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BIOC 202 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

Biochemistry

A

the study of chemical substances and the vital processes occurring in a living organism

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2
Q

~___ biomolecules within a cell

A

200

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3
Q

Biomolecule

A

an organic compound normally present as an essential component of living organisms

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4
Q

Types of Biomolecules

A
  1. Nucleic Acids
  2. lipids
  3. carbohydrates
  4. proteins
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5
Q

Nucleic Acids

A

informations storage (DNA/RNA)
Catalysis (ribozymes, ribosomes)
Energy transfer (ATP)
Components of cofactors such as NAD and FAD

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6
Q

lipids

A

Barriers (membranes)
Long term energy storage (fatty acids - triacyl glycerols)
Signaling (steroid hormones)
Insulation (blubber)

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7
Q

carbohydrates

A

Energy and energy storage (glucose, glycogen)
Cell recognition (glycosylation - sugars attached)
Structural (cellulose) (e.g. core of wood is sugar- but not able to break down)
Components of DNA and RNA (deoxyribose/ribose)

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8
Q

proteins

A

enzymes/catalysis (alcohol dehydrogenase)
Movement (actin & myosin)
Transport (hemoglobin)
Storage (ferritin)
Structural (keratin)
Defense (antibodies)
Regulation signaling/hormonal signaling (insulin - injected to retain protein structure)

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9
Q

Most biomolecules are composed of the following elements

A

carbon, nitrogen, oxygen, hydrogen

And elements to a Less extent: phosphorus and sulfur

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10
Q

biomolecules interact with each other and themselves by

A

bonding (different types of interactions) or molecular interactions

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11
Q

5 major types of interactions/bonding

A 
1. Covalent bonds
Noncovalent interactions:
2. Hydrophobic interactions
3. Van der Waals interactions
4. Ionic interaction
5. Hydrogen bonds
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12
Q

Covalent bonds

A

sharing of electrons between 2 adjacent atoms
short solid lines
Tend to be short
hard to break (strong)
Not easily reversible (stable)
High energy - small bond length
Resonance structures
CB bind atoms together to form biomolecules (e.g. adenine)
Can rotate above the single bonds (important for folding)

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13
Q

Geometry of carbon bonding with 4 single bonds

A

it adapts tetrahedral structure (109.5°) with free rotation about each bond

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14
Q

Geometry of carbon bonding with double bond

A

When carbon has a Double bond - adopts trigonal planar structure (120°) - no free rotation about double bond and a series of atoms are locked in a plane

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15
Q

Noncovalent interactions are all ____, meaning

A

electrostatic, meaning there are stationary or partial charges (allow for biomolecules to interact with each other and themselves -e.g. DNA structure, DNA replication, protein folding, and substrate folding)

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16
Q

_____ ______ of the phosphate groups in the DNA backbone

A

Electrostatic repulsion

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17
Q

Hydrogen bond

A

a hydrogen atoms partly (unequally) shared by 2 electronegative atoms
(with H donor + and H acceptor -)
This is a special form of an electrostatic interaction
H-bonds are weak (4-13kJ/mole) and longer (1.4 -2.6Å) than covalent bonds

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18
Q

Hydrophobic effect

A

Dispersion of lipids in H2O - each lipid molecule forces surrounding H2O molecules to become highly ordered
Cluster of lipid molecules: only lipid portions at the edge of the cluster force the ordering of water. Fewer H2O molecules are ordered and entropy is increased

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19
Q

Common H-bonds in biological systems

A

Bases in DNA can form H-bonds to form base pairs -> H-bonds in DNA base (A:T) pair
Water: Oxygen is partially negatively charged; Hydrogen is partially positively charged
Water’s structure allows for the formation of multiple hydrogen bonds
Water can disrupt H-bonding
Between neutral groups
Between peptide groups

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20
Q

Hydrogen donor

A

electronegative and tends to pull the electrons away from the hydrogen
The acceptor is also electronegative and thus has a partial negative charge and must have a lone pair of electrons

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21
Q

Cl and F does not act in biological systems but Negatively charged atoms can be ______ ______

A

electron donors

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22
Q

Ionic interactions

A

interaction of 2 charged atoms based on coulomb’s law (rolled into dielectric constant)
Attraction
Repulsion

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23
Q

F =q1q2/εr2

what are the variables?

