Chapter 3 & 4 Flashcards Preview

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Flashcards in Chapter 3 & 4 Deck (37):
1

Nonpolar amino acids

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

2

Aromatic amino acids

Phenylalanine, Tyrosine, Tryptophan

3

Polar amino acids

Serine, Threonine, Cysteine, Asparagine, Glutamine

4

Basic amino acids

Lysine, Arginine, Histidine

5

Acidic amino acids

Aspartate, Glutamate

6

What is the equation for isoelectric point?

pI = (pka1 + pka2)/2

7

What does the isoelectric point tell us?

What pH the molecule has no charge

8

How to find the pI of acidic amino acids

Take the pI of the two smaller pKas

9

How to find the pI of basic amino acids

Take the pI of the two larger pKas

10

Label the phi, psi, and omega bonds of
R O
I II
N --- C ---- C -_- N
I
H

Phi: between first carbon and nitrogen
Psi: between two carbons
Omega: between second carbon and nitrogen (with *O*)

11

Properties of alpha helix

-Lots of alanine (not glycine because it's too small and flexible)
-Right handed helix most common (can be left handed)
-Like a battery with the positive charge on top, and negative charge on bottom
-No proline
-Stabilized by hydrogen bonds

12

Properties of beta sheets

-Parallel or anti-parallel
-Rigid
-Beta turns
-Zig Zag like pattern
-Ring structure
-Stabilized by H bonds

13

What are beta turns?

Connect antiparallel and parallel beta sheets when the carbonyl of the first amino acid forms an H-bond with the amino of the fourth amino acid

14

How many types of beta turns exist?

2

15

What is a type I beta turn?

The most common beta turn where proline is in the cis formation, in the second position

16

What is a type II beta turn

The lesser common beta turn where glycine is in the third position

17

What characteristics of glycine makes it a destabilizer or stabilizer of protein structure?

Small R group present that allows it to fold in on itself. Too many glycine present leads to increased flexibility of beta sheet and increased instability

18

What characteristics of proline make it a stabilizer of protein structure?

R group is in cyclic formation which causes a rigid, stable structure

19

Primary structure example and which bonds?

Single amino acids connected by covalent bonds

20

Secondary structure example and which bonds?

Alpha helices and beta sheets with hydrogen bonding

21

Tertiary structure example and which bonds?

Multiple alpha helices and beta sheets connected together with disulfide bonds, hydrogen bonds, and motifs.

22

Quaternary structure example and which bonds?

Complexes of several proteins with hydrophobic and van der waals interactions

23

Alpha-keratin characteristics

-Two parallel right handed helix
*forms left handed super twist* that are connected with disulfide bonds and called pseudorepeats
-Pseudorepeats come together to make protofilaments, protofilaments come together to make protofibrils where the strands are kept together by H bonds
-Lots of alanine and glycine
-Tough
-Stabilized by cysteine disulfide bonds (15%)
-Present in hair and nails

24

Beta-keratin characteristics

-Parallel beta sheets
-Lots of alanine and glycine repeats
-Soft, flexible
-Present in silk fibroin (spider's web)

25

Collagen characteristics

-Left handed alpha helix with three amino acids per turn
*forms 3 alpha-chains
-The three alpha chains super twist into a right handed helix
-Tri repeat of Glycine - Proline - 4 hydroxyproline
-Covalently linked
-Insoluble
-Present in tendons and carilage

26

Fibrous protein characteristics

-Less common
-Strands/sheets
-One type of secondary structure
-Simple tertiary structure
-Strong, flexible support
-Insoluble and phobic amino acid

27

Globular protein characteristics

-More common
-Folded, spherical shape
-Many alpha helices and beta sheets
-Large

28

Describe a heat shock protein

Binds to regions of unfolded polypeptides that are rich in hydrophobic residues, thus protecting proteins subject to denaturation. Also protect other proteins from being folded if they need to be straight

29

Describe a chaperone protein

Assist unfolded, partially folded, or improperly folded proteins in finding their shape
-Require ATP

30

Prosthetic group

Organometallic structure that is tightly bound to proteins

31

Cofactor

Non-protein chemical compound that is required for protein's biological activity

32

Coenzyme

Organic or organometallic structure that is loosely bound to proteins

33

Motifs

A recognizable folding pattern involving two or more elements of secondary structure and the connections between them

34

Parallel Beta Sheets

N --> C
N --> C
Consistent ring size (12)
Bent H bonds

35

Antiparallel beta sheets

N --> C
C --> N
Alternate ring size (10/14)
Linear H bonds (stronger)

36

Peptide bond common conformation

Cis

37

Renaturation

Reformation of disulfide bonds that were broken during denaturation