Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOC 202 > MT 1 > Flashcards

MT 1 Flashcards

1
Q

Biochemistry

A

The chemical substances and vital processes occurring in a living organism

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

Cellular metabolism (aka chemical rxns in a cell)

Lite’s wiring diagram → dots biomolecules

Biomolecule: organic compound normally present as an essential compound of living organisms

This figure looks complex because all of the pathways are connected

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

List the types of biomolecules

A
  1. Carbohydrates (sugars)
  2. Lipids
  3. Proteins
  4. Nucleic acids
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Carbohydrates (sugars) Functions

A

Energy and energy storage (glucose & glycogen)

Cell recognition (glycosylation)

Structural (ie. in plants, cellulose)

Component of DNA (deoxyribose) and RNA (ribose)

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

Lipids functions

A

Energy and energy storage (triglycerides [TG], fats, fatty acids)

Structures/barrier (ie. membranes)

Signalling (steroid hormones)

Insulation (blubber)

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

Proteins functions

A

Catalysis (enzymes: lactase, alcohol dehydrogenase)

Signalling (hedgehog, ubiquitin, insulin)

Structure (collagen, histone)

Transport (membrane transporters, hemoglobin, LDL)

Defense (antibodies)

Storage (ferritin)

Movement (actin/myosin)

Synthesis (protein, DNA synthesis)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Nucleic acids functions

A

Information (DNA/RNA)

Energy (ATP, GTP)

Transport (tRNAs) ← beyond scope of the course

Catalysis (ribosomes)

Components of cofactors (NAD, FAD)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Most biomolecules are composed of…

A

Carbon

Hydrogen

Oxygen

Nitrogen

Phosphorus (nucleic acid & ATP/GTP)

Sulfur

Others too!

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

We study how biomolecules […].

These […] in biomolecules are known as […].

A

We study how biomolecules interact with each other and themselves. These interactions between elements in biomolecules are known as bonding.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

List the types of bonding

A
  1. Covalent bonds
  2. Ionic bonds
  3. Hydrogen bonds
  4. Van der Waal interactions
  5. Hydrophobic interactions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Covalent bonds

A

Sharing of electrons between 2 adjacent atoms

Drawn as solid lines

High energy

Not easily reversible (stable)

Relatively shorter (smaller bond length)

Bind together elements in biomolecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Geometry of carbon bonding

A

When carbon has 4 single bonds, it adapts tetrahedral structure, with bonds between carbons at 109 degrees with free rotation around each bond.

When carbon has a double bond, with trigonal (flat) planar structure with 120 degree angle → single bonds in same plane → 1 double bond, 2 single bonds

Triple bonds not important for biomolecules

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

Ionic bonds

A

Interaction of two charged atoms/particles

Described by Coulomb’s law: F = q1q2/E*r2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is E in Coulomb’s law?

A

E is dielectric constant; takes into account medium where interaction takes place. H2O has the highest dielectric constant, thus lowering the force of interaction. Electrostatic interactions determine helical structure of DNA

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

Hydrogen bonds

A

Definition: Hydrogen atom that is partially charged by electronegative atom

H-bond requires H-donor (with H-covalently bound to it) and H-acceptor (which has a lone pair of e-).

Both hydrogen acceptors and donors are usually oxygen and nitrogen (sometimes sulfur)

It is based on electrostatic interaction; electronegative donor tends to pull e- away from hydrogen. As a result, donor becomes partly negative and hydrogen becomes partly positive

Hydrogen bonds are weak (4-15 kjol/mole) and longer (relative to covalent or ionic)

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

Van der Waals Interactions

A

Attraction of two molecules

At any given time, charge distribution around an atom is not symmetric

This asymmetry causes complimentary asymmetry on other atoms, leading to attraction

Has small energy

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

If the atoms get too close, they repel

There is a “sweet spot”

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

Water in biochemistry

A

Almost all reactions in the body happen in aqueous solution

H2O has a huge effect on reactions

H2O molecule is bent and can form multiple H-bonds

H2O molecules form H-bonds with each other

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Based on water solubility, biomolecules can be divided into 3 groups. List them.

A

Hydrophilic, hydrophobic, amphipathic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Hydrophilic

A

Water soluble

Polar or charged (ie. NaCl)

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

Hydrophobic

A

Not soluble in water (ie. fats, oils)

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

Amphipathic

A

Molecules that containboth hydrophilic and hydrophobic parts (ie. tryptophan, tyrosine, lysine, methionine)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Very often, water needs to be […] to allow various […] to occur because […].

