FINAL MATERIAL Flashcards
(88 cards)
1
Q
what prefixes refer to how organisms get energy
A
- photo
- chemoorgano
- chemolitho
2
Q
what prefixes refer to how organisms synthesize complex organic compounds
A
- auto
- hetero
3
Q
name the only non-chiral amino acid
A
-glycine
4
Q
which amino acid is often found as a cis-peptide bond?
A
-proline
5
Q
what is the mutation in hemoglobin that leads to sickle cell anemia
A
-glutamic acid to valine
E6V
6
Q
Name the branched amino acids. What disease results from defects in the enzyme that catabolizes branched amino acids?
A
Leucine, Isoleucine, and valine
-Maple Syrup Urine Disease
7
Q
Phenylketonuria (PKU)
A
- defect in catabolism of phenylalanine
- extremely painful if untreated
- severe sequelae similar to MSUD
- can be controlled by dietary conditions
- extremely sensitive to artificial sweeteners
- can lead to mental disabilities, neurological issues, and such
8
Q
Tryptophan can be turned to ___
A
serotonin
9
Q
Lambert-Beer Law
A
- allows biochemists to measure concentration of protein
- larger side chain means larger UV absorption per mole
10
Q
Only ___ forms disulfides
A
cysteine
11
Q
The amide amino acids, glutamine and asparagine are sensitive to ___ hydrolyisis
A
acid or base
12
Q
Name the nonessential amino acids
A
alanine, asparagine, aspartate, glutamate, serine
13
Q
name the essential amino acids
A
-Histidine, isoleucine, leucine, lysine, methionine , phenylalanine, threonine, tryptophan, valine
14
Q
peptides are simply chains of ____ linked by ____ bonds made by ____ reactions between carboxylic acids and amino groups of amino acids
A
- amino acids
- amide bonds
15
Q
steps of Edman degradation
A
- ) label N-terminus with PTC and
- ) cleave N-terminal PTC-AA residue and separate it from the remaining peptide
- ) identify the PTH-AA by HPLC (high pressure liquid chromatography)
- ) repeat reaction with the remaining peptide to determine new N terminal
16
Q
PI of tyrosine
A
5.66
17
Q
pKa of R group of cysteine
A
8.18
18
Q
pKa of R group of Tyrosine
A
10.07
19
Q
pKa of R group of Lysine
A
10.53
20
Q
pKa of R group of Histidine
A
6
21
Q
pKa of R group of arginine
A
12.48
22
Q
pKa of R group of aspartate
A
3.65
23
Q
pKa of R group of glutamate
A
4.25
24
Q
Pyruvate dehydrogenase complex is made of _ enzymes
A
3
25
E1 of pyruvate dehydrogenase complex.
| Protein and function
pyruvate dehydrogenase:
- decarboxylates pyruvate via TPP
- oxidizes active acetylaldehyde
- transfers 2 electrons and acetyl to lipoic acid on E2
26
E2 of PDH. protein and function
- dihydrolipoyl transacetylase
| - transfers acetyl-group to CoA to make acetyl-CoA
27
E3 of PDH. Protein and function
- dihydrolipoyl dehydrogenase
| - reduces oxidized lipoic acid on E2 transfers 2 electrons via FADH2 to NAD+---> NADH
28
what reaction did we learn that utilized substrate channeling
PDH complex
29
what compounds inhibit PDH complex?
ATP, acetyl-CoA, NADH, fatty acids
30
what activates the PDH complex?
-AMP, CoA, NAD+, Ca2+
31
what enzymes are under regulation in the citric acid cycle?
