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Biochem I *ON OWN*
Unit 1
Lecture 3
Amino Acids & PRO Structure

Biochem I *ON OWN*
Unit 1
Lecture 3
Amino Acids & PRO Structure
Amino Acids:
What are the Nonpolar, Aliphatic amino acids?

GAP's
Very
Isolated
Leucy
Glycine
Alanine
Proline

Valine
Isoleucine
Leucine
Amino Acids:

What are the Aromatic Amino Acids?

Tyrone's
Phenomenol
Tryp
Tyrosine
Phenylalanine
Tryptophan
Amino Acids:

What are the polar, uncharged Amino Acids?

See
Three
Glued
Asparagas
Serine
Threonine
Glutamine
Asparagine
Amino Acids:

What are the Sulfur-Containing Amino Acids?

Me
Cyst
Methionine
Cysteine
Amino Acids:

What are the negatively charged, acidic Amino Aicds?

Aspen's
Glutton
Aspartate
Glutamate
Amino Acids:

What are the positive, basic Amino Acids?

His
Lyne's
"Arg"
Histidine
Lysine
Arginine
Amino Acids: Abbreviations

What are the abbreviations for Glycine?
gly
G
Amino Acids: Abbreviations

What are the abbreviations for Alanine?
ala
A
Amino Acids: Abbreviations

What are the abbreviations for Proline?
pro
P
Amino Acids: Abbreviations

What are the abbreviations for Valine?
val
V
Amino Acids: Abbreviations

What are the abbreviations for Leucine?
leu
L
Amino Acids: Abbreviations

What are the abbreviations for Isoleucine?
ile
I
Amino Acids: Abbreviations

What are the abbreviations for Phenylalanine?
phe
F
Amino Acids: Abbreviations

What are the abbreviations for Tyrosine?
tyr
Y
Amino Acids: Abbreviations

What are the abbreviations for Tryptophan?
trp
W
Amino Acids: Abbreviations

What are the abbreviations for Asparagine?
asn
N
Amino Acids: Abbreviations

What are the abbreviations for Glutamine?
gln
Q
Amino Acids: Abbreviations

What are the abbreviations for Serine?
ser
S
Amino Acids: Abbreviations

What are the abbreviations for Threonine?
thr
T
Amino Acids: Abbreviations

What are the abbreviations for Methionine?
met
M
Amino Acids: Abbreviations

What are the abbreviations for Cysteine?
cys
C
Amino Acids: Abbreviations

What are the abbreviations for Aspartate?
asp
D
Amino Acids: Abbreviations

What are the abbreviations for Glutamate?
glu
E
Amino Acids: Abbreviations

What are the abbreviations for Arginine?
arg
R
Amino Acids: Abbreviations

What are the abbreviations for Lysine?
lys
K
Amino Acids: Abbreviations

What are the abbreviations for Histidine?
his
H
All amino acids except _____ have the same structure?
Proline (pro, P)
Except for proline, components of amino acids:
1) A _____ group
2) A _____ carbon
3) An _____ group
4) A ____ chain
5) A ____ atom
1) Carboxyl (COOH or COO-)
2) alpha
3) Amino (N+H3)
4) R (side)
5) Hydrogen
Given their very similar structure, what differentiates the amino acids from one another?
The side chain (R group)
Given their very similar structure, what differentiates the amino acids from one another?
The side chain (R group)
The alpha carbon is what number carbon?
Carbon #2
In nature, almost all amino acids are in what conformation?
L-conformation
How many amino acids are coded for by DNA?
20
An amino acid that has both a positive and negative charge simultaneously is called what?

What is the net charge of a zwitterion?
Zwitterion

0
Negatively charged (acidic) amino acids (aspartate & glutamate) carry what charge?
-1
Positivgely charged (basic) amino acids (arginine, lysine & histidine) carry what charge?
+1
With exception to Proline, what are the 5 components of amino acids?
1) COO-
2) alpha-carbon (carbon #2)
3) N+H3
4) R-Group
5) H
Almost all amino acids occurring in nature are in what form?
"L"-form
1) In their most common form all amino acids will have what with relation to charges?

2) Where is the positive charge?