A

Very often, water needs to be excluded or manipulated to allow various electrostatic interactions to occur (ie. catalyst)

Water will disrupt hydrogen bonding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

The Laws of Thermodynamics

A
  1. Total energy of a system and its surroundings is constant. In other words, you don’t create or destroy energy; you can only change its form
  2. Total entropy (S=entropy=measure of randomness) of a system and its surroundings always increases for a spontaneous process. But entropy can decrease locally (ie. complimentary strands of DNA) but heat will be released, so 2nd law is still true.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Gibb’s Free Energy Equation and implications of ∆G, ∆H, ∆S

A

∆Gsys = ∆H - T∆Ssys

Where:

∆G = Gibb’s free energy (kJ/mole)

T = Temperature in K

If ∆G < 0, the reaction is spontaneous (exergonic)

If ∆G > 0, the reaction is non-spontaneous (endergonic)

∆H < 0, the reaction releases heat => ∆G is more negative => more spontaneous

∆S > 0 => more disorganized => ∆G is more negative => more spontaneous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What drives hydrophobic interactions?

A

When a non-polar molecule is added to H2O, the water molecules are forced into a shell. This lowers entropy. However, with time, non-polar molecules come together and H2O molecules form a shell only at the edge, and entropy increases.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

pH, buffers, Kw

A

Many biomolecules can act as weak acids and bases

Behaviour of biomolecules depends on ionization state, which is determined by pH

Because pH is important, it must be maintained at a certain level with buffers.

pH: A measure of concentration of H+ in solution

Buffer: A mixture of weak acid and conjugate base. It resists changes in pH. Buffering region is usually 1 pH unit on either side of pKa.

pH = -log[H+]

Scale = 0-14, where 0 is a strong acid and 14 is a strong base

H2O ⇌ H+ + OH-

Kw = ionization constant = 1 * 10-14

Kw = [H+][OH-]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Weak acid and bases review, Ka and pKa

A

Weak acids and bases don’t fully ionize in solution

CH3OOH ⇌ CH3OO- + H+

Ka = [A-][H+] / [HA] = [CH3OO-][H+] / [CH3OOH]

pKa = -log[Ka]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Henderson-Haselbach equation

A

If we titrate a weak acid with a strong base (NaOH), we can calculate pH using Henderson-Haselbach equation

pH = pKa + log[A- / HA]

If pH = pKa, [HA] = [A-]

If pH < pKa, [HA] > [A-]

If pH > pKa, [HA] < [A-]

There is a region where pH doesn’t change much => buffering region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

List the Three Key Buffers in Biological Systems

A
  1. Carbonate/Bicarbonate Buffer
  2. Phosphate Buffer
  3. Histidine and cysteine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Carbonate/Bicarbonate Buffer

A

CO2(dissolved) + H2O ⇌ H2CO3 (carbonic acid) ⇌ H+ + HCO3- (bicarbonate ion)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Phosphate Buffer

A

H2PO4- (dihydrogen phosphate ion) ⇌ H+ + HPO42- (monohydrogen phosphate ion)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Proteins

A

Linear polymers built out of α-amino acids (αα)

Proteins final 3D shape and function depends on its sequence of αα

Each αα has different functional groups, allowing for massive diversity

Proteins can be flexible or rigid

Proteins can interact with each other

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Amino Acids

A

Contain central carbon (α-carbon), attached to amino group, carboxylic acid group, hydrogen atom, and unique side chain (R)

Note: α-carbon is chiral

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Chiral center/Enantiomers/L vs D

A

Chiral center: Atom with its substituents arranged so that the molecule is NOT superimpossible on its mirror image

This means that there are 2 enantiomers for each amino acid (except glycine)

Enantiomer: pair of molecules, each with one or more chiral centre that are mirror images of each other

If the amino group is on the left, it is in the L-form (otherwise D-form)

In biological systems, only L-aa’s exist in proteins and all living things

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

At pH = 7, all amino acids exist in _______

A

At pH = 7, all aa’s exist in zwitterion

Zwitterion: ion with both (+) and (-) charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What determines amino acids variability?

