1.1 Amino acids and peptides Flashcards
What is the simple definition of Gibbs free energy?
It is the energy of the reaction available to do work
What is the equation relating the change in gibbs free energy to heat and entropy?

How are spontaneous reactions defined in terms of delta G?
Spontaneous reactions have a negative delta G
What is the difference between exergonic and endergonic?

What is the difference between exothermic and endothermic?

whats up
What does the sign of delta S indicate in terms of the change in entropy?
Delta S is negative: less disorder
Delta S is positive: more disorder
What is the equation linking delta G and delta G*?

How does the position of equilibrium relate to the change in Gibbs free energy?
The further away from equilibrium you start, the more work is done before you get there.

What are some ways through which a negative delta G can be achieved?
- Negative delta H (exothermic)
- Positive delta S (increase in entropy)
- Any combination that leaves delta G negative
What are the standard conditions in chemistry?
- 298 K
- Gases at a partial pressure of 101.3 kPa (1 atm)
- Reactants and products at 1 M concentrations
What are the standard conditions in biochemistry?
Same as those of chemistry but the reaction occurs in a well buffered aqueous solution at pH 7 with [H+] ion concentration 10-7 and Mg2+ = 1mM
If you look at the free energy equation and set all initial concentrations to 1, what happens?
Shows delta G is equal to delta Go when everything is at standard conditions

How does the free energy equation change when all concentrations are at equilibrium?
At equilibrium delta G=0 this means the reaction can do no more work.
This shows that delta G0 is a constant

What is used to predict where a reaction will be spontaneous?
The measure of whether a reaction will proceed spontaneously is delta G not delta Go.
How can the initial conditions of a reaction be altered in order to get a spontaneous reaction?

What are three ways of making unfavourable reactions go?
- Remove one or more of the products at a rate much faster than it is produced so that the reaction is now kinetically driven
- Replenish one or more of the reactants at a much faster rate than it is removed
- Couple the unfavourable reaction with a highly favourable reaction (in the active site of an enzyme)
Label the blanks on this ATP molecules


What is the difference between a nucleotide and nucleoside?
Nucleotide = base + sugar + phosphate
Nucleoside = base + sugar
What causes the release of energy via ATP?
Energy is released upon the hydrolysis of phosphoanhydride bonds
Show the equation for the release of energy via ATP including delta G

How is bond energy related to bond breakage/forming?
Energy is required to break any bond
Energy is released when any bond forms
Why is energy required to break any bond?
The bonded state is a more stable state that’s why it required energy to break
Why is the ATP reaction highly exergonic?
- ATP has a higher negative charge density than ADP (ATP less stable)
- Pi is very stable: multiple resonance states exist
- ATP phosphoanhydride bonds are relatively weak
- ADP phosphoanhydride bonds and Pi bonds are relatively strong
Why is tri phosphtate less stable than di phosphate?
Due to charge density, are there is a great accumualtion of negative charges and more strain and repulsion
What are some of the roles of proteins in the body?
- Catalysis
- Transport
- Structure
- Motion
- Signaling
What are some of the properties that make amino acids well suited to carry out a variety of biological functions?
- Capacity to polymerise
- Useful acid base properties
- Varied physical properties
- Varied chemical functionality
What is the basic structure of an amino acid?
The carbon always has four substituents and is tetrahedral.
All (except proline) have:
– an acidic carboxyl group connected to the carbon
– a basic amino group connected to the carbon
– a alpha hydrogen connected to the carbon

Which protein isomer is found in naturally occuring amino acids?
L amino acids
Where do the D and L names for amino acids originate from?
Based on the rotation of plane of polarised light viewed towards the light source or based on what you could chemically synthesise them from
How can you determine the chirality of the alpha carbon?

What amino acid is this?

Alanine
Alanine
What amino acid is this?


