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BIOL 311: Biochemistry I > Proteins (4), Carbohydrates (6/8), and Lipids (9) > Flashcards

Proteins (4), Carbohydrates (6/8), and Lipids (9) Flashcards

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1
Q

Enzymes

A

Catalysts involved in biochemical reactions. Increase the rate of reaction without being consumed.

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2
Q

Substrates

A

Molecule that acts as the reactant in an enzymatic catalyzed reaction. Binds to the enzyme at the active site.

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3
Q

Active Site

A

The location where the enzyme binds to on the substrate which allows catalysis to occur.

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4
Q

Lock and Key model

A

Only the correct substrate will fit to he active site on the enzyme.

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5
Q

Induced Fit

A

Interaction of the substrate and enzyme helps form the active site.

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6
Q

Enzyme Classification: Oxidoreductases

A

Catalyze reactions involving the gain or loss of electrons.

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7
Q

Enzyme Classification: Transferases

A

Transfers one group to another

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8
Q

Enzyme Classification: Hydrolases

A

Cleave a bond with water

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9
Q

Enzyme Classification: lysases

A

Break double bond with other means than oxidation and hydrolysis.

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10
Q

Enzyme Classification: Isomerases

A

Rearrangement of the molecule.

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11
Q

Enzyme Classification: Ligases

A

Join two molecules.

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12
Q

The two assumptions of Michaelis-Menten Constant

A
  1. k2 is much slower than k-1, as this allows for the establishment of an equilibrium at the ES complex.
  2. The ES complex forms rapidly and exists at a relatively unchanging concentration as the reaction proceeds until substrates is depleted.
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13
Q

Vmax

A

Theoretical maximal velocity for a given concentration of enzyme.

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14
Q

KM

A

Michaelis Constant: measures binding affinity of the ES complex.

  • Higher KM means lower affinity
  • Lower KM means higher affinity

KM = (k-1 + k2) / k1

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15
Q

Michaelis-Menten Equation

A

vo = Vmax [S] / KM + [S]

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16
Q

Lineweaver-Burke Plot

A

1/vo = (KM/Vmax)*1/[S] + 1/Vmax

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17
Q

kcat

A

Turnover Number: number of reactions the enzyme can catalyze per unit of time. Measures catalytic efficiency.

kcat = Vmax / [E]tot

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18
Q

Diffusion Controlled Limit

A

Occurrence when rate-limiting step becomes the diffusion of enzyme and substrate together.

Rate must be between 10^8 and 10^9 M-1 sec-1.

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19
Q

Suicide Inhibitors

A

Covalently modifies the actives site of the enzyme, irreversibly block its function. Directly poisons the enzyme.

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20
Q

Competitive Inhibitors

A

Recognize molecules similar to the shape of the substrate that binds to the active site which competes directly with the substrates. Can be overcome with substrate concentration is high.

vo = Vmax * [S] / KM*a + [S]

a = 1 + [I] / KI

Dissociation Constant KI = [E][I] / [EI]

Increase KM and Vmax remains the same.

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21
Q

Uncompetitive Inhibitors

A

Binds to the ES complex

vo = Vmax * [S] / KM + [S]*a’

a’ = 1 + [I] / KI’

KI’ = [ES][I] / [ESI]

Decrease KM and Decrease Vmax.

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22
Q

Mixed Inhibitors

A

A combination of competitive and uncompetitive inhibitors.

vo = Vmax * [S] / KMa +[S]*a’

Decrease or Increase KM and Decrease Vmax.

Note: If a = a’, the line will intersect on the x-intercept with different Vmax but same KM. This is known as the non-competitive or pure mixed inhibition.

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23
Q

General Principles of Enzyme Catalyzed Reactions

A
  • Enzymes bind to substrates with various weak forces (Van Der Waal, Ionic Bonding, Hydrogen Bonding, Dipole-Dipole Interaction) and entropy (delta S) decreases.
  • Enzyme binds to substrates with large number of weak forces known as electrostatic catalysis (sum total of the weak forces acting on the substrate).
  • In induced fit, enzyme bind substrates that favours the transition state.
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24
Q

Types of Catalysis: General acid-base catalysis

A

Amino acid side chains donate or accept protons. Polar and charged amino acids are important.