A

The side chains (R roups)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Glycine

A

Gly, G

No chiral carbon

Technically, not really hydrophobic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Isoleucine

A

Aliphatic

Has a second chiral center

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Methionine

A

Aliphatic

Contains thio-ether (-S-C) group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Proline

A

Contains a ring; changes 3D structure of amino acid

Still aliphatic

Twist in side chain; ring structure makes it more rigid/more restrained

Often introduces kinks in amino acid polypeptide chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Nonpolar, aliphatic amino acids

A

Aliphatic: Open chain structure (alkanes)

  1. Glycine, Gly, G
  2. Alanine, Ala, A
  3. Valine, Val, V
  4. Leucine, Leu, L
  5. Isoleucine, Ile, I
  6. Methionine, Met, M
  7. Proline, Pro, P

All of these are hydrophobic, often found in the center of a protein or in memebrane crossing domain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Aromatic Amino Acids

A

Contains aromatic group (phenyl ring)

Participates in hydrophobic interactions

  1. Phenylalanine, Phe, F
  2. Tyrosine, Tyr, Y
  3. Typtophan, Trp, W
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Tyrosine

A

Aromatic

Is like phenylalanine but has -OH, therefore making it more reactive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Basic amino acids

A

Positively charged

  1. Lysine, Lys, K
  2. Arginine, Arg, R
  3. Histidine, His, H

Charged, so found on the surface of proteins (interacts with water)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

Lysine

A

Basic amino acid; has an amino group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

Arginine

A

Basic amino acid; guanidinium group; side chains are positively charged at pH = 7 (pKa of the side chain is greater than 10)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

Histidine

A

Typically considered a basic amino acid

Has ionizable group with pKa ~6

That means that it can be charged or uncharged depending on its location

Often found in active site of enzymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Acidic amino acids

A

Negatively charged at pH = 7 (pKa < 4)

Contains carboxylic group

  1. Aspartate, Asp, D
  2. Glutamate, Glu, E

Charged, so found on the surface or proteins (interacts with water)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Polar amino acids

A

Not charged

Can form H-bonds (hydrophilic)

  1. Serine, Ser, S
  2. Threonine, Thr, T
  3. Cysteine, Cys, C
  4. Asparagine, Asn, N
  5. Glutamine, Glu, Q
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Serine

A

Polar amino acid

Contains hydroxy group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Hydroxy group

A

R-OH functional group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Threonine

A

Polar amino acid

Contains hydroxy group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

Cysteine

A

Polar amino acid

Contains sulfhydryl group (thiol group, -SH)

Can form disulfide bonds with another cysteine in the same chain or another. For example, insulin has 3 disulfide bridges.

Can form H-bonds, but they’re weak.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Asparagine

A

Polar amino acid

Derivative of aspartate

Contains carboxyamide instead of carboxyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

Glutamine

A

Polar amino acid

Contains carboxamide instead of carboxyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

pKa value of amino acids depend on ______

A

pKa value of amino acids depend on the environment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

Primary structure

A

Linear sequence of amino acids linked by peptide bonds to form a protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

Peptide bond

A

linkage of alpha-carboxyl of one amino acid to the alpha-amino group of another amino acid, with the loss of water

Not energetically favourable to form, but once formed, it is stable (requires energy to be made)

Peptide bond has double bond characteristics because of resonance between the peptide bond and the carbonyl; as a result, it is planar

There is no free rotation about hte peptide bond

Because of steric hindrance, almost all peptide bonds are in trans-configuration (R-groups of opposite sides of the plane) except X-Proline (both cis and trans occur, but trans is preferred)

The peptide bond is conformationally restrained, but the bonds between N-Cα and Cα-C=O are single and free to rotate; thus, polypeptides are flexible

60
Q

Polypeptide

A

A series of amino acids linked by peptide bonds

Has polarity; amino group is on the left and the free carboxylic group is on the right

Consist of repeated backbone with variable side chains

All carbonyl and amino groups in the backbone can H-bond (w/ the exception of proline); has an important role in 3D structure

61
Q

Write the single letter code sequence of this polypeptide

A

SGYAL

62
Q

Draw the polypeptide: SGYAL

A
63
Q

Draw the formation of a peptide bond

A
64
Q

Draw the formation of a disulfide bridge

A
65
Q

Dihedral angle

A

The amount of rotation; the angle between planes through two sets of three atoms

Ranges from -180° to 180°

N-Cα is called Φ (phi)

Cα -C=O is called Ψ (psi)

N-C=O is the peptide bond… no free rotation

In reality, not all combinations of Φ and Ψ are allowed, because of steric hindrance that limits the number of structures a protein can adopt

66
Q
A

Ramachandran plot

Shows the combinations of Φ and Ψ that are allowed

Areas of dark = favourable

Areas of light = borderline

Areas of white = not allowed

Each plot is for a particular amino acid; proline and glycine would have Ramachaundron plots that look very different from the other amino acids.