- citrate synthase
- isocitrate dehydrogenase
- a-ketoglutarate dehydrogenase complex
32
synthase
-condensation reactions occur without NTP
33
synthetase
-condensation reactions requiring NTP (may also be known as ligases)
34
phosphorylase
-breaks bonds using phosphate as a nucleophile
35
hydrolase
-breaks bonds using water as nucleophile
36
kinase
-transfers phosphoryl from NTP to acceptor
37
phosphatase
-removes phosphoryl by hydrolysis
38
amino acids can be joined together via ___ reactions to form ___
condensation reactions
| polypeptides
39
polypeptides can be cleaved to yield monomers via a ____ reaction
-hydrolysis
40
when we talk about peptide groups, we are refering to ___ atoms
6 atoms
| Ca1-CO-NH-Ca2
41
Describe the unique characteristics of the peptide bonds
- no free rotation around them because of partial double-bond character (thanks to resonance)
- the peptide bond (C-O and C-N bonds) fall between a single and a double bond length
42
a torsional angle, aka omega, refers to the __ bond, is usually ___, and means the molecule is in the __ configuration
Ca-C-N-Ca bond
- is usually 180 degrees
- 180 degrees refers to the trans configuration
43
the Phi bond refers to the bond between
N and Calpha
44
steric interference prohibits phi and psi angles of certain magnitudes like ____
0,0 or 180, 90
45
ramachandran plots
show backbone angles for all of AAs in a protein, or all of the backbon angles for a specific AA in a variety of protein
46
ramachandran plots
Visual display of φ & ψ angle sets showing sterically allowed conformations
47
1° structure
covalent arrangement of all amino acids in protein sequence plus disulfides
(plus non-amino acid stuff like prosthetic groups & glycosylations & fatty acids etc etc etc)
48
secondary structure
local spatial arrangements of groups of amino acids
Some stable, recurring arrangements with regular (or unchanging) φ & ψ angles for each residue in
some 2° structures are named, examples: α-helix, β-conformation (or β-strand) & β-turn
49
in an alpha helix protein, Hydrogen bonding occurs between:
the carbonyl oxygen of one peptide bond and the N-H group of the 4th amino acid away
50
there are approximately __ residues per turn in a polypeptides alpha helix
3.6 residues (5.4 Angstroms)
51
amphipathic
hydrophilic parts as well as hydrophobic
52
Levinthal’s paradox
➔ Protein folding cannot possibly operate as a random trial & error process
-if protein folding was a random process then: •If one assumes that each conformation requires ≥10-13 seconds to explore,
(since t = 10-13 seconds for single molecular vibrations)
then ≈10^(77) years required for small polypeptides to fold by random process
53
Application of Lambert-Beer Law:
- summarizes the light absorbing properties of the aromatic molecules
- is Abs=(path length)*(concentration)*(extinction coefficient)
- is used in then laboratory to quantify the protein concentration of samples
54
Keq provides information on ___, but not reaction ____
- thermodynamics (if Keq is positive number than products are thermodynamically favorable over reactants
- does not provide information on reaction rate
55
predict the net charge on peptide:
| K-L-A-E-H-S-D at pH 1, 7, and 14
+3, -1, -3
56
when molecular oxygen binds to a heme-containing protein like myoglobin, the two open-coordination bonds of Fe2+ are occupied by
-one O2 molecule and one amino acid R-group
57
the psi bond refers to
-C alpha and C
58
the omega bond refers to
-C-N bond
59
the structure and dynamics of a single domain (22 kDa) of a protein would be investigated using ___:
NMR, electron microscopy, or x-ray crystallography
-Nuclear Magnetic Resonance (NMR)
60
The structure of an 80 kDa enzyme bound to an inhibitor would best be investigated using ____:
NMR, electron microscopy, or x-ray crystallography
x-ray crystallagraphy
61
the structure of a large viral capsid (4 Mega Dalton) sample would best be investigated using ____:
NMR, electron microscopy, or x-ray crystallography
-electron microscopy
62
put the one letter amino acid code for:
| two amide R-groups that never carry any net charge at neutral pH
-N and Q
63
put the one letter amino acid code for:
| ionizable R group that often forms polypeptide crosslinks
-C
64
put the one letter amino acid code for:
| two acid R-groups that carry negative charges at neutral pH
-D and E
65
put the one letter amino acid code for:
| Heterocyclic R-group that can act as a general base in enzyme catalytics
-H
66
put the one letter amino acid code for:
