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Recap > BioChemistry > Flashcards

BioChemistry Flashcards

1
Q

Why is carbon extremely versatile?

A
  • it has a large structural diversity and therefore also a large functional diversity (bind to different receptors)
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2
Q

Orbitals

A

the shapes/volume in which electrons are distributed

S, P, D, F

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3
Q

Explain a covalent bond in terms of orbitals

A

1 orbital for each atom (carrying an unpaired electron) fuses into a molecular orbital which now contains 2 electrons

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4
Q

Triple bonds are…

A

instable

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5
Q

Chiral center

A

region in a molecule where C is bound to 4 distinct chemical groups

(achiral, also 4, but 2 are the same)

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6
Q

Enantiomers

A

2 different configurations of a molecule, with a chiral center (mirror images of each other)

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7
Q

Conformations

A

different forms/projections of molecules (e.g. single or double bonds)

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8
Q

Double bonds don’t allow…

A

for a rotation to take place

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9
Q

Single bonds allow…

A

free rotation

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10
Q

Staggered conformation has … potential energy

A

lower

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11
Q

Eclipsed conformation has … potential energy

A

maximum

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12
Q

Conformation

A

the (potentially flexible) spatial arrangement of atoms around fixed bonds in molecules

  • can readily be interconverted
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13
Q

Configuration

A

the FIXED arrangement of atoms dictated by the bonds of molecules

  • cannot easily be interconverted
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14
Q

Catabolism

A

the conversion of potential energy in food -> energy used by cells to work

  • generates energy and waste
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15
Q

Anabolism

A

the synthesis of biomolecules from building blocks

  • uses up energy
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16
Q

Lithnotrophs

A

require inorganic molecules for fuel

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17
Q

Energy

A

the capacity to do work

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18
Q

1st law of thromodynamics

A
  • constant amount of energy in the universe

- energy cannot be created or destroyed, but can change its form

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19
Q

2nd law of thermodynamics

A
  • energy is transferred in a way that increases the randomness (entropy) of the universe
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20
Q

Gibbs free energy formula

A

G = H - TS

G - free energy (the energy that is available to do work)
H - enthalpy
T - temp. (kelvin)
S - entropy

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21
Q

Enthalpy

A

total energy of the system (including bonds)

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22
Q

a system with a lot of free energy is

A

unstable

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23
Q

Spontaneous process

A

decrease in free energy (between substrate and product) as the system moves to a more stable state

delta G is negative

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24
Q

Exothermic

A

negative change in enthalpy, heat is released

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25
Q

Endothermic

A

positive change in enthalpy

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26
Q

Non-spontaneous (endergonic) reaction

A

products are less stable than substrates because they have a higher potential energy

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27
Q

Characteristics of a reaction:

A
  • spontaneity
  • equilibrium constant
  • directionality
  • velocity
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28
Q

Equilibrium constant (Keq)

A

when there is no net change in the concentrations of P or S

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29
Q

Directionality

A

most directions are reversible (move in both directions)

  • determined by Le Chatelier’s principle: when a dynamic equilibrium is disturbed, it changes to counteract the disturbance
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30
Q

Le Chatelier’s principle

A

when a dynamic equilibrium is disturbed, it changes to counteract the disturbance.

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31
Q

Protein

A

a linear polypeptide of amino acids linked by peptide bonds

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32
Q

What are the 4 groups coming off the central carbon in amino acids?

A
  1. hydrogen group
  2. amino acid group
  3. carboxylic acid group
  4. r group/ side chain
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33
Q

Zwitterion

A

has both a positive and a negative charge

34
Q

3 main types of non-covalent interactions

A

Non-directional:

  1. Van de Waals (weakest)
  2. Salt bridges (strongest)(between pairs of charged ions)

Directional:

  1. Hydrogen (only between polar. groups with permanent dipoles)(H donor and acceptor)
35
Q

A proteins functions are determined by its…

A

range movement / conformational flexibility

36
Q

Elements in amino acids

A

N, H, O, C, and sometimes sulfur

37
Q

Polar

A

can readily form H-bonds

38
Q

Aliphatic compound (proteins)

A
  • long chains (C in the middle, H attached)

- usually only single bonds

39
Q

Aromatic compounds (proteins)

A
  • rings
40
Q

3 Secondary protein structures

A
  1. Beta sheet (multiple H-bonds)
  2. Alpha helix
  3. Loops
41
Q

3 peptide bonds

A
  1. Cis (2 H side chains are parallel and tend to clash) (unfavorable)
  2. Trans (2 H side chains are adjacent)
  3. Omega
42
Q

In proteins ….. always comes before C

A

N

43
Q

In proteins ….. always comes before psi

A

phi

44
Q

Dihedral angles

A

between 2 intersecting planes or planes

  • Phi (between N and alpha carbon)

Psi (between the alpha and the carbonyl carbons)

45
Q

Imino acid

A

contains both imine and carboxyl functional groups

46
Q

Molecular models:

Red is:

Blue is:

A

oxygen

nitrogen

47
Q

Tertiary structure of a protein

A

arrangement of helices, sheets, and loops within the polypeptide

48
Q

Motif vs domain? (proteins)

A

Motif: assembly of several secondary structures
- a commonly repeating arrangement of a few secondary structure elements

Domain: 1+ motifs assembled to form a globular structure
- independent folding unit of a protein

49
Q

Loop regions usually hold the … of enzymes

A

active sites

50
Q

Protein fold

A

arrangement of secondary structure elements of a domain or protein

51
Q

Proteins only fold in…

A

aqueous environments (as it is entropically favorable to mask hydrophobic residues from water)

52
Q

What is the main force against protein folding

A

the loss of entropy (lot of conformational entropy when unfolded)

53
Q

Hydrophobic effect (proteins)

A

increase in the conformational entropy of water as less of it is interacting with the buried side chains

54
Q

…. stabilizes secondary structures

A

H-bonding

55
Q

3 favorable energetic components:

A
  1. hydrophobic effect
  2. non-covalent interactions
  3. reduction in entropy (going from many conformational options to a single one)
56
Q

2 main forces that promote protein folding:

A
  1. hydrophobic effect

2. enthalpy

57
Q

Main force that disfavors protein folding

A

chain conformational entropy

58
Q

Why does urea denature proteins

A
  • it is very polar

- alters H-bonds in the water, reduces hydrophobic effect

59
Q

Thermodynamic hypothesis

A

the most stable thermodynamic conformation of a protein is its native fold

60
Q

Folding is a … process

A

spontaneous

61
Q

During which part of protein folding is there the least free energy?

A

when a protein is in its native structure

62
Q

Protein structure is determined by…

A

its primary sequence

63
Q

Levinthal’s paradox (proteins)

A

the protein has no time to explore all the possible conformations as it would take longer than the existence of the universe

64
Q

How are the best protein conformations found?

A

through cooperativity, when one residue folds it makes it more favorable for another to fold as well

65
Q

2 models for how protein folding beings:

A
  1. Diffusion collision model
    • secondary structure forms and then the rest of the
      protein arranges itself
  2. Nucleation condensation model
    • first the hydrophobic core collapses, and the the
      secondary structures follow
66
Q

Cytosol

A

the aqueous component of the cytoplasm

  • is actually quite crowded with a lot of proteins and RNA, leading to the risk of aggregation
67
Q

Aggregation

A

when misfolded proteins clump together

68
Q

Chaperons

A

proteins that prevent aggregation, and help protein folding

  • prevent teenagers from getting too tangled up before they become adults
69
Q

…. interactions often lead to aggregation

A

hydrophobic interactions

70
Q

Are H-bonds directional?

A

yes

71
Q

Rapid protein folding may occur because of:

A
  1. hydrophobic interactions in the core

2. H-bonding networks in secondary structures

72
Q

Catalyst (enzyme) determine….

A

the speed of the reaction

73
Q

Substrate to enzyme equation

A

E + S <=> ES <=> EP <=> E + P

ES - enzyme-substrate complex
EP - enzyme-produce complex

74
Q

3 reasons why enzymes are good catalysts:

A
  1. formation of transient covalent bonds between substrate and enzyme (lowers activation energy)(decreases entropy)
  2. formation of weak covalent bonds (binding releases energy, decreases activation energy)
  3. exquisite specificity (induced fit)
75
Q

What are the functions of the rest of the enzyme?

A
  1. 3D fold allows for the correct positioning of residues (conformational change during binding)
  2. region for induced fit of substrate
  3. regulating and coordinating the enzyme
  4. regions involved in protein-protein interactions
  5. enzyme complexes
76
Q

How are enzymes regulated?

A
  • signals in the cell
77
Q

Stochastic

A

randomly determined

78
Q

Zymogens / proenzymes

A
  • synthesized as inactive precursors
  • cleaving activates them
  • reduce potential cell toxicity but allow for the quick release of active proteins
79
Q

Proteolysis

A

partial breaking down of proteins

- activates some proteins

80
Q

Insulin

A

released by the pancreas when there are high levels of glucose in the blood, stimulates glucose uptake by liver, adipose tissue, and muscles

81
Q

How do enzymes work?

A

decrease activation energy and then catalyze the reaction

DO NOT impact the equilibrium of reactions

82
Q

Reaction velocity

A

the amount of products formed over time PR the amount of substrate consumed

Recap (14 decks)

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