Lecture 3

Question 1

Big picture items

Answer 1

• There are 20 different amino acids
• Each amino acid has a common “backbone” but a different “side chain”
• The properties of the side chains span a wide range
• Modified amino acids play important functions
• Modification of amino acids in proteins is critical to life
• Amino acids can be linked together by peptide bonds
• Several oligopeptides have important cellular functions
• Proteins are synthesized by ribosomes

Question 2

Amino acid structure

Answer 2

R is the “side chain”

Question 3

Increasing hydrophobicity of the side chain

Answer 3

ala< lle < phe

Question 4

A zwitterionic α-amino acid

Answer 4

A zwitterionic α-amino acid

Question 5

Amino acids with an aliphatic, nonpolar side chain

Answer 5

Not many H-bond acceptors or donors in the side chain of all these amino acids. Only the S in the Met is a rather poor H-bond acceptor.

gly, ala, pro, val, leu, iso, meth

Question 6

Proline is unique

Answer 6

Its side chain makes a ring by bonding with its main chain nitrogen.

Question 7

Glycine is also unique

Answer 7

has no side chain.

Question 8

Isoleucine

Answer 8

is one of only two amino acids with a chiral side chain

Question 9

Amino acids with an uncharged, polar side chain

Answer 9

Plenty of H-bond acceptors and donors in the side chains of all these amino acids!

ser, thre, cyst. asparagine (asn), glutamine (gln)

Question 10

Cysteine is quite special

Answer 10

1. The pK of its SH is ~ 8.3
2. S– is a good nucleophile
3. It is good in coordinating metals
4. Can form disulfide bridges

Question 11

Amino acids with a positively charged side chain

Answer 11

lys, arg, hist

Question 12

Histidine (His) is very special:

Answer 12

1. Its pK of ~ 6 means that at neutral pH the imidazole ring is both in its protonated and unprotonated state; at a pH below the pK a larger fraction is protonated than unprotonated; at pH values above the pK a larger fraction of the side chain is unprotonated than protonated.
2. It is often involved in acid-base catalysis
3. The side chain is good in coordinating metals

Question 13

Amino acids with a negatively charged side chain

Answer 13

aspartate (asp), glutamate (glu)
• These side chains are very hydrophilic.
• The side chain carboxylates occur often in active sites
• The carboxylates can coordinate metals – in particular, Mg2+ and Ca2+ love them.

Question 14

Amino acids with an aromatic side chain

Answer 14

phen, tyr, trypt

Which two of these side chains could you call “amphiphilic”?

Question 15

The aromatic side chains of amino acids

absorb UV light

Answer 15

Phe absorbs at 258 nm – but is not shown because it absorbs much less than Tyr> and Trp.

Question 16

Below and above the pKa….

Answer 16

NOTE: The pKa of the same functional group can be different in different molecules.
• the pK of the side chain amino group of a Lys is different from that of the α-amino group of the N-terminus of a protein.
• the pK of the OH of a Ser side chain is so high that we do not consider it for this class, but the pK of the OH of a Tyr side chain is lower (and you have to know it).

Question 17

Biologically active amino acid derivatives

These are not incorporated into polypeptide chains of proteins

Answer 17

gaba, histamine, dopamine, thyroxine

Biologically active amino acids play crucial roles in cell-to-cell communication.
E. g. the top three are neurotransmitters, and thyroxine is a hormone

Question 18

Dopamine and the Synapse

Answer 18

Dopamine is an important neurotransmitter (among many others)
Neurotransmitters are compounds which travel across the “synaptic cleft” between two neurons
More precisely: from the axon of the presynaptic neuron to the dendrite of the postsynaptic neuron

Question 19

Dopamine and Parkinson’s Disease

Answer 19

Dopamine is synthesized in two enzymatic steps from the amino acid tyrosine, via 3,4-dihydroxyphenylalanine (also called “L-DOPA”)
Deficiencies in the dopamine production in the brain is correlated with “Parkinson’s disease”, which often starts with relatively mild tremors, but usually has many other effects including speech and motion disorders, and can progress to a truly devastating disease.
Giving Parkinson patients L-DOPA is one of the methods which gives some relief.