67
Q

Proteins have a series of […] on what […] they can adopt. They can foten hold into […] […] structure in […] conditions.

A

Proteins have a series of limitations on what orientations they can adopt. They can often hold into a single structure in physiological conditions.

68
Q

Why is knowing primary structure important?

A
  1. Determine 3D shape
  2. Understand function
  3. Understand dsease (ie. replacing a positiv AA with a negative AA is bad!)
  4. Understand evolutionary history
69
Q

Secondary structure

A

The spatial arrangement of amino acid residues that are relatively close to each other in linear sequence of polypeptide chain (alpha helices, beta sheets)

70
Q

Alpha helix

A

Polypeptide backbond forms the inner part of a right handed helix, with the side chans sticking outwards. It is stabilized by hydrogen bonds between NH and carbonyl (C=O) of the backbone

The C=O (i) forms H-bond with N-H (i+4) — he specifically said we need to know this

Has ideal dihedral angles of Φ = -60° and Ψ = -45°

All NH and C=O in the backbone are hydrogen bonded

Each aa in the a-helix increases the helix by 1.5Å (angstroms)

Proline/Glycine are the worst for alpha helix

R-groups in i+3 and i+4 are close to i

a-helix is right-handed; left-handed in possible but not stable due to steric hindrance

a-helical content vary in proteins (sometimes high, sometimes low)

Keratin consists of 2 intertwined helices

a-helix is shown as ribbons or rods in protein structures

71
Q

Antiparallel beta sheet

A

Two or more B-strands associated as a stack of chains in an extended zigzag; form stabilized by interstrand H-bond

Each aa extends B-strand by 35Å

The N-H and C=O of residue “i” in one B-strand from H-bond to a single residue “j” in the other B-strand

Φ= -139° and Ψ= +135°

72
Q

Parallel beta sheet

A

N-H of residue i of one strand forms H-bond with C=O of j in another strand, but C=O of i forms H-bond with N-H of j+2 residue in another strand

This makes strand shorter (3.25Å per residue)

Φ = -119° and Ψ= +113°

73
Q

Draw where the hydrogen bonds would form within an a-helix.

A
74
Q
A
75
Q

Is this antiparallel or parallel?

A

Antiparallel

76
Q

Is this antiparallel or parallel?

A

parallel

77
Q

Draw the hydrogen bonds on this beta sheet and state the Å

A
78
Q

Draw the hydrogen bonds and label the Å

A
79
Q

How are beta sheets depicted?

A

broad arrows pointing to C-terminus

80
Q

Turns and loops

A

Peptide chains reverse direction

Accomplished by B-turn (common) or by larger loops (no common structure)

81
Q

What is this?

A

A beta barrel – a transmembrane protein

82
Q

Tertiary structure

A

The spatial arrangement of aa residues that are far apart from each other in linear sequence as well as the pattern of disulfide bonds

Unique for every protein

83
Q

What is this? Describe it.

A

Myoglobin

153 amino acids, relatively small

Largely a-helices (70%)

Globular

Few voids (unorganized chain)

In red = heme (protoporphyrin ring) = where oxygen binds

Surface contour

Yellow = hydrophobic amino acids; mostly in protein core

Polar amino acids on the outside

84
Q

What is this? Describe it.

A

Troponin C

Ca2+ binding proteins

2 domains - parts of protein with defined function

85
Q

Quarternary structure

A

The spatial arrangement of multiple subunits (polypeptides) and their interaction

Some proteins are composed of more than one polypeptide chain (multimers) in order to function

86
Q

What is this? Describe it.

A

Hemoglobin; Hb

O2 transporter in blood of mammals

4 subunits: 2 alpha + 2 beta

Hb cannot function unless it forms tetramer (4 peptides)

87
Q

What is this? Describe it.

