3-3/4/5 (Amino Acids and Peptides)

What are proteins encoded by?

Genetic information stored in DNA.

How are proteins related to DNA sequences?

Each unique DNA sequence encodes a specific protein.

What are proteins made of?

Amino acid monomers linked into polymers.

What is a protein?

A folded polypeptide with biological function.

What determines protein folding?

Amino acid sequence and chemical properties.

What components form the amino acid backbone?

Amino group, alpha carbon, and carboxyl group.

Alpha carbon (Cα)

Central carbon atom to which all amino acid groups attach.

What four groups attach to the alpha carbon?

Amino group, carboxyl group, hydrogen, and R group.

What does the R group often contain?

A beta carbon connected to additional chemical groups.

Chirality

Property where a molecule cannot be superimposed on its mirror image.

What are mirror-image molecules called?

Enantiomers.

What property differs between enantiomers?

Their rotation of plane-polarized light.

What chirality form is found in biological amino acids?

L-amino acids.

What does the prefix L mean?

Levo, meaning rotates polarized light to the left.

What chirality form is rare in cells?

D-amino acids.

What structural feature causes chirality in amino acids?

Alpha carbon attached to four different groups.

Which amino acid is achiral?

• Glycine.

• Its side chain is hydrogen, so the alpha carbon has two identical groups.

Peptide bond

Covalent bond linking amino acids together.

How is a peptide bond formed?

• Through a condensation (dehydration) reaction.

• removes H2O per reaction

• forms between the carboxyl group of one amino acid and the amino group of another.

What type of chemical mechanism forms peptide bonds?

Nucleophilic addition-elimination reaction.

What initiates peptide bond formation?

Nucleophilic attack by the amino group.

Which atom is attacked during peptide bond formation?

The carbonyl carbon of the carboxyl group.

Dipeptide

Two amino acids linked by one peptide bond.

Polypeptide growth

Continued addition of amino acids through repeated peptide bond formation.

Why is the peptide bond rigid?

• It has partial double-bond character.

• so its bc os the Resonance delocalization of electrons.

• it’s Rigid and planar with restricted rotation.

Does peptide bond rigidity make proteins completely rigid?

No, rotation occurs around adjacent single bonds.

Which bonds in the backbone can rotate freely?

Cα–N and Cα–C bonds.

Why are rotating bonds important?

They allow protein folding into specific shapes.

What repeating pattern forms the polypeptide backbone?

Nitrogen–alpha carbon–carbonyl carbon sequence.

What determines polypeptide directionality?

• Different chemical groups at each end.

• N-terminus: Start of polypeptide with a free amino group

• C-terminus: End of polypeptide with a free carboxyl group.

Why do proteins fold into specific shapes?

Due to chemical interactions among side chains.

What determines protein structure?

Amino acid sequence.

How many rotating bonds exist per amino acid backbone unit?

Two freely rotating single bonds.

What defines the beginning of a protein sequence?

The N-terminal amino acid.

What defines the end of a protein sequence?

The C-terminal amino acid.

what are the non-polar aliphatic amino acids (7)

• NP and hydrophobic

• glycine (gly) G

• alanine (ala) A

• proline (pro) P

• valine (val) V

• leucine (leu) L

• isoleucine (ile) I

• methionine (met) M

ala, val, leu, ile

• cluster together within proteins

• stabilizes them through hydrophobic effect

gly and ala

• ambivalent (mixed)

• they can reside outside or inside

• since they have smaller side chains, their hydrophobic effects aren’t so extreme

why is proline unique?

• has a secondary amino group

• the side chain of proline forms a covalent bond with the amino group, making it cyclic

• it’s usually on the surface of proteins bc the rigid ring structure is suited for U turns in protein structures

• it’s still in the aliphatic classification

methionine

• one of the 2 sulfur containing aa in R group

• has a slightly nonpolar thioether side chain

what are the polar uncharged amino acids? (5)

• polar side chains that form H bonds with water/other polar molecules

• Serine (Ser) S

• Threonine (Thr) T

• Cysteine (cys) C

• Asparagine (asn) N

• Glutamine (gln) Q

ser and thr

• often found on protein surfaces

• they make great contact with (aq) end

• the -OH is a good nucleophile

  • serine typically found in enzyme active sites

  • threonine is secondary alcohol -OH so it’s not as good

cysteine

• can form H-bonds with water or other polar molecules

• often found on protein surfaces

• -SH group is a great nucleophile

• typically found in active sites of enzymes

asn and gln

• asparagine and glutamine

• have non-ionizable un-charged polar side chains

• they’re amide counterparts of asp (aspartic acid) and glu (glutamate)

what are the aromatic r group amino acids (3)

