Basic Concepts, Amino Acids, Proteins Flashcards
(88 cards)
1
Q
Milli-
A
10__
2
Q
Micro-
A
10__
3
Q
Nano-
A
10__
4
Q
M
A
mol/L
5
Q
%
A
weight/volume (usually g/dL)
6
Q
Equivalent
A
available charges of the particular ion
7
Q
Units of activity
A
Defined in terms of some effect
8
Q
Osmolarity
A
moles of solute particles in a solution
9
Q
Henderson-Hasselbach
A
pH= pKa + log ([A_]/[HA])
10
Q
α-amino acids
A
- Carboxylic acid with amine group on the α-carbon
- R-groups change (most are L-amino acids)
11
Q
Non Polar Aliphatic Amino Acids
A
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine
(GAP, LIV)
12
Q
Glycine
A
Gly
Non Polar aliphatic
13
Q
Alanine
A
Ala
Non polar Aliphatic
14
Q
Proline
A
Pro
Non Polar Aliphatic
15
Q
Valine
A
Val
Non Polar Aliphatic
Branched Chain
16
Q
Leucine
A
Leu
Non polar Aliphatic
Branched Chain
17
Q
Isoleucine
A
Ile
Non polar Aliphatic
Branched chain
most hydrophobic (charges are very balanced)
18
Q
Aromatic Amino Acids
A
Phenylalanine, Tyrosine, Tryptophan
19
Q
Phenylalanine
A
Phe
Aromatic
20
Q
Tyrosine
A
Tyr
Aromatic
21
Q
Tryptophan
A
Trp
Aromatic
22
Q
Polar, Uncharged Amino Acids
A
Asparagine, Glutamine, Serine, Threonine
Typically found on the surface
23
Q
Asparagine
A
Asn
Polar/Uncharged
24
Q
Glutamine
A
Gln
Polar, uncharged
25
Serine
Ser
Polar, uncharged
26
Threonine
Thr
Polar, uncharged
27
Sulfur-containing Amino Acids
Methionine, Cysteine
28
Methionine
Met
Sulfur-containing
29
Cysteine
Cys
Sulfur-containing, so can form disulfide bonds
Cystine = 2 cysteines bound by disulfide bond
30
Negatively charged Amino Acids
Aspartate, Glutamate
Acidic Amino Acids
31
Positively Charged Amino Acids
Arginine, lysine, histidine
Basic amino acid
32
Aspartate
Asp
Negatively charged (acidic)
33
Glutamate
Glu
Negatively charged (acidic)
34
Arginine
Arg
Positively charged (basic)
Most hydrophilic (very polar)
35
Lysine
Lys
Positive charge (basic)
36
Histidine
His
Positively charged (basic)
37
Hydropathy
How hydrophilic/phobic an anima acid is
38
pI
The pH at which the net charge on an amino acid is 0
39
Selenocysteine
* Modification fo a serine bound to a unique tRNA to selenocycteine
* Found in a few enzymes, where it is essential for activity
40
Types of amino acid modifications
* Carbohydrate addition
* Lipid addition (can anchor to protein membrane or be involved in regulation)
* Regulation
41
O-glycosylation
Occurs on the OH of ser, thr, tyr
Carbohydrate addition
42
N-glycosylation
Occurs on the NH2 of asn
Carbohydrate addition
43
Palmitoylation
Occurs on the internal SH of cys
Lipid addition
44
Myristolation
Occurs on the NH of the N-terminal of gly
Lipid addition
45
Prenylation
Occurs on the Sh of cys
Lipid addition
46
Phosphorylation
Occurs on the OH of ser, thr, tyr
is reversible
47
Acetylation
Occurs on the NH2 of lys (N-terminus)
Reversible
48
ADP-ribosylation
Occurs on the N of arg, gln, cys
Reversible
49
Carboxylation
Turns gutamyl residues into Ɣ-carboxylglutamyl residues
50
Oxidation
Pro/lys into hydroxylpro/hydroxylys
51
Peptide bond
* Bond b/t the α-carboxyl grp of 1 AA and the α-amino group of another AA
* Is planar
* Adjacent R-groups are almost always trans
52
Proteins
linear polymers of α-amino acids bound together by peptide bonds
53
Primary structure of proteins
* Amino acyl sequence of proteins
* N-terminal = amino
* C-terminal = carboxyl
54
Polymorphism
* genetic variation with a species
* Can produce a variation in phenotype which could be deleterious
55
Developmental variaion
* Different protein isoforms/isozymes may be expressed at different developmental stages of an organism
* Ex: HbF, HbA, and other hemoglobins
56
Tissue-specific Isoforms
* Different protein isoforms/isozymes are expressed simulteneously in one organism, but are restricted to different tissues
* Ex: creatine kinase isozymes and lactate dehydrogenase isozymes
57
Secondary Structures
Recurring, localized structures found within regions of a poly peptide chain
58
Alpha – Helix
* Helical structure stabilized by hydrogen bonds (b/t amino and carboxyl O atom of 2nd AA 4 residues down the chain)
* AA R-group projects outward from the axis of the helix
* Proline cannot be a part of a α-helix
59
Beta-Pleated Sheet
* somewhat planar surface stabilized by H-bonds b/t amide hydrograns and carboxyl Os
* AA R-groups are perpendicular to the plane of the sheet
* surfaces formed by β-sheets are often twisted
60
Parallel β-pleated sheets
2 polypeptide chains are oriented in the same direction relative to the N/C termini
61
Anti-Parallel β-pleated Sheets
2 polypeptide cains are oriented in opposite directions relative to their N/C termini
62
Domain
Part of a secondary structure that can exist on its own
63
Motif
* Type of supersecondary structure that is found in an array of different proteins (can make up a domain)
* Ex: helix-turn-helix motifs are found in many DNA-binding proteins
64
Teriary Structures
The folding pattern of the secondary structural elements into a 3D conformation
65
Forces involved in 3º structures
H-bonds, Salt bridges, Hydrophobic interactions, Van der Wall forces, Disulfide bridges
66
Globular protein properties
* Core is usually hydrophobic AA
* Surface is usually charged/polar AA (so hydrophilic) that interacts w/ a polar/aqueous environment and forms salt bridges to stabilize the structure
67
Transmembrane proteins typically have what types of 2º and 3º structures?
* 2º: usually α-helices that have hydrophobic residues that are embedded in the lipid/hydrophobic layer of the membrane
* 3º: hydrophilic residues interact extra/intracellularly
68
Quaternary structure
The individual subunits form a functional protein
69
What determines the protein type?
The number of subunits determines what about the protein?
70
Forces in 4º structure in globular proteins
H-bonding, Hydrophobic interactions, salt bridges/ionic bonds, rarely disulfide bonds (**no** covalent bonds)
71
Forces in 4º structure in fiborus/structural proteins
Extensive **covalent** bonds
72
What are the functional aspects of 4º structure
1. Increased stability (bc increased # of interactions b/t AA)
2. Cooperativity b/t subunits (Ex: hemoglobin-O2 binding)
3. Different subunits may have different activities
73
Protein folding
* 1º structure of protein determines folding
* Some fold spontaneously while others require specific cellular processes to promote proper folding
74
Heat Shock Proteins
* Some *prevent* improper folding
* Others requires ATP energy to promote folding
75
Cis-trans isomerases and disulfide isomerases promote what?
What non HSP function to promote proper protein folding?
76
Size Exclusion Chromatography
* Uses porous beads
* Larger proteins elude 1st bc smaller proteins get caught in the pores of the beads
77
Ion Exchange Chromatography (Cation)
* *bound* chemicals have a *negative* charge
* **Cations** adhere to the negatively charged column
* charges on proteins are pH dependent
78
Ion Exchange Chromatography (Anion)
* *bound* chemicals have *positive* charge
* **Anions** adhere to the positively charged column
* Charges on proteins are pH dependent
79
Hydrophobic Interaction Chromatography
* Medium contains *hydrophobic* groups
* Proteins w/ hydrophobic groups adhere to the column
80
Affinity Chromatography
* Medium has a bound, *protein specific* *ligand*
* Proteins that bind to the ligand adhere to the column
81
High-Pressure Liquid Chromatography (HPLC)
* Eluent pumped thru column under high pressure
* Typically looking for hydrophobic interaction chromatography (aka reversed phase)
* Separation is faster and at higher resolution
82
Electrophoresis
Separation based on mirgration of charged molecules applied in an electrical field
83
Native electrophoresis
* Separates by differences in charges due to the 1º structure
* Ex: hemoglobin isoforms, some isozymes (LDH, CK)
84
SDS-PAGE
* Protein molecules interact with the detergent (SDS) to produce proteins of about = charge-to-mass ratios
* SDS disrupts 4º structures (proteins become monomers
* migration thru the gel is based on size: smaller proteins go faster
85
Iso-Electric Focusing (IEF)
* Buffers generate a pH gradients within a PA gel
* Proteins migrate to pI=pH of gel
86
2D Electrophoresis
Uses both IEF and SDS-PAGE
87
Western blot
* Proteins are separated via electrophoresis and transferred to synthetic membrane (incubated w/ antibodies for specific protein
* 2nd antibody conjugated w/ reporter molecule to help visualize the specific protein
88
Mass Spect
* Separates molecules based on their mass
* Can identify proteins thru determination of masses of peptides produced thru tryptic digestion of proteins
* detects covalent modifications of a protein