For example: Lysozyme (Glu and Asp)

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25
Types of Catalysis: Metal ion catalysis
Active site metal ion can act as a redox active center. Site can also act as a Lewis base or acid. For example: Anhydrase
26
Types of Catalysis: Covalent catalysis
Nucleophilic or electrophilic attack on an atom which results in a covalent intermediate. Involves Ser, Asp, Lys, Tyr, Cys, and other cofactors. For example: Chymotrypsin (catalytic triad: Asp, Ser, His) and Chmotrypsinogen, the inactive form.
27
Proteases
Enzyme that degrades proteins. Many have Trypsin fold which are structures comprised of two Beta barrel domains, the active site being at the interface.
28
Affinity Labeling
Technique used to specifically label residues on the active site. Label only one amino acid residue, suggesting that the label amino acid is not the same as other amino acid residues.
29
Enzyme Regulation: Covalent modification -) Proteolytic cleavage
An inactive enzyme becomes active through cleavage or digestion of proteins and peptides (Irreversible) For example: Chymotrypsinogen (an inactive form) is activated by proteolytic cleavage to Chymotrysin
30
Enzyme Regulation: Covalent modification -) Phosphorylation
A form of protein activation, facilitated by protein kinases which add phosphate groups to the hydroxyl groups of serine, threonine, or tyrosine. Phosphatase remove phosphate groups. The regulation occurs through a series of singling steps termed a signalling cascade. (Reversible) For example: Src
31
Enzyme Regulation: Allosteric Regulation
Increases and decreases the enzymatic activity by binding at a site other than the active site. Most rapid and most direct form of regulation. Relaxed and Tense.
32
Monosaccharides Classifications
1. Number of carbon 2. Aldehyde vs Ketone 3. Based on stereochemistry on penultimate carbon. D-isomer if hydroxyl on the right and L-isomer if hydroxyl on the left.
33
Furanoses
5 Chair Conformation
34
Pyranoses
6 Chair Conformation
35
Epimer
Conformation when carbohydrates differ at one sterocenter
36
Anomeric Carbon
Former carbonyl carbon (C-1 or C-2) a - OH on bottom face of the ring B- OH on top face of the ring
37
Penultimate Carbon
Chiral carbon furthest away from the carbonyl besides the achiral carbon (C-5)
38
Mutarotation
Converting from numeric form to the other (a to B or B to a)
39
Haworth Projections
Monosaccharide in their cyclic form
40
Chemically modified: Amino sugars
Hydroxyls group can be replaced by amine
41
Chemically modified: Acylation
Addition of acyl group [R - C =O] ie: amine to amide
42
Chemically modified: Sugar alcohols
Carbonyl group is reduced to alcohols which makes it impossible for sugar alcohol to form a cyclic structure.
43
Chemically modified: Sugar acid
Monosaccharide can be oxidized, producing carboxylic acid modification.
44
Chemically modified: Deoxy sugars
Removal of hydroxyl on one or more carbons of a monosaccharide.
45
Monosaccharide
Glucose Galactose Fructose
46
Disaccharide
Reducing Disaccharide contains aldehyde and ketone Galactose + Glucose = Lactose (B-1,4 linkage) Glucose + Fructose = Sucrose (a,B-1,2 linkage) Glucose + Glucose = Maltose (a-1,4 linkage)
47
Raffinose
- Energy storage - Trisaccharide - Made up of glucose, galactose, and fructose - Galactose in an a-1,6 linkage to a sucrose
48
Inulin
- Energy storage - Oligosaccharide - Made up of fructose with glucose caps
49
Polysaccharide: Amylose
- Energy storage - Made up of several thousands glucose monomers - a-1,4 linkage
50
Polysaccharide: Amylopectin
- Energy storage - Made up of thousands to hundred thousands of glucose polymers - a-1,4 linkage with a-1,6 linkage branched point at every 24-30 residues