Cysteine

Aspartate

Glutamate

Phenylalanine

Glycine

Histidine

isoleucine

Lysine

Leucine

Methionine

Asparagine

Proline

Glutamine

Arginine

Serine

Threonine

Valine

Tryptophan

Tyrosine
Reversed prompt draw the amino acid
Cysteine

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Aspartate

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Glutamate

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Phenylalanine

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Glycine

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Histidine

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isoleucine

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Lysine

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Leucine

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Methionine

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Asparagine

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Proline

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Glutamine

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Arginine

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Serine

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Threonine

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Valine

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Tryptophan

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Tyrosine

What is the three letter code for aspartate?
D and Asp
What is the three letter code for glutamate?
E and Glu
What is the letter codes for phenylalanine?
F and Phe
What is the three letter code for isoleucine?
I and ile
What is the three letter code for Lysine?
K or Lys
What is the three letter code for asparagine?
N or Asn
What is the three letter code for glutamine?
Q or Gln
What is the three letter code for Arginine?
R or arg
What is the three letter code for tryptophan?
W or trp
What is the three letter code for tyrosine?
Y or Tyr
Which amino acids belong to the non polar aliphatic R groups?
Glycine, alanine, proline, valine, Leucine, Isoleucine, methionine
Which amino acids belong to the polar, uncharged R group category?
Serine, Threonine, Cysteine, Asparagine, Glutamine
Which amino acids belong to the aromatic R groups?
Phenylalaline
Tyrosine
Tryptophan
Which amino acids belong to the positively charged R groups? (basic)
Lysine
Arginine
Histidine
Which amino acids belong to the negatively charged R groups?
Aspartate
Glutamate
When is pKa equal to pH?

For the acidic side chains of aspartic acids and glutamic acid, in what state do these R groups exist at physiological pH?
Their pKa is 4.4 so at neutral pH they are completely ionsided and negatively charged
In what state do the basic side chains of Lysine and Arg have their R groups at physiological pH?
Lys has a pKa of 10 so the protonated, positively charged form dominates
Arg has a pKa of 12 so similarly completely ionised.
What are the special properties of basic side chain Histidine?
- HIghly used in enzyme active sites
- The imidazole ring is a H bond done or acceptor (electrophile or nucleophile) and chemically ambidextrous
- Effective nucleophile in its deprotonated form
What are some properties of the amide side chains asparagine and glutamine?
- Not very chemically reactive
- Polar
- H bond donor and acceptor
- THe can remove amide group to become carboxylic acids
What state does Tyrosine’s aromatic side chain exist at physiological pH?
- The phenol form dominates above pH 10, but below it phenolate is negatively charged

Why are the aromatic side chains responsible for UV absorbance and fluorescence properties?
- The extent and geomtery of conjugated double bond systems cause spectral differences

What properties does proline hold due to its unique geometry?
- It has no NH group so its an imino acid
- Can’t act as a backbone H bond donor
- Limites rotation between N-Cæ angle -60o
Compare the two sulfur containing side chains, cysteine and methionine

What are some examples of disulfide bonds being seen in proteins?



What are the rotation properties of the peptide bonds?
- The peptide bond has partial double bond character due to resonance
- Rotation around CO-NH bond is not free, groups are co-planer

What can be said about the size of the peptide bond?

Which peptide bond isomer is favoured energetically?
- The trans form is intrinically favoured energetically
- Due to severse steric hindrance (van der Waals) repulsion of the side chain in cis
What sort of peptied bond isomerisation is found in proline?
Similar steric hindrance in trans and cis but trans is still favoured for steric reasons

Label the terminology of the peptide bond


What happens when the peptide linkage is cis in nature? For bond angle

Label which one is the phi and si angle


Fill in the blanks about the phi angle


Fill in the blanks about the psi angle


Why are phi and psi so important?
Because assuming all peptide bonds are trans then all the conformation freedom in the backbone of the polypeptide is due to these two rotations, everything else is fixed
Fill in the blanks about side chain dihedral angles

