Midterm 1 Review Flashcards
1
Q
Disadvantages of cell compartmentalization
A
- having to develop the channels to get things through membranes → costs energy
2
Q
Velocity Curve
A
- rate of the reaction as a function of increasing substrate concentration
- an enzyme might have very low activity until you get higher substrate concentration
- km = rate of binding (k1) and the concentration of substrate to product (k2)
3
Q
Native Structure
A
- structure the protein needs to function
- stable bc its low energy
4
Q
Prions
A
- protein can become trapped in a non-native intermediate structure (mutation causes it to have a low energy state similar to that of the native structure)
- protein becomes trapped in a “energy trap” -> cant go back over to the native structure without putting energy to make it go over the energy humps
- have an intermediate structure that is low in energy so it doesn’t take the prion much to flip it
5
Q
Amyloid diseases
A
- unfolded intermediate that can self-assemble into fibrils
- neurons are being choked by aggregates of prion proteins
- prions can force a normally folded protein into the prion state → creating a big ball of rubber bands which is lethal
6
Q
Phosphorylation potential
A
free energy change of hydrolysis
7
Q
Le Chatelier’s Principle
A
- rxn change → new Keq
- dynamic equilibrium → never static, constant flow of going forward & backwards
8
Q
What are the bonds present in tertiary structure?
A
- Disulfide bonds
- Ionic interactions
- Hydrogen bonds
- Hydrophobic/ hydrophilic interactions (includes Van der Waals)
9
Q
Why do we phosphorylate a protein and not use amino acid
substitution?
A
It is a reversible process. A Kinase adds a phosphate
and a phosphatase removes a phosphate.
10
Q
How does post translational Modification affects protein function
A
DNA binding, translocation, change in conformation, change in stability
11
Q
What are histone
chaperones?
A
They are proteins that help guide histones as
they assemble to the DNA to form nucleosomes in
chromatin
12
Q
What are some heat
shock proteins?
A
They use energy to prevent aggregation of mis-folded
proteins that help guide them to their ultimate
structures
13
Q
what characteristics can influence equilibrium?
A
- concentration
- temperature
- pH
- pressure
14
Q
why do cellular processes use end-product regulation?
A
- to avoid overproduction of the product
- to avoid wasting energy to produce a product when it is no longer needed
15
Q
rnx coupling
A
- improves the energetics of the reaction
- delta G values get added to become more favorable
16
Q
Anabolism vs Catabolism
A
- anabolism -> reductive
- catabolism -> oxidative
17
Q
why would a pathway use to different reducing equivalents for anabolism and catabolism?
A
- no futile cycle
- not building something just to break it down again
18
Q
what makes ATP hydrolysis favorable?
A
- charge repulsion
- immediate ionization of ADP
- resonance stabilized Pi
19
Q
what does the addition of phosphate do to an organic compound?
A
- energizes it
- acts as an electron donot
- kinate adds it, phosphatase removes it
20
Q
What are the energetics of Pyruvate Kinase?
A
- exergonic, negative delta G
- PEP + ADP -> Pyruvate + ATP
21
Q
Creatine Kinase
A
- Forward → ATP is high
- Backward - ATP is low
- If the body is at rest, the reaction proceeds forward
22
Q
What do creatine pills do?
A
- allows for a more rapid phosphorylation of ATP
23
Q
Would the beginning or end of the ETC have the highest reduction potential?
A
- end
24
Q
D-stereoisomers
A
- glycine & cysteine
- both have R conformation instead of S
25
Psi bond
alpha carbon to carbonyl carbon
26
Phi bond
alpha carbon to nitrogen
27
Which AAs have high hydropathy index?
nonpolar AAs
28
Alpha helices
- secondary structure
- hydrogen bonds stabilize
- polar outside, nonpolar inside
29
which AAs are unstable in an alpha helix?
- proline, glycine
30
Collagen alpha helix
- G-P-X (glycine, proline, another AA)
- Proline is more rigid, allowing turns
- Glycine allows for the tight packing of collagen together
- stable, strong and flexible structure
- left handed helix
31
How does the isomerization of proline lead to the stabilization/ formation of beta turns?
- cis confirmation of prolines
- very rigid molecule
32
Net Charge
- pH protonated
- pH>pka -> deprotonated
33
examples of post-translation modification
- phosphorylation
- glycosylation
- acetylation
- methylation
- uniquitation
- these are all reversible
34
Hemoglobin
- R state has a higher affinity for O2
- low kd
- high affinity
- cooperative which is beneficial for transferring oxygen from Hb to the peripheral tissues
- composed of 2 alpha and beta hemoglobin structures (tetramer of 4 peptides)
35
Primary protein structure
sequence of chain of amino acids
36
Secondary protein structure
hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern
37
tertiary protein structure
a 3D folding pattern of a protein due to side chain interactions
38
quaternary protein structure
protein consisting of more than one amino acid chain
- the interactions of individual tertiary strucctures to form a polypeptide
39
Hydropathy Index
- measures how hydrophobic an amino acid is
- high hydropathy = hydrophobic
- F is the most hydropathic AA
40
why is a peptide bond planar
has a double bond nature between O-C-N
41
Collagen helix
- hydroxylation of prolines in collagen stabilizes the right-handed triple helix structure
- proline is forcing a turn and glycine allows this to happen
- doesnt use hydrogen bonds
42
examples of fibrous proteins
- collagen
- keratin
43
examples of globular proteins
- flavodoxin
- myoglobin
44
why is PTM a better strategy for the cell to use?
its fast & its reversible
44
consequences of protein phosphorylation
- conformation
- stability
- translocation
- DNA binding
45
Protein conformations can have consequences
- protein dissociation
- ion transport
- order ↔ disorder transition
- allosteric regulation
46
Ribonuclease
- a type of nuclease that catalyzes the degradation of RNA into smaller components.
- demonstrates that simple proteins can spontaneously refold into their "native state"
47
what type of mutations would affect protein structures?
TS mutations (temperarure sensitive mutations)
48
histone chaperones
proteins that help guide histones as they assemble onto DNA to form nucleosomes in chromatin
49
heat-shock proteins
use energy to help prevent aggregation of misfolded proteins and help guide them to their ultimate structures and/or complexes with other proteins
50
how many oxygens can hemoglobin bind?
4
51
cooperativity
the binding of one molecule or ligan or substrate increases the affinity of binding for additional molecules at the other sites
52
sigmoidal curve
a hybrid curve of an initially low affinity binding curve being converted to a high affinity binding curve
53
BPG
the binding of BPG to Hb stabilizes the T state of Hb
- allows more oxygen to achieve the R state)
- changes the conformation of the protein (allosteric effector)
54
Ras
- mutations in Ras can affect its ability to change shape through GTP Hydrolysis and can cause inappropriate activation of cell division
- Ras GTP (on) -> Ras*GDP (off) mutation that causes it to not stop replicating
55
PEP
- Phosphoenolpyruvate (PEP) is a high-energy metabolite in the final step of glycolysis. PEP is converted into pyruvate by pyruvate kinase.
56
The muscle protein myoglobin shows __________________ binding to oxygen
non-cooperative
57
The power stroke of muscle contraction occurs when
myosin releases Pi after ATP hydrolysis
