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BIOC1011 Molecular Basis of Life > Biological Chemistry > Flashcards

Biological Chemistry Flashcards

1
Q

Dalton’s atomic theory (4)

A 
1. All matter is made of atoms. Atoms
are indivisible and indestructible.
2. All atoms of a given element are
identical in mass and properties.
3. Compounds are a combination of two
or more different kinds of atoms.
4. A chemical reaction is a rearrangement
of atoms.
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2
Q

Molecule (definition)

A

an electrically neutral group of two or more atoms

held together by covalent chemical bonds

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3
Q

Compound (definition + example)

A

A pure substance made up of two or
more elements in a fixed ratio by mass

Ex) H2O2 (hydrogen peroxide)

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4
Q

Ways to represent molecules (4)

A

1) Molecular Formula
2) Structural Formula
3) Ball and Stick
4) Space filling model

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5
Q

Atoms are defined by: (3)

A
  1. MASS NUMBER = protons + neutrons
  2. ATOMIC NUMBER = protons (defines an element)
  3. ATOMIC WEIGHT = weight of all sub‐atomic particles

12 —-> Mass Number
C
6 —-> Atomic Number

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6
Q

Isotopes (definition)

A

Same atomic number (number of protons) but the Mass Number has chanced
Ex) C12 (most abundant) –> C13, C14 (iso.)

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7
Q

Ground‐State electron configuration: (def.)

A

The electron configuration of the lowest energy state of an atom
Quantized: e- can only be found in certain areas

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8
Q

Electron shells and corresponding #e-

A 
nucleus (protons + neutrons)
1st shell = holds 2 electrons
2nd shell = holds 8 electrons
3rd shell = holds 18 electrons
4th shell = holds 32 electrons
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9
Q

Electron configurations (song)

A

1s2, 2s2, 2p6, 3s2, 3p6, 4s2, etc.

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10
Q 
Covalent bond (def.)
Elements that form covalent bonds (4)
A

Formed by the sharing of one or more
pairs of electrons

Readily form covalent bonds (HCNO)
H-H is strongest (>Kj/mol) compared to others

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11
Q

Ranking Bonds (strongest to weakest)

A

Ionic bonds STRONGEST
Hydrogen bonds
Van der Waals
Hydrophobic interactions WEAKEST

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12
Q

A molecule will be polar if:

A

1) it has polar bonds, &
2) its centres of partial positive and partial negative charges lie at different places within the molecule.

Directionality always points TO PATIAL NEGATIVE

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13
Q

Dipole‐Dipole Interactions

A

These occur due to the electrostatic attraction of positive and negative dipoles between molecules

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14
Q

Forming an Ionic Bond

A

1) Lose or gain enough electrons to acquire a filled valence shell and become an ion.
2) An ionic bond is the result of the force of attraction between a cation (+) and an anion (‐).
3) An ionic bond is the result of the force of attraction between a cation and an anion

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15
Q

Electronegativity (EN): [definition]

A

The ability of an atom to lose or gain an electron is determined by its attraction for electrons

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16
Q

High EN

A

C, N, Cl, O

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17
Q

Low EN

A

Na, Ca

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18
Q

Hydrogen Bonds

A

Bond between a hydrogen (partial positive) and adjacent EN atom which is partially negative (usually N or O)

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19
Q

Bronnsted definitions of acids and bases

A
  • An acid has a tendency to lose a proton.

* A base has a tendency to accept a proton.

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20
Q

Water acting as either a Bronnsted Acid or base depending on scenario

A

Acting as Base: HCl + H2O -> Cl- + H3O+

Acting as Acid: 2Na + 2H20 -> 2Na+ + 2O- + 2H

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21
Q

pH is the measure of:

A

acidity

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22
Q

pH equation

A

pH = -log10 [(H3O+)]

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23
Q

pKa properties (2)

A

1) A pKa value tells us how acidic (or not) a given hydrogen atom in a molecule is (see titration diagrams).
2) pKa is defined as the pH at which a group has LOST HALF of its hydrogens.

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24
Q

Strong Acids vs. Weak Acids

A

Strong Acids: Completely dissociate in h20

Weak Acids: Dont completely dissociate in h20 (many biological proteins have functional groups that are weak acids)

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25
Q

Van Der Waals interactions (london dispersion)

A

1) the attraction between temporary induced
dipoles
2) strength increases as the mass & number of electrons in a molecule increases
3) Even though very weak, they contribute significantly to the attractive forces between large molecules as they act over large surface areas

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26
Q

Hydrophobic molecules

A

(hydro, water + phobos, fear)

are molecules which are NON-IONIC, NON-POLAR & therefore cannot form hydrogen bonds with water.