Question 20

Serine phosphorylation and dephosphorylation

Answer 20

Reversible modification of specific amino acids is extremely important in “signal transduction” in biology.

“Protein kinases” attach phosphoryl groups to specific Ser, Thr and Tyr side chains.

“Protein phosphatases” remove these phosphoryl groups

The selective phosphorylation or dephosphorylation of specific proteins allows cells to “sense” the environment, such as reacting to the presence of “insulin”.

Key: after phosphorylation at one or more sites, the properties of the protein differ.

Question 21

Protein Glycosylation

Answer 21

A very common type of modification of side chains on the protein surface.
One or more sugars are attached to one or more specific residues of a protein

In eukaryotic organisms:
• Almost all secreted and membrane-associated proteins are glycosylated.
• Protein glycosylation is important for many functions.

One of these functions is forming the “extracellular matrix (ECM)” in higher organisms
• The ECM is the mixture of proteins and oligosaccharides between cells
• The ECM is key to positioning cells properly with respect to each other
• The ECM is crucial in very complex processes like:
• Developmental biology
• Wound healing

Question 22

Protein Glycosylation 2

Answer 22

• Two major types of glycosylation are:
• O-glycosylation
• The oligosaccharide is attached to side chain O of a Ser or Thr
• N-glycosylation
• The oligosaccharide is attached to side chain N of an Asn:

Attaching sugars to a protein occurs during the secretion of a protein
There are often many types of saccharides joined together forming an “antenna”

The process of creating an oligosaccharide antenna is very complex
(For the exam you do need to know the concepts of “core” and “antenna”, but not the names of the different sugars).

Question 23

Biologically active (oligo)peptides

Answer 23

Aspartame is a dipeptide used as an artificial sweetener
• condensation of L-aspartic acid and (the methyl ester of) L-phenylalanine
• 200 times sweeter than sugar
• binds to the taste receptors TAS1R1 and TAS1R2

In Glutathione: a Glu is linked in an unusual way to a Cys, and the Cys is linked in the standard way to a Gly

Glutathione plays an important role in maintaining the reducing environment in cells.
(NOTE: the Glu-Cys-linkage (red arrows) is via the side(!) chain of the Glu!!)

Question 24

Condensation of two amino acids forming a peptide bond

Answer 24

The result is a “dipeptide”.
The red bond in the dipeptide is the “peptide bond”.
By repeating this condensation reaction, long “polypeptide chains” are obtained.
In all living organisms this process is carried out by the “ribosome”.

Question 25

A tetrapeptide

Answer 25

Ala-Tyr-Asp-Gly (three-letter code)
or
AYDG (one-letter code)

(The convention is to write peptide and protein sequences with the N-terminal residue at the left)

Question 26

The pKa of main chain termini

Answer 26

Although there are of course only two ends per peptide or protein chain,

it is still important to know that:
The pKa of the N-terminal -NH3 + is ~8;
the pKa of the C-terminal -COO- is ~4.

Example: it is the N-terminal amino group of influenza virus haemagglutinin which:
• senses the lower pH in the endosome, and becomes protonated,
• triggering the tremendous conformational change crucial for infection

Question 27

Protein synthesis is carried out by the ribosome

Answer 27

Characteristics of a bacterial ribosome
• Consists of 66% ribosomal RNA (wires) and 34% proteins (spheres)
• Total molecular weight ~ 2.5 MDa
• Binds message RNA (mRNA) which contains the codons encoding the sequence of amino acids in the polypeptide chain
• Binds a succession tRNA’s (transfer RNA’s) charged with amino acids
• The synthesis of the polypeptide chain is carried out by ribosomal RNA, hence the ribosome is a ”ribozyme”

The ribosomes in eukaryotes are similar but somewhat more complex.

A few major ribosome features
• Two subunits:
• small (yellow – called “30S”)
• large (blue – called “50S”)
• Three tRNA binding sites (magenta, green and gold)
• The growing polypeptide chain exists via a tunnel