• they’re hydrophobic and absorb UV light at 280nm

• this can be used to measure protein concentrations

• phenylalanine (phe) F

• tyrosine (tyr) Y

• tryptophan (trp) W

phenylalanine

• phe, F

• most hydrophobic among the aromatic amino acids

Tyrosine

• tyr, Y

• has an ionizable group that can form H-bonds

• so it’s important in some enzymes

tryptophan

• trp, W

• bulky af

negatively charged R grouped amino acids (2)

• they’re (-) at pH 7 and hydrophilic

• they’re usually found on protein surfaces

• aspartate (aspartic acid) (asp) D

• glutamate (glutamic acid) (glu) E

positively charged R grouped amino acids (3)

• they’re basic at pH 7

• they’re very polar and found on the protein exterior

• histidine is the least basic

• Lysine (lys) K

• arginine (arg) R

• histidine (his) H

alanine info and side chain

• ala, A

• CH3 side chain

• NP and aliphatic

• ambivalent (mixed)

• can reside outside or inside bc of a smaller side chains

valine info and side chain

• val, v

• CH bound to CH3 and CH3 side chain

• NP and aliphatic

• clusters inside protein bc it’s hydrophobic

leucine info and side chain

• leu, L

• CH2 - CH where the CH is bound to CH3 and CH3 sidechain

• NP and aliphatic

• clusters inside protein bc it’s hydrophobic

isoleucine info and side chain

• ile, I

• CH bound to a CH3 and CH2-CH3 side chain

• NP and aliphatic

• clusters inside protein bc it’s hydrophobic

glycine info and side chain

• gly, G

• H side chain

• NP and aliphatic

• ambivalent (mixed)

• can reside outside or inside bc of a smaller side chains

proline info and side chain

• pro, P

• 4 C ring including the secondary carbon (pentagon ring)

• has NH within the ring

• NP and aliphatic

• good for U turns

phenylalanine info and side chain

• phe, F

• has a CH2 - benzene side chain

• aromatic amino acid

• most hydrophobic among the aromatics

tyrosine info and side chain

• tyr, Y

• has a CH2 - benzene - OH side chain

• aromatic (hydrophobic)

• can form H-bonds

• so it’s important in some enzymes

tryptophan info and side chain

• trp, W

• has 2 rings side chain

• aromatic (hydrophobic)

• bulky af

serine info and side chain

• ser, S

• CH2 - OH side chain

• polar and uncharged

• often found on protein surfaces

• the -OH is a good nucleophile

  • serine typically found in enzyme active sites

threonine info and side chain

• thr, T

• CH bound with OH and CH3 side chain

• polar and uncharged

• often found on protein surfaces

• the -OH is a good nucleophile, but not the best bc secondary alcohol

cysteine info and side chain

• cys, C

• CH2 - SH side chain

• polar and uncharged

• usually found on protein surface

• -SH is a great nucleophile so it’s in enzyme active sites

methionine info and side chain

• met, M

• CH2 - CH2 - S - CH3 side chain

• NP and aliphatic

aspartic acid info and side chain

• asp, D

• CH2 - C which is bound to (=O) and OH (or O-) side chain

• (-) charged amino acids at pH 7

• hydrophilic and found on protein surface

glutamic acid info and side chain

• glu, E

• CH2 - CH2 - C which is bound to (=O) and OH (or O-) side chain

• (-) charged amino acids at pH 7

• hydrophilic and found on protein surface

asparagine info and side chain

• asn, N

• CH2 - C that is bound to (=O) and (-NH2)

• amine derivative of aspartic acid

• polar uncharged amino acid

glutamine info and side chain

• gln, Q

• CH2 - CH2 - C that is bound to (=O) and (-NH2)

• amine derivative of glutamic acid

• polar uncharged amino acid

lysine info and side chain

• lys, K

• CH2 - CH2 - CH2 - CH2 - NH2 or NH3+ side chain

• (+) charged at pH 7, basic and polar

arginine info and side chain

• arg, R

• CH2 - CH2 - CH2 - NH - C bound to NH2 and (=NH or =NH2+)

• (+) charged at pH 7, basic and polar

histidine info and side chain

• his, H

• CH2 - 5 point ring

  • 3C and 2 N

• (+) charged at pH 7, basic and polar

• least basic among the (+) charged amino acids

SDS Polyacrylamide gel electrophoresis endgoal

seperate proteins based on size

SDS Polyacrylamide gel electrophoresis mechanism

• SDS added to a sample of proteins and heated

  • denatures them

  • surrounds them with uniform charge

  • subunits are also seperated

• when put through Polyacrylamide gel from the top

  • it goes towards the bottom (+) bc the polypeptides are (-)

  • the smaller ones go faster and further

• since the charge:mass ratio is the same, the difference in travel is only due to MW

  • low MW proteins are more mobile