A

Minute virus of mice

9 VP1 + 51 VP2 = viral capside (quarternary structure)

Large enough to fit DNA

88
Q

Three examples of quarternary structures

A
  1. Proteasome
  2. Spliceosome
  3. Ribosomes (+ RNA)
89
Q

In nature, polypeptides […] folds into one structure in seconds.

A

USUALLY, NOT ALWAYS

90
Q

How do we predict the final 3D conformation?

A

We cannot predict the final 3D conformation using primary structure. RIP.

91
Q

What do we know about protein folding, if we can’t predict the final 3D conformation then?!

A

What we do know:

Folding is driven by thermodyanmics: finding the most stable complex (most negative ∆G), but the difference between folded and unfolded protein is small (~20-60 kJ/mole)

Driven mostly by entropy (ie. the hydrophobic side chains are going to be exluded from water in the core, while polar amino acids are at the surface)

In order to fold, hydrogen bonds must form

Unpaired charged or polar groups will destabilize structures.

What can we do?

Though we cannot predict final 3D structures, we can predict secondary structures.

Certain amino acid residues are more likely to form a-helix or B-sheets

A, L, K, M form stable a-helix

Proline and glycine destabilize a-helix

P doesn’t have H and it is rigid (steric hindrance)

G is too flexible

However, even peptides with the same sequence can adopt different secondary structure in different proteins

Folding is usually an all-or-none process (either folded or misfolded/unfolded)

Folding is cooperative (if one portion of the protein folds, it will influence how another portion of the same protein folds)

We usually visualize protein folding as a free energy funnel

Normal tertiary structure = native structure = functional protein

In a protein’s unfolded state, there are many possible structures with high free enrgy, but as a series of folding happens, free energy decreases with every structure formed. The number of possible conformations decrease until you reach the native (folded) state

Note: Not all proteins have one single conformation

Some might only form a final structure when bound to a substrate or regulator; some exist in equilibrium between two different structures

92
Q

What are the three ways to determine the final 3D structure of proteins?

A

Cryoelectron microscope: uses a beam of electrons to image many, many native proteins

X-ray crystallography: measure e- density (ie. myoglobin)

NMR (nuclear magnetic resonance): measures the location of nuclei

93
Q

Posttranslational modifications

A

Modifications to proteins after it has been synthesized

  1. Phosphorylation - adding phosphate to amino acids with -OH (ie. Ser, Tyr, Thr); ie. signal transduction to activate or deactivate proteins
  2. Glycosylation - addition of sugars to a residue (usually Asn and Ser); ie. cell recognition (immune system); ie. glycoprotein
  3. Hydroxylation - usually protein (hydroxyproline); ie. collagen - triple helix
  4. Carboxylation - addition of a carboxyl group; glutamate (ie. blood and clotting)
  5. Acetylation - addition of acetyl group; lysine - regulation of gene expression (epigenetics)
  6. Proteins can be trimmed (ie. trypsinogen –> trypsin)
94
Q

Label these posttranslational modifications

A
  1. Hydroxylation
  2. Carboxylation
  3. Glycosylation
  4. Phosphorylation
95
Q

Enzyme

A

Biological macromolecule that acts as a catalyst for biochemical rxns. Usually proteins.

96
Q

Catalyst

A

Chemical that increases the rate of rxn without being consumed

97
Q

Kcat

A

of molecules of substrate converted to product per molecule of enzyme per second

98
Q

Specificity

A

Enzymes are very specific; they will catalyze only one specific reaction or a set of rxns

Specificity is based on a series of weak interactions between substrate and enzyme, especially in the active site

The shape of the enzyme determines specificity and function

99
Q

Trypsin

A

Digestive enzyme

Cleaves peptide bond on the carboxyl side of Lys or Arg

100
Q

Papain

A

Cleaves any peptide bond

101
Q

Thrombin

A

Involved in blood clotting

Cleaves Arg (or Gly) peptide bonds

102
Q

What digestive enzyme is this?

A

Trypsin

103
Q

What digestive enzyme is this?