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27
Q

Amphipathic molecules

A

(amphi, both + pathos, passion)
- Are both hydrophobic and hydrophilic.

Ex) Detergents are amphipathic: SDS

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28
Q

Chemical Kinetics: (def)

A

The study of the rates of chemical reactions

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29
Q

Factors affecting rates of reaction (6)

A

1) molecular collisions
2) activation energy
3) nature of the reactants
4) concentration of the reactants
5) temperature
6) catalyst

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30
Q

2 Types of Energy Diagrams

A

1) Exothermic reactions

2) Endothermic reactions

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31
Q

Exothermic Reactions

A

Reactants higher E than products

Release of energy

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32
Q

Endothermic Reactions

A

Reactants lower E than products

Energy needs to be put into the system

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33
Q

Nature of Reactants:

ex) Faster reactions
ex) Slower reactions

A

Fast) Reactions between ions in aqueous solution are very fast (their activation energies are very low).

Slow) Reactions between covalent compounds, whether in water or another solvent, are slower (their activation energies are higher).

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34
Q

Temperature Affecting Rate of reaction

A

Approximation: 10°C increase in temperature, the reaction rate doubles.

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35
Q

Catalyst

A

A substance that increases the rate of a chemical reaction without itself being used
up.

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36
Q

Equilibrium constant

A

Reaction: aA + bB ↔ cC + dD

K = Products^# / Reactants^#
K = [C]^c[D]^d / [A]^a[B]^b
37
Q

Is there a relationship between rate of reaction and equilibrium constant (k)?

A

No
Rate of reaction = refers to how quickly a reaction will reach equilibrium
K = where on the spectrum the equilibrium will occur

Any combination of the two is okay.

38
Q

Hydrolysis

A

Break apart

39
Q

Synthesis

A

Build

40
Q

How many AA’s are there?

A

20

41
Q

Components of AA

A

1) Alpha carbon (wants 4 bonds)
2) Alpha Amino
3) Alpha Carboxyl
4) alpha hydrogen

42
Q

Aromatic R-groups with ascending size

A

Phenylalanine: Phe, F
Tyrosine: Tyr, Y
Tryptophan: Trp, W

43
Q

Non-polar, Aliphatic, R-groups

Hydrophobic

A

GAVLIMFWP
Grandma Always Visits London In May For Wes’s Party

Glycine Gly G, Alanine Ala A, Valine Val V, Leucine Leu L, Isoleucine Ile I, Methionine Met M, Phenylalanine Phe F, Tryptophan Trp W, Proline Pro P

Phenylalanine, Tryptophan, Proline are NOT aliphatic

44
Q

Polar, uncharged, R-groups

A

STCNQY
Santa’s Team Crafts New Quilts Yearly

Serine Ser (S)
Threonine Thr (T)
Cysteine Cys (C)
Arspargine Asp (N)
Glutamine Gln (Q)
Tyrosine Tyr (Y)
45
Q

Electrically Charged R-groups

A

DEKRH
Dragons Eat Knights Riding Horses
DE are positively charged
KRH are negatively charged

Aspartic Acid Asp (D)
Glutamic Acid Glu (E)
Lysine Lys (K)
Arginine Arg (R)
Histidine His (H)
46
Q

Charged side chains at pH 7

A 
Dragons Eat Knights Riding Horses
Glu and Asp (pKa <5) 
Lys (pKa ~10)
Arg (pKa ~13) 
His (pKa ~6.5)
47
Q

Hydrogen bonders

A

Hydrogen ST. North. QWY
H.ST.N.QWY

Ser, Thr, His, Asn, Gln, Tyr, Trp

48
Q

Proteins are (2)

A

1) Linear polymers of amino acids

2) linked by peptide bonds.

49
Q

AA writing convention

A

5’ -> 3’

N-terminus –> C-terminus

50
Q

Disulphide bonds

A
  • Covalent bond
  • Oxidation of two cysteine side chains
  • Can be reversed by treating with reducing agent

Oxidation: make dusilphide bonds
Reduction: Breaks disulphide bonds

51
Q

Fibrous Protein

A
  • Shape is linear, regular, often with repeating units, e.g. collagen
  • Polypeptide chain is extended
  • There are non‐covalent bonds between adjacent polypeptide chains
  • They usually have a structural role
52
Q

Globular Protein

A
  • Polypeptide folds into a roughly spherical shape e.g. hemoglobin
  • Most non‐covalent bonds are within one polypeptide chain
  • Most proteins are globular
53
Q

Secondary Structure (2)

A

Hydrogen bonding between peptide bond atoms results in two main structures:

1) alpha-helix
2) beta (pleated) sheet

54
Q

Is a-helix a left handed or right handed helix?