3) Where is the negative charge?
1) Both a + and - charge

2) On the N+H3 (N+H2 for Proline)

3) On the COO-
Categories / Properties of Amino Acids:
1) Non-polar, aliphatics are ___
2) Polar, aliphatics are ____
3) Aromatics contain ____
4) Sulfur containing have ____
5) Negatively charged are ____
6) Positively charged are ____
1) Hydrophobic
2) Hydrophilic
3) Rings
4) Sulfur
5) Acidic
6) Basic
Properties of Amino Acids:
What is the pKa of Carboxyls for all Amino Acids?
pKa = 2.0
Properties of Amino Acids:
1) What is the pKa of the amino group of Proline?

2) What is the pKa of the amino group of Cysteine?

3) What is the pKa of the amino group of every other amino acid besides Proline and Cysteine?
1) 11

2) 10.3

3) 9
How many amino acids contain an R-group that can be protonated or deprotonated and can therefore effect charge?
9
Properties of Amino Acids: pKa of R-Group

1) What is the pKa of Tyrosine, Lysine & Arginine?

2) What is the pKa of Serine and Threonine?

3) What is pKa of Aspartate and Glutamate?
1) 10

2) 14

3) 4
Properties of Amino Acids: pKa of R-Group

1) What is the pKa of the R-Group of Histidine?

2) What is the pKa of the R-Group of Cysteine?
1) 6

2) 8.4
1) What is hydropathy?

2) Hydropathy = ? = ?
1) How much something hates water

2) Hydropathy = Hydrophobic = Lipophilic
1) For carboxyl groups of ALL amino acids, if the pH is the sol'n is less than the pKa of the carboxyl group, the carboxyl is what?

2) For carboxyl groups of ALL amino acids, if the pH is = to the pKa of the carboxyl group, 1/2 the carboxyls are what?

3) For carboxyl groups of ALL amino acids, if the pH is the sol'n is greater than the pKa of the carboxyl group, the carboxyl is what?
1) Protonated

2) Deprotonated

3) Deprotonated
Realize that the pH of the solution that an amino acid is in effects whether the following are protonated or depronated?

1) Carboxyl Groups
2) 9 R Groups
3) Amino Groups
Realize that the pH of the solution that an amino acid is in effects whether the following are protonated or depronated?

1) Carboxyl Groups
2) 9 R Groups
3) Amino Groups
1) If the pH of a sol'n is lower than the pK of an AA's carboxyl group, R-group or amino group, then they will be what?

2) If the pH of a sol'n is equal to the pK of an AA's carboxyl group, R-group or amino group, then they will be what?

3) If the pH of a sol'n is higher than the pK of an AA's carboxyl group, R-group or amino group, then they will be what?
1) Protonated

2) In a state where 1/2 is protonated and 1/2 is deprotonated

3) Deprotonated
What is the isoelectric point (pI)?
The pH @ which the overall charge on an Amino Acid / PRO = 0.
Disulfide bonds b/t 2 cysteines makes what?

Cysteines with disulfide bonds can also form mixed disulfides such as what?
Cystine

Glutathione
Modified Amino Acids:
1) When serine is bound to a specific tRNA it can form what?
1) Selenocysteine
Modified Amino Acids: Carbohydrate Addition: O-glycosylation

1) O-glycosylation occurs with what amino acids?

2) O-glycosylation is the addition of a carbohydrate to the ____ of the R-groups OH
1) ser, thr, tyr

2) Oxygen
Modified Amino Acids: N-Glycosylation

1) N-glycosylation takes place with what amino acid?

2) N-glycosylation is the additino of a carbohydrate to the _____ of the R-group's NH2
1) asn

2) Nitrogen
What are the 3 types of Amino Acid modificatino that are involved in regulation?
Phosphorylation

Acetylation

ADP-Ribosylation
Phosphorylation:

1) Takes place with what 3 amino acids?

2) Phosphorylation is the addition of a _______ to the _____ of the R-Group's OH
1) ser, thr, tyr

2) phosphate, oxygen
Acetylation:
1) Acetylation takes place with what 2 things?

2) Acetylation is the addition of an ______ to the ____ of the R-group's NH2
1) lys
A terminal NH2

2) Acetyl Group
Nitrogen
ADP-Ribosylation:

1) ADP-Ribosylation occurs with what 3 amino acids?

2) Ribosylation is the addition of an ______ to the _____ of arg & gln's R-group's NH2
OR
the S of cys's R-group's SH
1) arg, gln, s

2) ADP-Ribose, Nitrogen
Other ways to modify amino acids:

1) Hydroxylation is the ____ or pro & lys

2) gamma-Carboxy-glutamation is the Carboxylation of ____.
1) oxidation

2) glu
Saccharides Bound to PRO can form what 2 substances?
GlycoPRO
Proteoglycans
1) Sacchardies can be bound to what 3 Amino Acids via "O-Linkage?"