| amino acid serving as the initiator for the biological protein synthesis
-M
67
put the one letter amino acid code for:
| largest R group with the most absorbance of UV light at 280 nm
W
68
put the one letter amino acid code for:
| three R-groups that can readily be phosphorylated
S, T, Y
69
put the one letter amino acid code for:
| -only secondary amine R-group and often located in B-turns
-P
70
put the one letter amino acid code for:
| two basic r groups that carry full positive charges at neutrall pH
K and R
71
smallest R group and often located in B-turns
G
72
Two isomeric aliphatic R-groups, one with a second chiral center
-I and L
73
put the one letter amino acid code for:
| a large aromatic R-group with almost no polar character whatsoever
F
74
put the one letter amino acid code for:
| smallest branched-chain R-group with virtually no polar character
V
75
smallest chiral R group that prefers to fold as in alpha helix
A
76
Mass Spectrometry
- Molecules first must be ionized in a vacuum (MALDI*, ESIˇ)
- Molecules introduced into an electric plus magnetic field
- Then molecules follow path through the field as a function of their mass-to-charge ratio = m / z
- Easily automated ! now often analyze peptides derived from proteins
- MS can be used to confirm the identity of your purified protein
- MS can even identify chemically modified versions of your protein
77
is lactose a reducing sugar?
- Lactose and maltose are two examples of reducing sugars, but sucrose is not.
- to be a reducing sugar the anomeric carbon must be FREE!!!
- The reducing end of a disaccharide is the monosaccharide with a free anomeric carbon that is not involved in a glycosidic bond and is thus capable of converting to the open-chain form
78
chymotrypsin and trypsin cleave with different specificities. What feature gives chymotrypsin its substrate specificity?
-chymotrypsin's hydrophobic pocket has the perfect space and geometry to fit aromatic R groups
79
chymotrypsin and trypsin cleave with different specificities. What feature gives trypsin its substrate specificity?
- Trypsin favors basic residues like lysine and arginine
- An important difference is that residue 189 is a negatively charged Asp in trypsin
- The aspartate residue (Asp 189) located in the catalytic pocket (S1) of trypsin is responsible for attracting and stabilizing positively charged lysine and/or arginine, and is, thus, responsible for the specificity of the enzyme. This means that trypsin predominantly cleaves proteins at the carboxyl side (or "C-terminal side") of the amino acids lysine and arginine
80
Simple diffusion:
| -describe and define and identify a solute transported by each mechanism
simple diffusion is how O2 gets into tissues. It does not require energy nor is a channel needed. The substance just goes down its concentration gradient
81
Facilitated diffusion
| -describe and define and identify a solute transported by each mechanism
- Facilitated diffusion is the process of spontaneous passive transport of molecules or ions across a cell's membrane via specific transmembrane integral proteins.
- this is how glucose enters cells
82
Primary Active transport
| -describe and define and identify a solute transported by each mechanism
- requires energy-usually in the form of ATP
| - this channel requires energy to pump ions or substrates against their concentration gradient like in the Na-K+ ATPase
83
Secondary active transport
| -describe and define and identify a solute transported by each mechanism
-Secondary active transport uses electrochemical gradients established to move certain solutes against their concentration gradients. Like the Na+-Glut transporter in the small intestines. Na+ flows down its concentration gradient and glucose goes along for the ride
84
Identify 3 traits that distinguish channels from carriers
- • Solutes diffuse through the pore of channel proteins, whereas career proteins bind solutes on one side of membrane and release it on the other side
- channels are not saturable, but carriers can be
- Carrier proteins can transport molecules or ions against the concentration gradient, while channel protein cannot.
- • Carrier proteins move across the membrane, whereas channel proteins do not move while transporting molecules or ions.
85
Lineweaver-Burk Equation
= (Km/Vmax)(1/[S] + 1/Vmax
86
Scatchard plot equation
[Bound]/[Free] = 1/Kd * (Bmax - [RL])
87
epinephrine and glucagon are ___
-kinda similar
88
PFK 2 is active when ____ and makes
- dephosphorylated
| - fructose 2,6 phosphate
