Lectures 2 - 6 Flashcards Preview

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Flashcards in Lectures 2 - 6 Deck (48):
1

generic amino acid structure

      COO-
       
|
H3N+ -​ Calpha - H
      |
       R-group


An C-H with an amino, an acid, and a sidechain.

2

Central Dogma

DNA makes RNA and RNA makes PROTEINS

3

compounds of life

1. Amino acids and proteins

2. Nucleotides and polynucleptides

3. Saccharides and poly saccharides

4. Lipids

4

Post-translational modifications (PTM)

Purpose of PTM is to add diversity to proteins.

Phosphorylation is the most common PTM.

5

Chirality

Chiral molecules are non-superimposable mirror images. Amino acids are chiral! Only L-isomer is found in amino acids. 

 

Note: GLY is not chiral (the side chain is just an additional 'H'.)

6

pKa

pKa = pH when there is a 50:50 ratio of protonated and deprotanated species for a specific ionizable group (ex: the acid part, the amino part, and/or the R-group part)

7

Isoelectric point

aka pI. Where the net charge is zero. (Often the middle of the steep part of the S curve)

8

Zwitterion

When the amino acid is neutral

9

If the pH is lower than the pKa for an ionizable group...

...that group will be PROTONATED (add an H)

10

If the pH is higher than the pKa for an ionizable group...

...then that group will be DEPROTANATED (lose an H)

11

If the pH is equal to the pKa for an ionizable group...

...then that group is likely be in equal states of protonated and deprotonated.

12

Non-polar, aliphatic R groups

These are mostly HYDROPHOBIC.

Mall store chains, GAP v. LIM?
 

Glycine (H - small), Alanine (CH3), Proline (ring!), Valanine,
Leucine, Isoleucine, Methionine (has an S)

easy 3-letter codes:
GLY, ALA, PRO, VAL, LEU, ILE, MET

13

Aromatic R groups

These are very HYDROPHOBIC

The AROMA of feet and tires ruins trips.

Phenylalanine, Tyrisine, Tryptophan

14

Tyrosine

TYR

In the aromatic R group / hydrophobic

Has a polar group (-OH)

Can be phosphoroylated

15

Positively charged R groups

These are HYDROPHILLIC.

Last Action Hero got POSITIVE reviews.

Lysine, Arginine, Histidine

LYS, ARG, HIS


Note: They have extra amines that add an extra +. At neutral pH, they have basic pKas (10, 12, 7)

16

Lysine

LYS

Part of the Positive charged R group. 

Hydrophillic

Can be deprotonated in the right environment

17

Histidine

HIS

Part of the + charged R group / Hydrophillic

Is a common proton donor / acceptor in enzymes

Has a ring

Can be phosphorylated (when deprotonated)

Common in bacteria

18

Negatively charged R groups

These are HYDROPHILLIC.

Glue makes aspirin BAD to eat.

Glutamate, Aspartate
GLU, ASP (each ends in -ate)


Note: At neutral pH, they have pKas that are acidic (4-5). Each has an extra COO-. Often act as proton donor and acceptors in enzymes.

19

Polar, uncharged R groups

These are HYDROPHILLIC

Three sisters: Sarah, Ashley, Glenda, love swimming.

Threonine (-OH), Cysteine (has a S), Serine (-OH), Asparagine (C=O), Glutamine (C=O)
THR, CYS, SER, ASN, GLN

20

Serine

SER

Part of the polar, uncharged R group / hydrophillic

Can be phosphorylated (-OH)

21

Threonine

THR

Part of the polar, uncharged R group / Hydrophillic

Can be phosphorylated (-OH)

22

Cysteine

CYS

Part of the polar, uncharged R group / hydrophillic

Includes an 'S' atom. Two CYS residues can create a disulfide bond (S-S) under oxidizing conditions, usually outside the cell. Disulfide bonds are crosslinks in a folded protein and add stability.

At neutral pH, its pKa is ~9. Can be deprotonated in the right environment.

(Cytoplasm is a reducing environment.)

