Amino Acids/Proteins/Peptides Flashcards Preview

Biochemistry > Amino Acids/Proteins/Peptides > Flashcards

Flashcards in Amino Acids/Proteins/Peptides Deck (34):
1

Amino Acid Chemical Structure

The smallest protein constituents chemically composed of:
1. Amino group (-NH2)
2. Carboxylic group (-COOH)
3. R group (determines property of amino acid)
4. Alpha carbon

***Note:
1. Amino & carboxylic groups do not have to branch from the same carbon
2. Not all amino acids are coded for by codons/not all of them are incorporated into proteins
3. Modification of some amino acids to others is possible

2

Proteinogenic Amino Acids

20 Alpha, chiral amino acids coded for by the human genome

***Glycine is the only achiral proteinogenic amino acid

3

Amino Acid Classes based on their Side Chain Property

1. Nonpolar/Nonaromatic
2. Polar
3. Aromatic
4. Negatively Charged
5. Positively Charged

4

Nonpolar Amino Acids

1. Glycine - [smallest amino acid -achiral with H R-group]
2. Alanine- [CH3]

CH3
3. Valine - [CH2-CH3]

CH3
4. Leucine-[CH2-CH2-CH3]

CH3
5. Isoleucine [CH2-CH2-CH3

6. Proline - [Involves Amino group's Nitrogen in a penta
cycline)

7. Methionine- [CH2-CH2-S-CH3]

Glaciers in Alaska victoriously Located Isolated Prowlers

5

Aromatic Amino Acids

1. Phenylalanine [with a benzene group-is nonpolar]
2. Tyrosine [Phenylalanine w -OH/relatively polar]
3. Tryptophan [Double ring-contains N]

People still go to Alaska b/c of aroma of Pine, Timber & and other trees

6

Polar/NonAromatic Amino Acids

1. Serine
2. Threonine
****Both are highly polar due to their -OH group*****
3. Asaparagine
4. Glutamine
****Both have an amide group that does not become charged upon changes in pH******
5. Cysteine
****Contains a thiol group (-SH) that is prone to oxidation*********

7

Negatively Charged Amino Acids
***at physiological pH of 7.4****

1. Aspartic acid/Aspartate
2. Glutamic acid/Glutamate

***These amino acids, unlike asparagine and glutamine that carry amide groups, carry carboxylic groups.

****Aspartate and Glutamate are the deprotonated forms of these amino acids****

8

Positively Charged Amino Acids

1. Lysine [has primary amino group]

2.Arginine [has positive charge delocalized over all 3 nitrogens in its side chain]

3. Histadine [Has an aromatic ring with two nitrogen atoms]

9

Hydrophobic Vs. Hydrophilic Amino Acids

1. Hydrophobic AA [Alanine, Valine, leucine, isoleucine, phenylalanine]
2. Hydrophilic AA [(Negatively Charged: aspartate & glutamate) + (Positively Charged: lycine, arginine, histadine) + glutamine and aspargine]

The rest of the amino acids [ serine, threonine, cysteine, tyrosine, tryptophan, methionine, glycine & proline] lye somewhere in b/w with regards to their hydrophobic/philic nature

10

Amino Acid Acid/Base Behavior

Amino acids are amphoteric with 2 pkas for their 2 ionizable species (carboxylic acid & amino group)

-at ph

11

Buffer Solution

a solution in which the pH does not fluctuate much with acid or base titration

12

Pka1

Point at which only half of the carboxylic species of an amino acid are deprotonated

13

pI

Isoelectric point

Point at which all carboxylic species in an amino acid have been deprotonated and point at which amino acids exist as zwitterions or neutral species

-for acidic amino acids, pI can be obtained by averaging the pKa of carboxylic group and pKa of R-group
-for neutral amino acids, pI can be obtained by averaging pKa1 & pKa2
-for basic amino acids, pI can be obtained by averaging pka of amino group and that of the Rgroup.

14

pKa2

Point at which half of the amino groups of an amino acid are deprotonated

15

pH>pKa2

pH range in which all amino groups of an amino acid are deprotonated and the overall charge is positive

16

Titration Curve

Curve that shows the change in pH of a species with addition of base or acid

Elements of a titration curve consist of
pka1 ----nearly flat horizontal line b/c at pka1, [HA]=[A]; therefore solution serves as a buffer with little pH change

pI-----nearly vertical line b/c pH of neutral species is very sensitive to change w/ addition of acid/base.

pka2----nearly flat horizontal line [see above]

17

Protonation/Deprotonation

pKa1= [deprotonated species of carboxylic acid]=[protonated species of carboxylic acid]

pI= [entirely deprotonated COOH]=[entirely protonated NH2]

pKa2= [deprotonated species of NH2]=[Protonated species of NH2]

18

Peptide Constituents/Types

Residues (amino acid subunits); dipeptides; tripeptides; oligopeptides; polypeptides

19

Peptide Bond

Aka Amide bond is formed through a condensation/dehydration rxn where the nucleophilic amino group of one amino acid attacks the electrophilic carbonyl carbon of another amino acid to connect the N of amino with with C of carbonyl while eliminating a water molecule.

***This reaction creates resonance structures where partial double bond character exists b/w Carbonyl C & O and between Carbonyl C and Amino N due to presence of delocalized electrons in the Carbonyl pi bond and on N as a lone pair.

The resonance Structure limits possibility of free rotation in peptide backbones, giving them very rigid structures.

Peptide bonds are read and drawn from N-Terminus (Free amino end) to (C-Terminus: free carbonyl end)

20

Peptide Breakdown Mechanism (Enzymes & Reactions)

Hydrolytic enzymes that break down Peptides in our bodies:

1. Trypsin (starts cleavage at C-terminus of arginine & lysine)
2. Chemotrypsin (starts cleavage at C-terminus of Phenylalanine, Tryptophan and Tyrosine)

Rxn:

1. A hydrogen is added to the amino group and a hydroxide is added to the carbonyl group.

21

4 Levels of Protein Structure

1. primary
2. secondary
3. tertiary
4. quaternary

22

Primary Protein Structure

1. Sequence of amino acids coded by DNA genes
2. linearly linked with covalent, peptide bonds
3. determined using SEQUENCING, a laboratory technique

23

Secondary Protein Structure

1. hydrogen-bonded neighboring primary structures
2. 2 types: [Alpha helices & Beta-Pleated Sheets]

24

Alpha Helices

1. Intramolecularly hydrogen bonded peptide chains that coil clockwise around a central axis
I: Side chains point away from the central axis
II: Hydrogen bonds exist b/w carbonyl oxygen of one
residue and amino hydrogen of another residue 4
residues down the chain
2. is a keratin component

****Contains proline only at its begining due to its bulky structure****

25

Keratin

a fibrous protein component of hair, nail and skin

26

B-Pleated Sheets

1. one type of 2ndary amino structure
2. Structure with parallel or antiparallel primary protein
structures hydrogen bonded together in a pleated
manner
I: Amino acid side chains point up and down, away
from the plain of the sheet
II: hydrogen bonds exist b/w carbonyl oxygen of one
residue and amino hydrogen of another residue in
the parallel/antiparallel chain
III: pleats exist to maximize H-Bonding
3. is a component of fibroin that makes silk fibers

***Contains proline only at its turns b/w pleated chains***

27

Protein Types

1. Fibrous --(formed by 1 & 2ndary structures)--ex: collagen
2. Globular---(formed by 3 & 4nary sturctures)---ex: hemoglobin

28

Tertiary Protein Structure

3 dimensional protein structure folded with respect to 1. hydrophillic/hydrophobic interactions of amino acid side chains and with respect to 2. disulfide bonds
I: hydrophobic groups lie on the inside and further
hydrogen bond /hydrophillic groups lie on the
outside and hydrogen bond (this layout maximizes
protein stability & solvation in H2O)
II: disulfide bonds create loops/waves in protein
structure

Involve 3 types of interactions

1-Hydrophobic/Hydrophillic
2-Disulfide bonds
3. Hydrogen Bonds

29

Disulfide Bonds

1. Bonds that form from oxidation of 2 cysteine molecules
2. One of the important bond types in proteins' tertiary structures
3. create waves/loops in protein structure and remain responsible for waviness of hair

30

Denaturation

Destruction of a protein's 3 dimensional shape that leads into the protein's loss of function

Can be:
1. reversible
2. irreversible

Caused by
1. solutes--[directly hydrolyze H-bonds, disulfide bonds
& other interactions, breaking down 2, 3 &
4ternary structures] - ex: SDS
2. heat --[increased T, increases KE which overcomes
the hydrophobic interactions in a protein--
>protein collapses]

31

Quaternary Structures of Proteins

1. Functional protein units that form from aggregation of numerous polypeptide chains/sub-units (3tiary structures)---Ex: Hemoglobin & Myoglobin

2. Functions:
I: Increase stability of protein by reducing protein's
surface area
II: Bring catalytic sites closer together to inc rate of
Rx
III: induce cooperativity & allosteric effects

***Not all proteins have 4nary structures****

32

Cooperativity/Allosteric Effect

Conformation change in one subunit of a quaternary protein structure that induces enhancement or reduction of activity of other subunits

33

Conjugated Proteins

Proteins whose function depends on the prosthetic element they carry.

Ex:
1. Glycoproteins---[prostethic element: carbohydrate]
2. Lipoproteins---[prosthetic element: lipid]
3. Nucleoproteins---[prosthetic element: nucleic acid]

***These proteins are inactive in absence of their prosthetic group***

34

Prostethic groups

Minerals & vitamins, carbs, nucleic acids, & lipids that attach to a protein and determine its function

Ex: iron heme of hemoglobin--