Lysozyme
- one polypeptide chain
- conformation stabilised
- by intrachain disulfides
Explain pos charged amino (basic) acid structures in detail
- Lysine
- Aliphatic side chain (methyl groups) capped with amino group (capped with amino group)
- very polar
- potent nucleophile - reactive centres
> A nucleophile is a chemical species that donates an electron pair to form a chemical bond — usually to an electron-deficient atom (called an electrophile). - Arginine
- long aliphatic side chain of methyl group capped with guanindino group (HN = C(NH2)2)
- guanindino group is planar and stabilised by resonance charge which is delocalised over whole group (partial double bonds)
- very polar
- pos charged form predominates - Histidine
- highly used in enzyme active sites
- Imidazole ring has special properties and is aromatic
Has an imidazole ring
→ This is a 5-membered ring with two nitrogen atoms.
→ It’s aromatic (stable and has a special ring structure like benzene).
Can act as a nucleophile
→ When deprotonated (one nitrogen loses a hydrogen), it has a lone pair of electrons, so it can attack other molecules.
Can both give and take hydrogen bonds
→ So, it can act like a nucleophile (donating electrons) or an electrophile (accepting electrons).
→ That’s why it’s called chemically ambidextrous.
Versatile
→ Its ability to change charge easily near physiological pH makes it very reactive and flexible, perfect for enzyme chemistry.
Explain aromatic amino acid structures in detail
- Phenylalanine
- nonpolar
- unreactive - Tyrosine - Overall Polar
- largely nonpolar ring
- somewhat polar (OH)
- OH can hydrogen bond
- hydroxyl group pKa ~ 10
- resonance structures - Tryptophan - Non-polar overall
- largely non-polar
- Indole ring
- largest side chain
- conjugated double bonds
- Absorbs UV light and fluorescence
- Indole NH H-bond donor
- electron-rich - charge transfer
> Indole is an organic compound with the chemical formula C8H7N, a fused benzene and pyrole ring
> because of this extensive delocalisation through pi orbitals, theres high electron density, its also very useful in electron transfer reactions
Summary:
- The above aromatic side chains are responsible for most UV absorbance and fluorescence properties of proteins
- Extent and geometry of conjugated double bond systems cause spectral differences
- useful for detection of proteins in solution
- The spectral properties are sensitive to their immediate environment making them useful probes of protein structure
Beer-Lambert Law: can measure spectral properties of amino acids and proteins
Difference between polarity and hydrophilicity
🔁 Think of it like this:
Polarity is the cause (how electrons behave in a molecule).
Hydrophilicity is the effect (how the molecule behaves in water).
‘Read’ amino acid sequences in single letter and three letter code
YES
Rules of aromaticity
- they are rings
- planar (sp2 hybridised usually)
- follow Huckels rule - 4n+2 electrons where n is integer in conjugated p orbitals (double-bonds)
Describe hydrophobic effect
The hydrophobic effect arises because nonpolar molecules (like hydrocarbons) do not interact favorably with water. This is critically dependent on the fact that carbon and hydrogen have very similar electronegativities, meaning C–H bonds are nonpolar.
✅ Therefore:
Molecules made mostly of C–H bonds (like lipids) are hydrophobic.
They don’t form H-bonds or strong dipole interactions with water.
So, in aqueous environments, water excludes these molecules, pushing them together — this is the hydrophobic effect.
From sequence information, identify the ionizable groups in
polypeptides and draw the structure of their protonated and
deprotonated states.
