Chapter 3: Amino Acids, Peptides, Proteins

Helpfulness: 0
Set Details Share
created 6 years ago by kristenmilenki
51 views
Med Chem TUSP PY1
updated 6 years ago by kristenmilenki
show moreless
Page to share:
Embed this setcancel
COPY
code changes based on your size selection
Size:
X
Show:
1

Amino Acids

Building Blocks of Proteins

Proteins are linear heteropolymers of alpha-amino acids

2

Protein function

Capacity to polymerize

useful acid/base properties

varied chemical properties + chemical functionality

3

L-alpha- Amino Acid

Basic Amino group + Acidic Carboxylic Group + alpha Carbon + R group (all except Proline)

in b/w molecule therefore charge = 0

All AA Chiral Except Glycine

4

Proteins only contains

L-AA

5

AA pK1 (-COOH)

2

6

AA pK2 (-NH3+)

9

7

AA PI

6

8

Get Approximate # of AA In A Protein By:

MW of Protein/ 110

9

Serotonin (5-HT)

In depression, not enough serotonin, drugs block intake so there is an increase of serotonin in synaptic cleft

10

Catecholamines

Dihydroxy Phenylalanine: DOPA

11

DOPA

Treat Parkinsons

Parkinsons patients have low levels of DOPA

12

GABA

If add Carboxylic Acid Group (-COOH) ---> GLUTAMINE

Important in neutrotransmission

13

Triiodothyronine T3

Important in Syn of Thryoxine

Only natural compound that contains Iodine

14

Zwitterionic Form

Net Charge=0

15

Fully Protonated AA

@Acidic pH:

Carboxyl --> Protonate

AA --> Cationic

16

Zwitterion AA

@Neutral pH:

Carboxyl --> Deprotonate

AA-> Protonated

Netcharge =0

17

Fully Deprotonated AA

@Basic pH

Amino group --> Neutral

AA --> Anionic form

18

Zwitterion + pH =6

Around pH=6, zwitterion dominated

pI=pH

AA in zwitterion form

**Only True For AA w MONO Carboxylic acid and MONO amino group

19

Amphoteric Nature of AA

AA can act as:

acid(Proton donor)

or base (proton acceptor)

20

AA Can Act As Buffer:

AA w uncharged side chains have 2 pka values, 2 + 9

can act as buffer in two pH regions

21

At net charge =0

Zwitterion

AA least soluble in water

AA does not migrate in electric field

22

Chemical Enviro Affects

pKa values

alpha carboxy more acidic than in carboxylic acid

alpha amino slightly less basic in amines

23

The Side Chain pKa is higher bc

Electronic Distribution

24

Ionizable side chains show up in

titration curve

25

pKa values recognized if

2 pKa values are more then 2 pH units apart

26

Peptide

Small Condensation Products of AA

"Small" compared to proteins

27

Polypeptide

Covalently Linked Alpha AA

28

Condensation

Lose H2O

29

Peptide Stability

Very Stable

Equilibrium on hydrolysis side

Slow ---> Kinetically Stable

Absence of Catalyst, Last Very Long Time

30

Peptide Ends

NOT SAME

31

Terminal Amino + Carboxyl + Ionizable R Group Contribute to

PI

32

Can Change Alpha Carbon Location w/ same groups

different compounds

ex. Glutamylcysteinyl glycine ---> Glutathione

-Same Groups: Glutamin, Cysteine + Glycine

33

Proteins

Polypeptide + Cofactors + Coenzymes + Prosthetic Groups

34

Cofactors

* Think Metals *

Functional Non AA Component

Metal Ions or Organic Molecules

35

Coenzymes

* Think Organic *

Organic Cofctors

NADH (CHECK THIS) In Lactate Dehydrogenase

36

Prosthetic Groups

Covalently Attached Cofactors

Heme In Myoglobin

37

Small Protein

Large Polypeptide

38

Lipoprotein

Prosthetic Group: Lipids

39

Glycoproteins

Prosthetic Group: Carbohydrates

40

Phosphoproteins

Prosthetic Group: Phosphate Groups

41

Hemoproteins

Prosthetic Group: Heme (Iron Porphyrin)

42

Flavoproteins

Prosthetic Group: Flavin Nucleotides

43

Metalloproteins

Prosthetic Group: Iron, Zinc, Calcium, Molybdenum, Copper

44

Primary Structure

Linear array of AA

Covalent Bonds --> Disulfide Bonds

AA sequence

AA Residues

45

Secondary Structure

Alpha Helix

Stable Arrangement of AA residues in pattern

46

Tertiary Structure

3D polypeptide folding

Protimers

Polypeptide Chain

47

Quaternary Structure

Arrangement in space of protein w 2+ polypeptide unties

Assembled Subunits

48

Slight Change In Primary Structure

Carries on to Quaternary Structure

49

How Can A Mixture Of Proteins Can Be Separated?

Relies on differences in physical and chemical properties

  • Charge
  • Size
  • Affinity for a ligand
  • Solubility
  • Hydrophobicity
  • Thermal Stability

**Chromatography used to separate*

50

Column Chromatography

Most Powerful Method

Protein Charge, Size, Binding Affinity and Other Properties

  1. Porous Solid Material Held In Column
  2. Buffered Solution Migrates Through It
  3. Protein Placed On Top
  4. Protein Moves Down through Solid
51

Ion Exchange Chromaotgraphy

Protein Mixture Added to Column Containing Cation Exchangers

Cation Exchangers--> Move Slower

Anion Exchangers--> Move Faster

Exploits Difference in sign and magnitude of net electric charges of proteins at given pH

52

Size-Exclusion Chromatography (Gel Filtration)

Protein Mixture Added to Column Containing Cross-Linked Polymer

Larger Molecules --> Pass More Freely

Separates Proteins According to Size

53

Affinity Chromatography

Protein Mixture Added to column containing a polymer bound ligand specific for protein of interest

  • Unwanted Proteins are washed through

Solution of Ligand Is added to Column

  • Protein of interest is eluted by ligand solution

Separated Protein by their binding specificities

54

Electrophoresis

Separation in analytical scale

Electric Field pulls proteins according to their charge

Gel Matrix hinders mobility of proteins according to their size and shape

55

pH > pI

Protein/AA charge is negative

56

pH < pI

Protein/AA charge is positive

57

Isoelectric Focusing

can be used to determine pI of a protein

  1. Put protein sample on end of gel
  2. change pH along gel
  3. electric field is applied
  4. After Staining, proteins shown to be distributed along pH gradient according to pI values

High pI/pH------> Low pI/pH

58

Ninhydrin

reagent used to indicate presence of AA

end result--> highly conjugated ( a lot of double bonds)

59

Sanger Method

for terminal AA identification

FDNB

Dansyl Cl

Dabsyl Cl

Fluorescamine

60

Edman Degration

extension of Sanger Method

advantage** --> peptide remains intact and can be recycled through process