A

Thrombin

104
Q

Active site

A

Region of an enzyme that binds the substrate. It contains the residues that directly participate in the rxn. The nonaxtive site residues are important for structure of the protein or regulation of enzyme (ie. phosphorylation/inhibitors)

105
Q

Characteristics of an active site

A
  1. They are clefts in the enzyme made up by residues from all over the primary structure
  2. Takes up a small volume of an enzyme
  3. Water is usually manipulated or excluded from an active site

– This changes the behaviour of the resiudes

  1. Substrate is bound by weak interactions in active site
  2. There is a partial complimentarity between substrate and active site
106
Q

Models for how substrates may bind in the active site of an enzyme

A
  1. Lock and Key
    - Active site is complimentary to match to a substrate
  2. Induced Fit
    - Binding of a substrate causes the active site to assume a matching shape
107
Q

Cofactors

A

Enzymes may require cofactors in order to function

Cofactor: inorganic ion or small organic compound required for enzyme activity

108
Q

Cofactor vs Coenzyme

A

Cofactor - only inorganic ions (ie. Mg2+)

Coenzyme - organic compounds (ie. FAD)

109
Q

Prosthetic group

A

Cofactor that is tightly bound to an enzyme (heme in myoglobin)

110
Q

Apoenzyme

A

Enzyme that requires a coenzyme but doesn’t have the cofactor (no function)

111
Q

Holoenzyme

A

Enzyme that requires a cofactor and has the cofactor (functional)

112
Q

Ni2+

A

This is a cofactor that is found in tap water and needed for DNA synthesis

113
Q

Enzymes Thermodynamics

A
  1. Enzymes do not alter ∆G; they obey laws of thermodynamics; do not change how spontaneous rxn is
  2. Enzymes do not alter the final equilibrium of products to reactants
  3. Enzymes do speed up rxns; enzymes accelerate rxns by decreasing the activation energy (∆G‡) by facilitating the formation of the transition state (X‡​)

The energy needed to get to X‡​ is known as activation energy (∆G‡)

∆G‡s→​p = Gx‡ - Gs → forward rxn

∆G‡p→​s = Gx‡ - Gp → reverse rxn

Only a fraction of substrate (s) will have enough energy to form X‡

The activation energy cotnrols the rate (rate limiting step)

Activation energy is not a part of the ∆G of the rxn

∆G‡cat < ∆G‡uncat

This is how enzymes work:

S+E ⇌ ES ⇌ EP ⇌ E + P

Enzymes will interact with transition state such that the activation energy is lowered: the rxn will speed up as a greater fraction of S has energy to react (to convert to X‡)

114
Q

Where does the energy to lower ∆G‡​ come from?

A

It comes from the enzyme binding and stabilizing the transition state in the active site. Active site is most complimentary to X‡

115
Q

Binding energy

A

∆GB = binding energy

Defined as the energy derived from the non-covalent interactions between the enzyme and substrate

116
Q

How can we measure the rate of rxn for

A → P

A

We can measure the rate (or velocity) of this rxn as eithr disappearance of substrate A over time or the appearance of product (P) over time.

V = -∆A/∆t = ∆P/∆t (usually expressed as moles/unit of time)

If we measure the disappearance of A, then we can express the rate as directly related to [A]

V = k[A] k - rate constant (not an equilibrium constant!)

k = proportionality constant that relates to [S] at a specific temperature.

This is known as first order rxn and k has units of sec-1 or min-1

117
Q

Second order kinetics

2A → P

A + B → P

A

2A → P where v = k[A]2

A + B → P where v = k[A][B]

These 2nd order rxns usually have k as units of M-1sec-2 or M-1min-1 or moles-1sec-1

118
Q

Michaelis-Menten Kinetics

A

Series of tubes with fixed amount of enzyme, mixed with different amount of substrate. Then they measured the amount of product formed over time.

119
Q

Draw a graph of free energy G vs reaction coordinate for an exergonic reaction. Label reactants, products, activation barrier/transition state (‡), ∆G‡cat, ∆G‡uncat​ and ∆G

A
120
Q

Draw a graph of free energy G vs reaction coordinate. Label S (ground state), Transition State (‡), P (ground state), ∆G‡S→​P, ∆G‡P→​S, ∆G’°

A
121
Q

Draw a graph of free energy G vs reaction coordinate. Label S, P, ES, EP, transition states (‡), ∆G‡​uncat, ∆G‡​cat​, ∆Grxn​

A
122
Q

Who are these people?

A

Leoner Michaelis

Maud Menten

123
Q

Assumptions about enzyme kinetics

A
  1. We only examine early times in the rxn when [P] is low. We can ignore reverse rxn.