2) Saccharides can be bound to what amino acid via an "N-Linkage"?
1) Serine, Threonine, Tyrosine

2) Asparagine
When lipids are added to amino acids they can perform what 2 functions?
1) Anchor PROS to Membranes
2) Be involved in regulation
Types of lipid addition:

1) Palmitoylation of _____

2) Prenylation of _____

3) Myristoylation of ______
1) Cysteine

2) Cysteine

3) Glycine
Reversible regulatory modifications to amino acids:

1) Phosphorylation of ___(3)___

2) Acetylation of _____

3) ADP-Ribosylation of _____
1) serine, threonine, tyrosine

2) Lysine

3) Arginine, Glutamine, Cysteine
Peptide Bonds:
1) Occur b/t the ____ of one amino acid AND the _____ of another amino acid

2) The configuration of a peptide bond makes it a _____ bond

3) The R-Groups of the 2 amino acids involved in a peptide bond are in what configuration?
1) alpha-carboxyl, alpha-amino

2) Planar

3) Trans Configuration
Structure of PRO:
1) What is the primary structure of AA?

2) Secondary Structure?

3) Tertiary Structure?

4) Quaternary Structure?
1) Order of Amino Acids

2) Formation of alpha-helices and beta-pleated sheets

3) Folding of alpha-helices and beta-pleated sheets into a 3-d structure

4) Multiple polypeptide subunits combining into 1 unit
Primary Structure: Order of Amino Acids

1) 1st Residue is called what?
2) The 1st Residue is the amino acid with a free _____ group
3) The last residue is called what?
4) The last residue is the amino acid with the free ____ group?
1) N-Terminal
2) alpha-amine
3) C-Terminal
4) Carboxyl Group
Variations in Primary Structure:
1) HbF & HbA are different what of eachother?

2) Creatine Kinase & Lactate Dehydrogenase Isoenzymes are what?
1) Isoforms / Isozymes

2) Tissue Specific
Secondary Structure: alpha-helix and beta-pleated sheets

The alpha helix has hydrogen bonds b/t the ______ of the 1st amino acid and the ______ of the 2nd amino acid which is 4 AA downstream from the 1st AA
Amide Hydrogen

Carbonyl Oxygen
Secondary Structure:

In the alpha helices of the secondary structure of PRO, the R-groups will be aligned in which direction?
The R-groups will project out
Secondary Structure:

Is proline present in an alpha-helix?
NO
Secondary Structure: beta-pleated sheets

beta-pleated sheets are formed by hydrogen bonds b/t _____ & _____
amide hydrogens
carbonyl oxygen
Secondary Structure:
In beta-pleated sheets the amino-acyl "R-Groups" are _____ to the plane of the sheet AND they _____
perpendicular
alternate sides
______ are repetitions / motifs of secondary structures that can bind and hydrolyze ATP
Nucleotide Binding Domains (NBD)
Tertiary Structure:
What are the 5 forces involved in the tertiary structure of PRO?
1) Hydrogen Bonds
2) Salt Bridges
3) Hydrophobic Interactions
4) Van der Waal's Forces
5) Disulfide Bridges
Quaternary Structure:

What are the 4 forces involved in the quaternary structure of PRO?
1) Hydrogen Bonds
2) Hydrophobic Interactions
3) Salt Bridges & Ionic Bonds
4) Rarely Disulfide Bonds
Quaternary Structure: Properties of quaternary structure

1) Quaternary Structure increases the stability of PRO via ____

2) Quaternary structure effects the _____ b/t subunits

3) Quaternary Structure effects ______
1) amino acid interaction

2) Cooperativity

3) Regulation
When you have soluble, globular PRO in water:

1) The inner core of globular PRO will consist of hydrophobic, _____ AA

2) The outer surface of globular PRO will consist of hydrophilic, _______ AA

3) The outer surface of soluble globular PRO in water can form what?
1) Non-Polar

2) Polar

3) Salt Bridges
Trans-Membrane Soluble PRO:
1) Their will be a Hydrophobic portion of the PRO adjacent to the _____ in the internal part of the membrane

2) Their will be a _____ portion of the PRO that will be outside of the membrane.
1) Lipids

