Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

BIOC1011 Molecular Basis of Life > Biological Chemistry > Flashcards

Biological Chemistry Flashcards

(88 cards)

Start Studying
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.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Molecule (definition)

A

an electrically neutral group of two or more atoms

held together by covalent chemical bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Ways to represent molecules (4)

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Isotopes (definition)

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Electron configurations (song)

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Ranking Bonds (strongest to weakest)

A

Ionic bonds STRONGEST
Hydrogen bonds
Van der Waals
Hydrophobic interactions WEAKEST

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Dipole‐Dipole Interactions

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Electronegativity (EN): [definition]

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

High EN

A

C, N, Cl, O

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Low EN

A

Na, Ca

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Hydrogen Bonds

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

pH is the measure of:

A

acidity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

pH equation

A

pH = -log10 [(H3O+)]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Van Der Waals interactions (london dispersion)
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
26
Hydrophobic molecules
(hydro, water + phobos, fear) | are molecules which are NON-IONIC, NON-POLAR & therefore cannot form hydrogen bonds with water.
27
Amphipathic molecules
(amphi, both + pathos, passion) - Are both hydrophobic and hydrophilic. Ex) Detergents are amphipathic: SDS
28
Chemical Kinetics: (def)
The study of the rates of chemical reactions
29
Factors affecting rates of reaction (6)
1) molecular collisions 2) activation energy 3) nature of the reactants 4) concentration of the reactants 5) temperature 6) catalyst
30
2 Types of Energy Diagrams
1) Exothermic reactions | 2) Endothermic reactions
31
Exothermic Reactions
Reactants higher E than products | Release of energy
32
Endothermic Reactions
Reactants lower E than products | Energy needs to be put into the system
33
Nature of Reactants: ex) Faster reactions ex) Slower reactions
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).
34
Temperature Affecting Rate of reaction
Approximation: 10°C increase in temperature, the reaction rate doubles.
35
Catalyst
A substance that increases the rate of a chemical reaction without itself being used up.
36
Equilibrium constant
Reaction: aA + bB ↔ cC + dD ``` K = Products^# / Reactants^# K = [C]^c[D]^d / [A]^a[B]^b ```
37
Is there a relationship between rate of reaction and equilibrium constant (k)?
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
Hydrolysis
Break apart
39
Synthesis
Build
40
How many AA's are there?
20
41
Components of AA
1) Alpha carbon (wants 4 bonds) 2) Alpha Amino 3) Alpha Carboxyl 4) alpha hydrogen
42
Aromatic R-groups with ascending size
Phenylalanine: Phe, F Tyrosine: Tyr, Y Tryptophan: Trp, W
43
Non-polar, Aliphatic, R-groups | Hydrophobic
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
Polar, uncharged, R-groups
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
Electrically Charged R-groups
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
Charged side chains at pH 7
``` Dragons Eat Knights Riding Horses Glu and Asp (pKa <5) Lys (pKa ~10) Arg (pKa ~13) His (pKa ~6.5) ```
47
Hydrogen bonders
Hydrogen ST. North. QWY H.ST.N.QWY Ser, Thr, His, Asn, Gln, Tyr, Trp
48
Proteins are (2)
1) Linear polymers of amino acids | 2) linked by peptide bonds.
49
AA writing convention
5' -> 3' | N-terminus --> C-terminus
50
Disulphide bonds
- 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
Fibrous Protein
* 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
Globular Protein
* Polypeptide folds into a roughly spherical shape e.g. hemoglobin * Most non‐covalent bonds are within one polypeptide chain * Most proteins are globular
53
Secondary Structure (2)
Hydrogen bonding between peptide bond atoms results in two main structures: 1) alpha-helix 2) beta (pleated) sheet
54
Is a-helix a left handed or right handed helix?
Right handed
55
Examples of a-helixes (3)
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
Keratin
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
Collagen
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
Protein Domain
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
Native Structure
1) Present under physiological conditions 2) biologically active structure 3) Stabilized by many non‐covalent bonds
60
Protein Denaturation
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
Are disulphide bonds (S-S) broken by increased temperature and pH change?
No. S-S bonds are broken by reducing agents such as 1) b‐mercaptoethanol 2) dithiothreitol.
62
Protein folding in cells is often assisted by interaction with other proteins called:
Chaperones
63
BSE (Bovine Spongiform Encephalitis)
- 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
General Globular Protein Architecture (5)
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
Myoglobin
Stores O2 in muscles
66
Catalysts (3)
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
Oxidoreductases
One compound oxidizes a second one. | Oxidation & reduction.
68
Hydrolases
A compound is split into two products.
69
Lyases
A compound is split into two products, but | not by hydrolysis.
70
(Isomer)ases
A compound is rearranged by moving one | part of the molecule to another place.
71
Ligases
Two compounds are joined together
72
Transferases
Part of one compound is transferred to a | second one.
73
Examples of Transerases (1)
1) Kinase
74
Example of Hydrolase (1)
(1) Trypsin
75
General reaction of enzymes
E + S ES --> E + P
76
Induced Fit Model
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
Vmax
the maximum velocity Vmax at high (“saturating”) substrate concentrations.
78
Km
The Michaelis constant is the substrate concentration for which the velocity is half maximal.
79
Michaelis Mentis Kinetics Equation
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
How do enzymes lower Ea
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
Some enzymes require a _____ to function
co-enzyme
82
Co-enzymes can be (2)
1) metal ion (mg, fe, zn, k) | 2) small organic molecules (vitamins)
83
Apoenzyme.
An enzyme that is missing its coenzyme
84
Haloenzyme
Apoenzyme + Coenzyme = Haloenzyme
85
Inhibitor
A compound that decreases the rate of an | enzyme‐catalysed reaction
86
Competitive inhibitors
- 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
Km of an inhibitor is:
1/Km
88
Efficacy of HIV and Anti-influenza drugs are limited by (3)
1) Side effects 2) Bioavailability 3) Resistance

BIOC1011 Molecular Basis of Life (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions