Chapter 4 Amino Acids Revised 2/ - PowerPoint Presentation

Slide1

Chapter 4Amino Acids

Revised 2/

18

/2014

Biochemistry I

Dr. Loren WilliamsSlide2

Proteinogenic Amino Acids

An amino acid contains

an amine group

a carboxylic acid group,

a side-chain (or R-group,

all attached to the same chiral carbon atom (the Cα)There are twenty 'standard' amino acids, distinguished by their sidechains. The standard amino acids are encoded by the genetic code throughout the tree of life.The are three non-standard (non-canonical) amino acids pyrrolysine (found in methanogenic organisms and other eukaryotes), selenocysteine (present in many noneukaryotes as well as most eukaryotes), N-Formylmethionine.Slide3

stereochemistry at the

CaSlide4

CORN

C’O, R, NH and H are bonded to the chiral Ca atom. Rotate the molecule so the Ca-H bond is directed out of the page (with the hydrogen atom toward the viewer), if C’O, R, NH groups are arranged clockwise around the C

a atom, then it is the L-form. If counter-clockwise, it is the D-form.

stereochemistry at the

C

aSlide5

stereochemistry at the

C

aSlide6

L

D

stereochemistry at the

C

aSlide7

stereochemistry at the

C

aSlide8

Optically active molecules rotate

a plane of linearly polarized light about the direction of

propagation. Optical activity occurs in solutions of chiral molecules such as amino acids, sugars, etc.

Optical ActivitySlide9

Optically active molecules rotate

a plane

of linearly polarized light about the direction of propagation. Optical activity occurs in solutions of chiral molecules such as amino acids,

sugars, etc.

The

a helix & b sheet (proteins) and A & B helices of nucleic acids have CD signatures representative of their 3D structures [caused by differential absorption of RH and LH circularly polarized light].Optical Activity

Circular DichroismSpring 2014, not covered Slide10

alanine Ala (A) arginine Arg (R)asparagine Asn (N) aspartic acid Asp (D)cysteine

Cys (C)glutamic acid Glu (E)glutamine Gln (Q)glycine

Gly (G) histidine His (H)isoleucine Ile

(I)leucine Leu (L)lysine Lys (K)methionine Met (M)phenylalanine Phe (F)proline Pro (P)

serine

Ser (S)threonine Thr (T) tryptophan Trp (W)tyrosine Tyr (Y)valine Val (V) the 20 standard amino acidsSlide11

the 20 standard

amino acidsSlide12

Table 4-1 part 1

flexible

small

hydrophobic

hydrophobic

hydrophobic

hydrophobic

rigidSlide13

Table 4-1 part 2

hydrophobic

metal binder

hydrophobic

no NH

hydrophobic

aromatic

hydrophobic

aromaticSlide14

Figure 4-5Slide15

Figure 4-4Slide16

Table 4-1 part 3

hydroxyl

hydroxyl

amide

amide

aromatic

hydroxyl

thiol

redox, metalSlide17

Table 4-1 part 4

base

base

acid/base

acid

acidSlide18
Slide19

http://www.russell.embl-heidelberg.de/

aas/Slide20
Slide21

This is how I want you to draw peptides

N to C (---->)correct stereochemistry at C

acorrect ionization states (

His,Cys)draw all H, except those bonded to Cno chemical mistakesSlide22

Histidine

(protonation state)

pH < pK

a

pH > pK

aSlide23

HA

H

+

+ A

–

There is a sign error here that

microsoft won’t let me fix.Slide24

anion above pH 3.1

anion above pH 4.1

neutral above pH 6.0

cation below pH 8.0

neutral below pH 8.3

neutral below pH 10.9cation below pH 10.8cation below pH 12.5Slide25

amino acid jewelrySlide26

Selenocysteine

exists naturally in all kingdoms of life.

Selenocysteine

is found in several enzymes (for example glutathione peroxidases,

tetraiodothyronine

5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases, selenophosphate synthetase 1, methionine-R-sulfoxide

reductase B1, and some hydrogenases).

Selenocysteine

is encoded by a UGA codon (normally a stop codon) using ‘translational recoding’. The UGA codon is made to encode

selenocysteine

by certain sequences and secondary structures in the mRNA.

Amino Acid 21:

Selenocysteine

Spring 2014, not covered Slide27

Pyrrolysine (Pyl or O) is a genetically coded amino acid used by some methanogenic archaea and one known bacterium. Pyrrolysine is used in enzymes that are part of methane-producing metabolism. Pyrrolysine is similar to lysine, but with an added pyrroline ring linked to the end of the lysine side chain. It forms part of an unusual genetic code in these organisms.

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Amino Acid 22:

Pyrrolysine

Spring 2014, not covered Slide28

N-

Formylmethionine

(

fMet

) is a derivative of methionine in which a

formyl group has been added to the amino group. It is used for initiation of protein synthesis in bacteria, mitochondria and chloroplasts, and may be removed post-translationally.

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Amino Acid 23: N-

Formylmethionine

Spring 2014, not covered Slide29

Figure 4-3

Formation of

a Peptide Bond

condensation dehydrationSlide30

Formation of

a Peptide Bond

in the ribosomeSlide31
Slide32
Slide33

Figure 4-6

Oxidation and Reduction of Cysteine

Oxidized

ReducedSlide34

Oxidation and Reduction of CysteineSlide35

Page 88

reduced

oxidized

Oxidation and Reduction of

Glutathione

Spring 2014, not covered Slide36

Figure 4-14

Modified Amino Acids

Spring 2014, not covered Slide37

Spring 2014, not covered Slide38

Figure 4-15

Spring 2014, not covered