51
Polysaccharide: Glycogen
- Energy storage - Made up of ten thousands glucose polymers - a-1-4 linkage with high a-1,6 branched linkage every 6-12 residues
52
Polysaccharide: Starch
- Plant Energy storage - Similar to Glycogen
53
Polysaccharide: Cellulose
- Structural - Linear polymers of hundreds to thousands glucose monomers - B-1,4 linkage
54
Polysaccharide: Chitin
- Structural - B-1,4 linkage of N-Acetylglucosamine
55
Polysaccharide: Alginate
- Structural - Copolymer of mannose and glucaronate
56
Energy Storage polysaccharide
- Can be linear or branching - Typically has a a-1,6 linkage (branching)
57
Structure polysaccharide
- Linear for structural purposes - Typically has a B-1,4 linkage (linear)
58
The 3 control points in glycolysis
Step 1, 3, and 10 (committed irreversible steps) Note: step 3 is considered the first committed stage as step 1 can lead to other pathway
59
Input and Output of Glycolysis
Input: 2 ATP, Glucose, 1 NAD+ Output: 4 ATP total (2 Net), 2 Pyruvate, 1 NADH
60
The 2 control points in glucogenesis
Step 1 and 2
61
Fatty Acids
- Amphipathic - Even number of carbon atoms - Insulate and cushion vitals - Components of neutral lipids, phospholipids, and eicosanoids - Generally found as esters and amides (as it is more stable)
62
Saturated Fatty Acids
- Do not contain double bond - Solid at room temperature - Unhealthy
63
Unsaturated Fatty Acids
- Contain double bond - Liquid at room temperature - Monounsaturated: only one double bond - Polyunsaturated: has multiple double bond - Cis (same direction): Naturally occurring fatty acids - Trans (different direction): Hydrogenated fatty acids
64
18:1 delta 9 (w9)
- 18 number of carbons - 1 number of double bonds - 9 the position of the double bond from the carboxylic acid end - w9 the position of unsaturated bond from the omega end (away from carboxylic acid)
65
Neutral Lipids
Classification of fatty acids that do have a charged groups as the carboxylic acid is esterified to either glycerol or cholesterol. Allows for safe storage due to the detergent nature of charged groups.
66
Triglycerides
- How we store lipids - Unsaturated acid in a triacylglycerol (TAG) is attached to the carbon 2 in the glycerol - TAG rarely repeats a fatty acid - To mobilize TAGs, we require cholesterol
67
Cholesterol Esters
- Fatty acids esterified to cholesterol - Can be stored in the body as a cholesterol reserve
68
Steroids
- Groups of lipids with diverse functions but a common skeleton consisting of four fused rings - Made from cholesterol
69
Cholesterol
- Maintains membrane fluidity - Transport across the membrane - Diffusion of proteins within the membrane - Membrane integrity
70
Bile Salt
Detergents synthesized from cholesterol by the liver and stored in the gall bladder.
71
Waxes
Hydrophobic, long-chain fatty acids esterified to a long chain alcohol
72
Micelle
Spherical sphere composed of aggregates of fatty acids at high concentration Illustration of hydrophobic effect
73
Phospholipids
Amphipathic lipid molecules which makes up the main structural components of membranes. Divided into: glycerophosholipids and sphingolipids
74
Glycerophosholipids
Lipid containing glycerol head, two fatty acyl chain, and a phosphoalcohol
75
Sphingolipids
Lipid containing one fatty acyl chain and a spingosome backbone and a phosphoalcohol.
76
Eicosanoids
Molecules derived from 20 carbon polyunsaturated fatty acids - Signalling molecules - Regulating functions such as blood pressure, pain, inflammation, and labour/deliver.

BIOL 311: Biochemistry I (1 decks)

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