A

Right handed

55
Q

Examples of a-helixes (3)

A

1) Keratin (the protein that forms fur, hair, feathers, claws, horns, etc.
2) Myosin (a major protein of muscle fibres)
3) Fibrin (responsible for creating the network that holds blood
clots together).

56
Q

Keratin

A

Helical: hair fibres are made of bundles of microfibrils, with each microfibril comprised of pairs of a-helices wound together like a rope, forming stretchy fibres.

57
Q

Collagen

A

1) most abundant single proteinin most vertebrates
2) Repeating sequence, Gly‐X‐Y, where X is often proline and Y is proline or hydroxyproline
3) Forms a triple‐helix of 3 polypeptide chains

58
Q

Protein Domain

A

1) conserved, can function, and exist
independently
2) can often be independently stable and folded.
3) can vary from about 25-500 amino acids in length.

59
Q

Native Structure

A

1) Present under physiological conditions
2) biologically active structure
3) Stabilized by many non‐covalent bonds

60
Q

Protein Denaturation

A

1) Biologically Inactive
2) There are large and opposing enthalpic and entropic changes on denaturation.
3) Increase T = – increased kinetic energy leads to breaking of non‐covalent bonds
4) pH changes lead to ionization of side chains

61
Q

Are disulphide bonds (S-S) broken by increased temperature and pH change?

A

No. S-S bonds are broken by reducing agents such as

1) b‐mercaptoethanol
2) dithiothreitol.

62
Q

Protein folding in cells is often assisted by interaction with other
proteins called:

A

Chaperones

63
Q

BSE (Bovine Spongiform Encephalitis)

A
  • Prion diseases
  • Infective protein (PrPSc = prion protein, scrapie form) causes mis‐folding of its natural counterpart (PrPC = prion
    protein, cellular form) in the host animal.
  • Mis‐folded protein then behaves like PrPSc triggering the mis‐folding of other molecules of PrPC resulting in a chain reaction
64
Q

General Globular Protein Architecture (5)

A

1) Compact
2) Charged side chains are on the surface.
3) Hydrophobic side chains are inside.
4) The side chain and peptide groups which can form hydrogen bonds may be either on the surface or inside.
5) Adopt the minimum energy structure.

65
Q

Myoglobin

A

Stores O2 in muscles

66
Q

Catalysts (3)

A

1) speed up reactions rate at which equilibrium is attained.
2) The position of the equilibrium is not altered.
3) not used up in reaction

67
Q

Oxidoreductases

A

One compound oxidizes a second one.

Oxidation & reduction.

68
Q

Hydrolases

A

A compound is split into two products.

69
Q

Lyases

A

A compound is split into two products, but

not by hydrolysis.

70
Q

(Isomer)ases

A

A compound is rearranged by moving one

part of the molecule to another place.

71
Q

Ligases

A

Two compounds are joined together

72
Q

Transferases

A

Part of one compound is transferred to a

second one.

73
Q

Examples of Transerases (1)

A

1) Kinase

74
Q

Example of Hydrolase (1)

A

(1) Trypsin

75
Q

General reaction of enzymes

A

E + S ES –> E + P

76
Q

Induced Fit Model

A

Proposes that the initial interaction between the enzyme and the substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding to allow catalysis

77
Q

Vmax

A

the maximum velocity Vmax at high (“saturating”) substrate concentrations.

78
Q

Km

A

The Michaelis constant is the substrate concentration for which the velocity is half
maximal.

79
Q

Michaelis Mentis Kinetics Equation

A

The equation which describes this relationship is:
v = Vmax [S]o/(Km + [S]o)
v is the rate
[S]o is the initial substrate concentration

At low [S]o (<>Km), v is independent of [S]o

80
Q

How do enzymes lower Ea

A

The active site fits better to the transition state. Therefore, the transition state is easier to attain and the activation energy is, therefore, lower

81
Q

Some enzymes require a _____ to function

A

co-enzyme

82
Q

Co-enzymes can be (2)

A

1) metal ion (mg, fe, zn, k)

2) small organic molecules (vitamins)

83
Q

Apoenzyme.

A

An enzyme that is missing its coenzyme

84
Q

Haloenzyme

A

Apoenzyme + Coenzyme = Haloenzyme

85
Q

Inhibitor

A

A compound that decreases the rate of an

enzyme‐catalysed reaction

86
Q

Competitive inhibitors

A
  • Resemble the substrate and are thus able to fit the active site
  • Compete with the substrate for binding to the enzyme and inhibit it.
87
Q

Km of an inhibitor is:

A

1/Km

88
Q

Efficacy of HIV and Anti-influenza drugs are limited by (3)

A

1) Side effects
2) Bioavailability
3) Resistance

BIOC1011 Molecular Basis of Life (2 decks)

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