2) Hydrophilic
PRO Folding:
What 2 things can promote proper PRO folding?
Certain heat shock PRO (hsp)
cis-trans isomerases / disulfide isomerases
PRO Folding:
Can some hsp also prevent improper folding?
YES!!
Chromatography separates cmpds based on their affinity for what 2 phases?
1) Stationary Phase
2) Mobile Phase
What are the 5 types of chromatography?
1) Size Exclusion (Gel Filtration) Chromatography
2) Ion Exchange Chromat
3) Hydrophobic Interaction Chromat
4) Affinity Chromatography
5) High-Pressure Liquid Chromatography (HPLC)
Size Exclusion (Gel Filt) Chromat
1) Separates cmpds based on ___

2) Medium?

3) Mechanism:
Smaller PRO enter pores in beads ---> exit column ____

Larger PRO DO NOT enter pores in beads ---> exit
1) Size

2) Porous Beads

3) Slowly
Quickly
Ion Exchange Chromatography:

1) Separates cmpds based on ____

2) Medium?

3) Mechanism:
Cation Exchange: what is it?
Anion Exchange: what is it?
1) Charge

2) Resin beads which bear a charge

3) cation exchange: Beads have a - charge & cations stick to the column

anion exchange: beads have a + charge & anions stick to column
When making use of Ion Exchange Chromatography, how can you elute stuck cations or anions?
By adding more cations or anions respectively
Hydrophobic Interaction Chromatography:

1) Separates cmpds. based on what?

2) Medium?

3) Mechanism: What will stick to the column?

4) How would you elute (displace) the stuck hydrophobic groups?
1) Hydrophobic groups

2) Hydrophobic Groups

3) PRO w/ hydrophobic surfaces

4) Decrease the polarity of the eluent
Affinity Chromatography:
1) Separation of compds based on what?

2) Medium?

3) Mechanism: What will stick to the column?

4) How do you displace the stuck PRO?
1) PRO-ligand binding

2) PRO specific ligand

3) The PRO which binds to the ligand

4) Add excess ligand
High Pressure Liquid Chromatography (HPLC):

1) Separation of cmpds based on what?

2) Their mechanism and medium are the same as what?

3) What's the difference b/t them?
1) Hydrophobic groups

2) Hydrophobic Interaction Chromatography

3) Separation is fast and @ a higher resolution
Electrophoresis:
1) Separates cmpds based on what?

2) What are the 3 types of electrophoresis?
1) Charge in an electric field

2) SDS-Polyacrylamide Gel Electrophoresis (PAGE)

Iso-Electric Focusing (IEF)

2-Dimensional Electrophoresis
SDS-Polyacrylamide Gel Electrophoresis (PAGE)

1) Separation is based on what?

2) Medium?

3) Mechanism:
A) SDS does what 2 things?
B) Which PRO will migrate through the PA gel faster?
1) Size

2) SDS PRO
A) Produces PRO of = charge:mass ratio;
Breaks down Multimeric PRO to Monomeric PRO
B) Smaller PRO
Iso-Electric Focusing (IEF)
1) Separation is based on what?

2) Medium?

3) Mechanism: PRO migrates to part of the gel where the pH = ?
1) PRO pI

2) PA gel w/ a pH gradient (Range)

3) pI
2-Dimensional Electrophoresis uses what 2 methods?
Iso-Electric Focusing (IEF)

SDS-PAGE
1) Western Blot is used for visualizing what?

2) Mechanism:
A) PRO separated by ____
B) ___ specific for a particular PRO is added
C) 2nd Ab w/ a _____ & that's specific for 1st Ab is added and that's specific for 1st Ab
1) PRO

2 A) electrophoresis (PAGE)
B) Ab
C) Reporter Molecule
Edman-Sequencing

1) Uses what substance?

2) PITC attacks what?

3) The product of this attack is removed, analyzed and the ___ is determined.

4) This entire process removes the entire what?
1) Phenylisothiocyante

2) The N-terminal of a polypeptide

3) The specific amino acid

4) Amino Acid
Mass Spectrometry (MS):

1) Separates molecules based on what?

2) Is used to do what 2 things with PRO?
1) Mass

2) ID PRO
Detect Covalent Modifications of PRO
How can Mass Spectrometry ID PRO:

1) PRO digested by ____?

2) From this, masses of individual peptides are ID'ed which allows you to do what?
1) Trypsin

2) ID the PRO