23

Amino Acids that can be Phosphorylated

TYR

SER, THR

24

Hydrophillic R groups

Positively charged R groups

Negatively charged R groups

Polar, uncharged R groups

25

Hydrophobic R groups

Non-polar, aliphatic R groups

Aromatic R groups

26

Peptide Bond

A covalent bond made between the acid group of 1 AA and the amine group of another AA. There is a loss of H2O. 

27

Why are peptide bonds less soluble than amino acids in water?

Each amino acid has a N and C terminus, that's two charges for water to interact with. A peptide is the comibination of multiple AA and it also only has two end terminals.

 

5 AA = 10 terminals for water to act on.

1 peptide with 5 AA = 2 terminals for water to act on.

28

Proteins

A folded polypeptide (>30 AAs) with a specific 3-D structure. Its structure determines its function.

29

Name the 4 Levels of Protein Structure

1. Primary

2. Secondary

3. Tertiary

4. Quaternary 

30

What is Primary Structure?

The sequence of amino acids from N-to-C. 

Ex: GLY-ALA-TYR-TRP-GLY-ARG
Covalent bonds hold AA together.

Determine the sequence by Edman method (expensive, hard) or by sequencing the DNA that codes for a protein.

Limitations: Primary structure does not tell you what a protein does or how it works. 

31

What is Secondary Structure?

The arrangement of the polymer backbone or "main chain." It can describe an entire polypeptide or a segment of a poly peptide. 

 

Relies on phi, psi, omega values to determine path/shape. Wants as many H-bonds to form as possible in interior of protein.

32

What is Tertiary Structure?

The arrangement of all atoms (main chain and side chains) in a single protein polymer. 

33

What is Quaternary Structure?

The arrangement of multiple polymers into a "complex." 

34

How to source protein

Source protein can be gotten from animal tissue (cow brain, rat liver) or by overexpression in a host organism (e coli, yeast). The ladder is an example of genetic engineering.

35

What is Chromatography?

A way to purify the protein for experiments.

36

Types of Chromatography

  • Ion-Exchange (separate by charge) or other properties like size, hydrophobicity. 
     
  • Natural Affinity (using an antibody, substrate)
     
  • Affinity Tagging (add extra HIS residues to terminal); type of genetic engineering

37

Homologs

Are proteins similar in primary sequence.

38

Consensus Sequences

Short stretches of "highly conserved" sequences of proteins. 

* means identical
: means similar
. means similar but not as much

39

Methods to "see" proteins

1. XR Crystallography

2. NMR

3. Cryo-electron Microscopy (Cryo-EM)

40

XR Crystallography

Requires a lot of pure protein to work.

Grow protein crystals then measure diffraction patterns. Note: Crystals are hard to grow.

41

NMR

Produce the protein by feeding the protein source (an animal) a heavy-isotope labeled amino acid (N15 or C13). Measure the chemical shift. 

Limited: small-medium size proteins

42

Cryo-EM

Requires pure protein, but less than XR crystallography or NMR. 

Limitations: Works best for very large proteins. Equipment is expensive. 

43

Bonds and Interactions

Covalent Bonds - 200-500 kJ/mol

Ionic Bonds (or better: Electrostatic Interactions)

Hydrogen Bonds (H-bond) - 10-40 kJ/mol 

vanderWaals - 5-10 kJ/mol

Hydrophobic interaction - 5 kJ/mol

44

Hydrophobic Interaction

This is the most important interaction for proteins -- it is critical for protein folding -- even though it's relatively weak (5kJ/mol)

45

Constrains of a polypeptide backbone?

1. Planar peptide bond (6 atoms form a plane)

2. Steric hinderance

*A fully extended polypeptide is PHI = PSI = 180º
Proline may be cis.

*Omega is the Carbonyl-Amide bond. It's a partial double bond, hence no free rotation.

46

Ramachandran Plot

Shows allowed phi / psi combinations.

47

Regular Secondary Structures

1. alpha helices

2. beta sheets

3. poly-pro or left handed helices (collagen)

(These elements have repeating phi/psi values.)

* Turns - is a common structure but not regular

* Coil - structured but no pattern

* Loops - "unstructured" because of multiple conformations

48