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BIOL301 > Midterm 1 Review > Flashcards

Midterm 1 Review Flashcards

1
Q

Disadvantages of cell compartmentalization

A
  • having to develop the channels to get things through membranes → costs energy
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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)
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3
Q

Native Structure

A
  • structure the protein needs to function
  • stable bc its low energy
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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
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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
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6
Q

Phosphorylation potential

A

free energy change of hydrolysis

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7
Q

Le Chatelier’s Principle

A
  • rxn change → new Keq
  • dynamic equilibrium → never static, constant flow of going forward & backwards
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8
Q

What are the bonds present in tertiary structure?

A
  1. Disulfide bonds
  2. Ionic interactions
  3. Hydrogen bonds
  4. Hydrophobic/ hydrophilic interactions (includes Van der Waals)
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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.

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10
Q

How does post translational Modification affects protein function

A

DNA binding, translocation, change in conformation, change in stability

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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

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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

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13
Q

what characteristics can influence equilibrium?

A
  • concentration
  • temperature
  • pH
  • pressure
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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
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15
Q

rnx coupling

A
  • improves the energetics of the reaction
  • delta G values get added to become more favorable
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16
Q

Anabolism vs Catabolism

A
  • anabolism -> reductive
  • catabolism -> oxidative
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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
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18
Q

what makes ATP hydrolysis favorable?

A
  • charge repulsion
  • immediate ionization of ADP
  • resonance stabilized Pi
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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
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20
Q

What are the energetics of Pyruvate Kinase?

A
  • exergonic, negative delta G
  • PEP + ADP -> Pyruvate + ATP
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21
Q

Creatine Kinase

A
  • Forward → ATP is high
  • Backward - ATP is low
  • If the body is at rest, the reaction proceeds forward
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22
Q

What do creatine pills do?

A
  • allows for a more rapid phosphorylation of ATP
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23
Q

Would the beginning or end of the ETC have the highest reduction potential?

A
  • end
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24
Q

D-stereoisomers

A
  • glycine & cysteine
  • both have R conformation instead of S
25
Q

Psi bond

A

alpha carbon to carbonyl carbon

26
Q

Phi bond

A

alpha carbon to nitrogen

27
Q

Which AAs have high hydropathy index?

A

nonpolar AAs

28
Q

Alpha helices

A
  • secondary structure
  • hydrogen bonds stabilize
  • polar outside, nonpolar inside
29
Q

which AAs are unstable in an alpha helix?

A
  • proline, glycine
30
Q

Collagen alpha helix

A
  • 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
Q

How does the isomerization of proline lead to the stabilization/ formation of beta turns?

A
  • cis confirmation of prolines
  • very rigid molecule
32
Q

Net Charge

A
  • pH<pka -> protonated
  • pH>pka -> deprotonated
33
Q

examples of post-translation modification

A
  • phosphorylation
  • glycosylation
  • acetylation
  • methylation
  • uniquitation
  • these are all reversible
34
Q

Hemoglobin

A
  • 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
Q

Primary protein structure

A

sequence of chain of amino acids

36
Q

Secondary protein structure

A

hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern

37
Q

tertiary protein structure

A

a 3D folding pattern of a protein due to side chain interactions

38
Q

quaternary protein structure

A

protein consisting of more than one amino acid chain
- the interactions of individual tertiary strucctures to form a polypeptide

39
Q

Hydropathy Index

A
  • measures how hydrophobic an amino acid is
  • high hydropathy = hydrophobic
  • F is the most hydropathic AA
40
Q

why is a peptide bond planar

A

has a double bond nature between O-C-N

41
Q

Collagen helix

A
  • 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
Q

examples of fibrous proteins

A
  • collagen
  • keratin
43
Q

examples of globular proteins

A
  • flavodoxin
  • myoglobin
44
Q

why is PTM a better strategy for the cell to use?

A

its fast & its reversible

44
Q

consequences of protein phosphorylation

A
  • conformation
  • stability
  • translocation
  • DNA binding
45
Q

Protein conformations can have consequences

A
  • protein dissociation
  • ion transport
  • order ↔ disorder transition
  • allosteric regulation
46
Q

Ribonuclease

A
  • 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
Q

what type of mutations would affect protein structures?

A

TS mutations (temperarure sensitive mutations)

48
Q

histone chaperones

A

proteins that help guide histones as they assemble onto DNA to form nucleosomes in chromatin

49
Q

heat-shock proteins

A

use energy to help prevent aggregation of misfolded proteins and help guide them to their ultimate structures and/or complexes with other proteins

50
Q

how many oxygens can hemoglobin bind?

A

4

51
Q

cooperativity

A

the binding of one molecule or ligan or substrate increases the affinity of binding for additional molecules at the other sites

52
Q

sigmoidal curve

A

a hybrid curve of an initially low affinity binding curve being converted to a high affinity binding curve

53
Q

BPG

A

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
Q

Ras

A
  • 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
Q

PEP

A
  • Phosphoenolpyruvate (PEP) is a high-energy metabolite in the final step of glycolysis. PEP is converted into pyruvate by pyruvate kinase.
56
Q

The muscle protein myoglobin shows __________________ binding to oxygen

A

non-cooperative

57
Q

The power stroke of muscle contraction occurs when

A

myosin releases Pi after ATP hydrolysis

BIOL301 (20 decks)

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