Protein Structure

Question 1

NONPOLAR AMINO ACIDS

Answer 1

Girls Are Pretty Very Large In Masr, with an AROMA that Trips The People.

Glycine, Alanine, Valine, proline, Leucine, Isoleucine, Methionine (aliphathic)

Tryptophan, tyrosine, phenylalanine (aromatic)

Question 2

POLAR AMINO ACIDS

Answer 2

Ladies Are Hairy (positively charged)

Seriously, Three Scissors, And Glue (polar uncharged) Are Gone (negatively charged)

Lysine, Arginine, histidine, serine, threonine, cyseine, , , asparagine, glutamine, aspartate, glutamate.

Question 3

GLYCINE

Answer 3

Gly (G)

Question 4

Alanine

Answer 4

ALA / A

Question 5

PROLINE

Answer 5

PRO / P

Usually, the alpha-carbon to primary amino group bound has some double bond character. but the secondary amino group does not allow any internal rotatoin of the N or the carboxyl group.

It is stiff and causes a bend/change of direction of the peptide chain.

Question 6

VALINE

Answer 6

VAL / V

Question 7

LEUCINE

Answer 7

Leu / L

Question 8

ISOLEUCINE

Answer 8

ILE / I

Question 9

Methionine

Answer 9

MET / M

Has thio-ether group

Question 10

Aromatic Amino Acids

Answer 10

Tryptophan (TRP / W)

Tyrosine (TYR / Y) 10

Phenylalanine ( PHE/ F)

Aromatic AA residues allow us to determine concentrations because they absorb UV and flouresce.

Question 11

Basic Amino Aicds

Answer 11

Lysine (LYS/ K) 10

Arginine (ARG / R) 12

Histidine (HIS/ H): it remain dissociated 6.5

Lysine and Arginine are present in histones.

Question 12

ACIDIC AMINO ACIDS

Answer 12

Aspartic Acid (ASP/ D) 4.4

Glutamic Acid (GLU / E) 4.4

Question 13

POLAR (uncharged) AMINO ACIDS

Answer 13

Serine (SER / S)

Threonine (THR / T)

Cysteine (CYS / C)

Asparagine (ASN / N)

Gluatmine (GLU / Q)

Question 14

Cysteine Oxidation

Answer 14

CYS / C

It can oxidize to form disulfide bonds. This can occur between chains, known as interchain disulfide bonds.

Example: reducing disulfide bonds bask to SH allows hair to be flexible, which can allow manipulation or engineering, and then later oxidized to keep it firm.

Question 15

Modified Amino Aicds

Answer 15

These are post-translational modifications.

Question 16

Peptide Bonds

Answer 16

Dehydration reaction, although it is thermodynamically unstable.

The peptide bond itself is between the carboxyl carbon and the nitrogen, which has partial double-bond character, thus there is limited to no rotation. therefore, rotaiton occurs around alpha-carbon.

The oxygen therefore has a partial negative charge, while the N has a partial positive charge.

30-40% of Amino acids are non-polar.

Question 17

Conjugated Proteins

Answer 17

Lipoproteins,

Glycoprotiens

Phosphoproteins

Hemoproteins

Flavoproteins

Metalloproteins

**These are added after translation. **

Question 18

Alpha Helix

Answer 18

Due to rigidity of peptide bond, the peptide chain wraps in a helix and hydrogen bonds to itself. The hydrophilic residues are on the outside. The hydrogen bonds allow it to be lined up.

Can be stretched and absorbs water (wool)

Question 19

Beta Sheets

Answer 19

The peptide sheets are in extended lines and held in rows by hydrogen bonds. between carboxylic oxygen and side chains

Side chains are sticking up and down, which determine chemical charecteristics.

Cannot strecth or absorb water (silk)

Question 20

Turns and Flexibility

Answer 20

Turns: Proline

Flexibilities: Glycine

Question 21

Primary Structure

Answer 21

Sequence of amino acids and location of disulfide bridges (Cysteine).

Determined by covalent bonds.

Question 22

Secondary Structure

Answer 22

Relationship of amino acids that are close to each other to form motifs

(alpha-helices, B-sheets, and collagen helix)

Question 23

Tertiary Structure

Answer 23

3-D conformation of secondary structures. How secondary structurse are arranged based on side chain chemistry to make subunits.

Question 24

Quaternary Structure

Answer 24

Number of subunits and their packaging in relation to each other (packaging of domains).

Different subunits are usually folded independently.

Question 25

Answer 25

Primary: amino acid chain and disulfide bonds

Secondary: B-sheets

Tertiary: adjcaent B-sheet subunits

quaternary: two idential subunits that combine

Question 26

Cytochrome C

Answer 26

Does not have an identifiable secondary structure motif.

Since it is a monomer, there is no quaternary structure.

Question 27

Hemoglobin

Answer 27

tetramer of four myoglobin subunits

primary structure: AA peptide chain

secondary: alpha helices
tertiary: myoglobin subunit
quaternary: tetramer of 4 myoglobin subunits.

Question 28

Domains

Answer 28

Some single chains can form multiple globular regions to form domains, like in Troponin C.

Substrates usually bind in between domains.

Question 29

Different Structural patterns

Answer 29

Question 30

What is the linkage between beta barrell and green mice?

Answer 30

The B-barrel is GFP, which has a chromophore in the middle, which can sponteaneously flouresce.

Question 31

What Factors determine protein folding?

Answer 31

The amino acid sequence determines the folding.

Proteins can spontaneously fold.

B-mercaptoethanol, urea, and guanidine was used to denature protiens and reduce disulfide bonds. When these substances were taken out, the proteins spontaneously re-folded back to its original state.

Some proteins that have been post-translationaliy modified after folding may not be able to refold.

Question 32

Immunoglobulins

Answer 32

primary structure: sequence of AA and disulfide bridges

secondary structure: Beta sheets form constand and variable regions or domains.

Tertiary structures: beta sheets arranged in 2 heavy chains and 2 light chain subunits

Quarternary: subunits form a tetramer.

They do not have a unique AA sequence, in the variable region of each light chan domain of each subunit in its N-terminus.

changes in AA allow for different antigen specificity.