E + S ⇌ ES → P

  1. [S] >> [E], we can assume that [ES] doesn’t affect [S]
  2. A steady state exists such that the rate of [ES] formation = rate of [ES] consumption
124
Q

Caculating the initial velocity

A

We can calculate the initial velocty, V0 (initial rate, μM/time)

Based on an earlier assumption, we can describe how initial velocity depends on [S]

V0 = Vmax ([S]/([S}+Km))

[S] = concentration of substrate

V0 = initial velocity

Vmax = maximum velocity of rxn, when all the active sites are saturated with subtrate

KM = Michaelis constant; [substrate] at which the enzyme catalyzed rxn proceeds at 1/2 Vmax rate. It is a rate constant.

125
Q

Michaelis constant

A

KM = K-1 + K2 / K1

When [S] << KM => V0 = Vmax ([S]/KM)

[S] = KM => V0 = Vmax (KM/2KM) = 1/2 Vmax

[S] >> KM => V0 = Vmax ([S]/[S]) = Vmax

KM is an important characteristic of enzymes; it’s a rough estimate of affinity of the enzyme to its subtrate

KM high = affinity is low

KM ​low = affinity is high

It depends on the type of enzyme, pH, temperature, ionic strength

126
Q

Vmax

A

Maximum rate of enzyme

It will change with [enzyme]

127
Q

What is this called?

A

Lineweaver-Burk plot

128
Q

What is the x-intercept of the Linweaver-Burk plot?

A

-1/KM

129
Q

What is the y-intercept of the Lineweaver-Burk plot?

A

1/Vmax

130
Q

Do all enzymes follow Michaelis-Menten kinetics?

A

No.

131
Q

List the 4 types of enzyme inhibition

A
  1. Irreversible inhibition
  2. Competitive inhibition
  3. Non-competitive inhibition
  4. Uncompetitive inhibition
132
Q

Can KM and Vmax be used for comparing enzymes?

A

No, because they change depending on the concentration of enzyme used.

133
Q

How can we compare enzymes, if not with KM or Vmax ?

A

We can use Kcat !

134
Q

Kcat

A

The minimum amount of subtrate an enzyme can convert into product in a given time (min-1 or sec-1)

Kcat = Vmax/[E]T

[E]T = enzyme total concentration = [E] * # of active sites

Higher number = better / more efficient enzyme

135
Q

Specificity constant / Catalytic efficiency constant

A

Kcat / KM

sec-1M-1

136
Q

Label the axes, the slope, and the intersepts

A
137
Q

Irreversible inhibitor

A

AKA suicide inhibitor

Inhibitor stays boundt o enzyme for long periods (often forever). Usually covalently attached in active site => inhibitor blocks active site

138
Q

Competitive inhibitor

A
  • inhibitor binds to the active site and competes with the substrate for it
  • only one can bind at a time
  • Vmax doesn’t change but amount of subtrate needed to reach Vmax – as well as half of Vmax – is increased (KM increases)
  • Adding inhibitor increases KM but Vmax remains unchanged
  • Can be overcome by adding more subtrate
  • In a double-reciprocal plot, Y-intercept stays the same; X-intercept increases (KM increases, because -1/KMi > -1/KM => KMi > KM
139
Q

Non-competitive inhibitor

A
  • Inhibitor binds at a site other than the active site
  • Inhibitor doesn’t block active site (ie. substrate can bind to active site, but products are not formed)
  • can’t compete by adding more substrate
  • KM doesn’t change, but Vmax decreases
  • In effect, you are lowering the number of functional enzymes
  • In double-reciprocal plot: x-intecept is the same, but y-intercept is different (increases)
140
Q

Uncompetitive inhibitor

A
  • Inhibitor only binds to ES, forming ESI complex
  • Like non-competitive inhibition, this results in lower Vmax (lowering # of functional enzymes)
  • But it also decreases KM because as ES → ESI => [ES] ↓ ! This promotes increased substrate binding to enzyme, lowering KM
  • In the double reciprocal plot: both X and Y-intercepts change => parallel lines

– x-intercept decreases (moves left) and y-intercept increases (moves up)

141
Q

What type of inhibition is this?

A

Uncompetitive

142
Q

What type of inhibition is this?

A

Noncompetitive

143
Q

What type of inhibition is this?

A

Competitive

144
Q

Draw the line corresponding to competitive inhibition on this plot.

A
145
Q

Draw the line corresponding to noncompetitive inhibition on this plot.

A
146
Q

Draw the line corresponding to uncompetitive inhibition on this plot.

A

BIOC 202 (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions