Lecture 1 Flashcards
(96 cards)
1
Q
What are proteins composed of?
A
Amino acids
2
Q
What are the 20 AAs referred to as?
A
Common or Standard AAs
3
Q
What is physiological pH?
A
7.4
4
Q
Which AA has a secondary amino group and what is another name for it being a secondary amine?
A
Proline
Imino
5
Q
What is a significant AA present in collagen?
A
Proline
6
Q
Amino acids are bound via what type of bond?
And through which type of rxn?
A
Peptide linkage/
Amide bond
Condensation/dehydration rxn
7
Q
AAs can act as an acid or a base, commonly known as…
A
Amphoteric
8
Q
Neutral molecules which contain both positive and negative charges are called
A
Zwitterions
9
Q
Where are nonpolar side chains typically found?
A
Interior of proteins in aqueous solutions or on outer surface in hydrophobic environments (membrane in lipid bilayer)
10
Q
Does proline enhance or interrupt the a-helices found in globular proteins?
A
Interrupt
11
Q
Where and what is being replaced to cause sickle cell anemia?
A
At the 6th position of the b-subunit of hemoglobin, glutamate is being replaced by valine
12
Q
Typical life span of healthy red blood cell?
A
90-120 days
13
Q
Which AAs contain Sulfur?
A
Cysteine and Methionine
14
Q
Which group often serves as an attachment site for phosphate groups?
A
Hydroxyl groups
-OH
15
Q
Which group(s) can serve as an attachment site for oligosaccharide chains in glycoproteins?
A
Amide and hydroxyl groups
16
Q
Which group(s) are important components of the active site of enzymes?
A
Sulfhydryl groups
-SH
17
Q
What bond is formed when a sugar binds to Asparagine in a condensation rxn?
A
N-Glycosidic bond
18
Q
What bond is formed when a sugar binds to Serine in a condensation rxn?
A
O-Glycosidic bond
19
Q
Nonessential AAs
A
Alanine Arginine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine Tyrosine
20
Q
All essential AAs
A
Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine
21
Q
Which chiral form of AAs are found in the proteins, D or L?
A
L
22
Q
Asymmetric mirror images are called
A
Enantiomers
Optical isomers
23
Q
Difference between stereoisomer and enantiomer
A
Stereoisomer- differ only in spatial arrangement of their atoms
Enantiomer- non-superimposable mirror images
24
Q
What does a standard buffer contain?
A
A weak acid and its conjugate base (weak base)
25
Relationship between Ka, pKa and acid strength
Larger Ka -> smaller pKa -> stronger acid
Smaller Ka -> larger pKa -> weaker acid
26
Ka equation
Ka = [H+][A-] / [HA]
27
pKa equation
pKa = -log Ka
28
Henderson-Hasselbalch equation
pH = pKa + log [A-]/[HA]
29
How many pH units should a buffer be within of the acid's pKa value?
+/- 1 pH unit
30
What form is predominantly present in a buffer solution when the pH > pKa?
Deprotonated
31
How many pKa values do AAs have?
At least 2
32
The pH at which a molecule possesses no net charge...
Isoelectric point
33
How to solve for isoelectric point?
Take average of the 2 pKa values.
If basic, take average of upper 2
If acidic, take average of lower 2
34
Type of bonding in primary structure
Covalent peptide bonds
35
Type of interaction in secondary structure
H-bonding between amino and carbonyl groups
36
Type of interaction in tertiary structure
Hydrogen bonds
Disulfide bons
Ionic interactions
Hydrophobic interactions
37
Interaction in quaternary structure
Interaction of more than one polypeptide chain
38
How to break peptide bonds?
Hydrolyzed nonenzymatically by prolonged exposure to strong acid or base at high temps
Enzymatically, peptidases (proteases)
39
2 categories of peptidases
Exopeptidases
Endopeptidases
40
Types of exopeptidases and where they cut
Aminopeptidases- cuts amino end
Carboxypeptidases- cuts carboxyl end
41
Which direction to read an AA peptide sequence?
From N-terminus to C-terminus
42
What is a residue?
An individual component AA in a polypeptide
43
When naming a polypeptide, what happens to the endings of AA residues?
All changed to -yl except last AA residue stays same
44
What type of bond usually present in peptide bonds (cis/trans) and why?
Usually trans because of steric hindrance between the -R groups
45
What does DEGENERATIVE mean?
Multiple codes code for same AA
46
Where are bond formations in secondary structure?
H-bonds between C=O and N-H groups
47
In a-helices, how often are H-bond interactions unto itself?
Approximately every 4 AAs
48
Which is tighter, a-helix or b-pleated sheet?
a-helix
49
Which direction do R-groups face in a-helix
Outward
So they can interact in the tertiary structure and avoid steric interference
50
What AA disrupts the a-helix?
Proline
51
Individual segments of b-pleated sheets are called...
b-strands
52
T/F
| b-sheets can be parallel and antiparallel
True
53
What are the specific interactions that occur between R-groups in tertiary structures?
Hydrogen bonds
Disulfide bonds
Ionic interactions
Hydrophobic interactions
54
What are Chaperones?
Specialized group of proteins that help in proper folding of many proteins
55
Denaturation...
The unfolding and disorganization of the proteins tertiary and secondary structures (no hydrolysis of peptide bonds)
56
Examples of denaturing agents
```
Heat
Organic solvents
Mechanical mixing
Strong acids/bases
Detergents
Ions of heavy metals (Pb, Hg)
```
57
How are subunits held together in quaternary structure?
```
Noncovalent interactions
(Hydrophobic interactions, H-bonds, ionic bonds)
```
58
Isoforms...
Proteins that perform the same function but have different primary structures
59
Isozymes...
Protein isoforms that function as enzymes
60
What typically happens to misfolded proteins?
Tagged and degraded by the cell
61
What large factor contributes to the accumulation of misfolded proteins?
Age
62
Examples of diseases that can result from accumulation of misfolded proteins and where implicated...
Amyloid disease- implicated in Alzheimer's
Prion disease- induces normal protein to become abnormal. Implicated in
- bovine spongiform encephalopathy (mad cow)
- scrapie (in sheep)
- Creutzfeldt-Jakob (humans)
63
Are hemoglobin and myoglobin tertiary or quaternary?
Myoglobin- tertiary
| Hemoglobin- quaternary
64
What is at the center of the heme structure?
Fe
65
What are the 5th and 6th things to bind to the Fe group in heme?
O2 and Histidine
66
Where is myoglobin found?
In heart and skeletal muscle.
| If found in blood, means something is wrong
67
Where is hemoglobin found?
Red blood cells
68
Function of hemoglobin?
Main: transport O2 from the lungs to the capillaries of tissues
Also: can transport H+ and CO2 from the tissues to the lungs
69
Structure of hemoglobin?
2 a and 2 b subunits, each of which has a heme bi ding pocket
70
What are the two states of hemoglobin and when are they in those states?
R (relaxed) state- oxygenated form (less ionic and H-bonding between dimers)
T (taut) state- deoxygenated form
71
Type of O2 dissociation curve for hemoglobin?
Sigmoidal
72
Myoglobin has what type of O2 dissociation curve?
Hyperbolic
73
Hemoglobin and myoglobin both demonstrate what type of binding? Define
Cooperative binding- as first O2 binds, binding of additional O2 is enhanced
74
Bohr effect
Effect of a change in the O2 binding affinity of Hb, due to the binding of other ligands
75
Other ligands that bind to Hb?
H+
2, 3-bisphosphoglycerate
CO2
76
A decrease in pH leads to a decrease/increase in oxygen affinity of Hb?
And the dissociation curve to shift left/right?
Decrease
| Right
77
Increased 2,3-BPG leads to an increase/decrease of O2 affinity in Hb?
And causes shift in dissociation curve left/right?
Decrease
| Right
78
A decrease in CO2 causes an increase/decrease in O2 affinity of Hb?
Shift in dissociation curve left/right?
Increase
| Left
79
What happens to O2 affinity in Hb when CO is bound?
Extreme increase in affinity of O2, so much so that it cannot release O2 to the tissue
80
Hemoglobinopathies examples
Sickle cell anemia (Hb S) - glutamate is substituted with valine
Hemoglobin C (Hb C)- glutamate substituted with lysine
Hemoglobin SC - (Hb S + Hb C)
81
Fibrous proteins tend to be mainly for what?
Structure
82
Fibrous protein examples
Collagen
Elastin
a-keratin
Silk fibroin
83
Most abundant protein in the human body
Collagen
84
Composition of collagen...
Right handed triple helix, each individual helix itself is Left handed
85
Type of collagen found in teeth, bone, skin and tendons
Type 1
86
AA composition of collagen
~33% glycine
Up to 30% proline and 4-hydroxyproline
3-hydroxyproline and 5-hydroxylysine also occur
87
A high % of hydroxyproline and hydroxylysine suggest the presence of...
Collagen
88
Where does collagen synthesis occur?
Both inside and outside the cell
89
Main steps of Collagen Biosynthesis
- after transcription
1. selected proline and lysine residues are hydroxylated
2. Selected hydroxylysine residues are glycosylated with glucose and galactose
3. A triple helix is formed and procollagen is produced
4. The N-terminal and C-terminal propeptides are cleaved by procollagen peptidases, producing tropocollagen
5. Self-assembly of tropocollagen into fibrils with cross-linking to form mature collagen fibers
90
Defects in collagen
Ehlers-Danlos syndrome (EDS)- fragile stretchy skin and loose joints
Osteogenesis imperfecta (OI)- bones that easily bend and fracture
91
Where are elastin fibers found?
Lungs
Walls of large arteries
Elastic ligaments
92
Where is keratin found?
```
Hair
Wool
Skin
Horns
Fingernails
```
93
Nonpolar amino acids
```
Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline
```
94
Uncharged polar amino acids
```
Serine
Threonine
Tyrosine
Cysteine
Glutamine
Asparagine
```
95
Acidic amino acids
Aspartate
| Glutamate
96
Basic amino acids
Lysine
Arginine
Histidine