A

Where F is the force of the interaction
ε is the dielectric constant
Takes into account the medium the atoms are in
In biological systems the atoms are in water and water has a high dielectric constant
Negatively charged backbone of DNA repel each other

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24
Q 
Hydrophobic interactions
(special type of interaction)
A

Properties of water and thermodynamics: entropy driven event
Water will decrease entropy (randomness) when a nonpolar molecule is in an aqueous environment
When a nonpolar molecules (hydrophobic) is added to water, the water molecules are forced into a shell (cage) around the molecule (they can’t interact with it-> lowers entropy
When 2 non-polar molecules come together, fewer water molecules are needed to form a shell, and entropy increases (even though the hydrophobic molecules are clustering together)
Favors nonpolar molecules coming together
Nonpolar molecules cause water to surround the molecule in an ordered manner

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25
Q

Hydrophobic molecules coming together -> leads to

A

decrease in entropy, but the water molecules are becoming more disordered -> increase in entropy
Even though the entropy of the liquids has decreased, the entropy of the water molecules has increased by a greater amount

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26
Q

Van der Waals interactions

A

attraction of any 2 atoms in close proximity
- a specific form of an electrostatic interaction
Van der Waals interactions in DNA
At any given time, the charge distribution around an atom is not symmetric
That asymmetry causes complimentary asymmetry in other atoms resulting in the 2 atoms being attracted to each other
Van der waals Contact distance- distance between two atoms of maximal attractions between 2 atoms - overlapping electron cloud
The attraction increases until the 2 atoms electron clouds start to repel
Van der Waals interactions in DNA - maximal attraction between
Weak interactions are weak with 2-4 kJ/mole

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27
Q

importance of water

A

Almost all biochemical reactions/processes occur in an aqueous solvent
Water plays a huge role in these reactions or interactions
Water is cohesive - can interact with itself and anything with charges or partial charges
Water has a bent shape making the molecule polar and capable of forming multiple H-bonds
Water is an excellent solvent for polar (hydrophilic) molecules

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28
Q

Water can form up to hydrogen bonds

A

4

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29
Q

Amphipathic molecule

A

hydrophilic (water loving) and hydrophobic (water fearing) properties; molecules that contain polar and nonpolar groups

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30
Q

Water molecules can weaken electrostatic interactions by …

A

competing for their charge

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31
Q

effects of water in relation to dielectric constant, and H bonds

A

Water molecules can weaken electrostatic interactions by competing for their charge
Water reduces electrostatic interaction by ~80x
Water has a high dielectric constant
This has serious consequences for biological systems - often water needs to be excluded (or manipulated to allow the various electrostatic interactions to occur

Water is needed to dissolve thing but can also interfere with electrostatic interactions

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32
Q

why must Water be removed for DNA formation

A

Water must be removed for DNA formation for H-bonds to form between base pairs
Water can disrupt H-bonds by forming its own H-bonds

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33
Q

Thermodynamics laws:

A
  • All biological events are governed by a series of physical laws
    1. The total energy of a system (matter in a defined space), and the surroundings is constant
    2. The total entropy of a system and its surrounding always increases for a spontaneous process
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34
Q

explain: The total energy of a system (matter in a defined space), and the surroundings is constant

A

cannot create or destroy energy- can only change its form (e.g. burning wood - converting chemical energy into heat and sound, or dropping ball- PE to KE)

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35
Q

Enthalpy: H:

A

heat content of the system and its surroundings

- When heat is released, makes the universe more disordered but the reaction is ordered (decrease in entropy)

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36
Q

Entropy: S

A

measure of randomness

It always increases for a spontaneous process

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37
Q

explain: The total entropy of a system and its surrounding always increases for a spontaneous process
and 2 examples

A

For any spontaneous process increase E.g. increase in entropy mixing 2 strands of complementary DNA
But things can become ordered. Entropy can be decreased locally in the formation of ordered structures only if the entropy of the universe is increased by an equal or greater amount
E.g. of annealing of 2 strands of complementary DNA; entropy decreases (2 molecules to 1 molecule) but heat is released, causing the entropy of universe to increase
randomness

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38
Q

Using △Hsys and △Ssyst: △G = △H - T△S

what are the variables and what is it used for

A

T is temperature in Kelvins
Where △G is known as the Gibbs Free energy, measured in kJ/mole
Used to determine spontaneity of a reaction spontaneously: how likely the reaction is to occur

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39
Q

Spontaneity doesn’t define how ___ a reaction will occur, just that it …

A

fast; can (or cannot occur)

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40
Q

If △G < 0

A

reaction is spontaneous (exergonic reaction)

  • when △H < 0, △G becomes more negative and the reaction becomes more spontaneous
  • when △S > 0 (i.e. the reaction becomes more disordered), △G becomes more negative, and the reaction becomes more spontaneous
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41
Q

If △G > 0

A

reaction is nonspontaneous (endergonic reaction)

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42
Q

__ is very useful because all reactions in a biological system must be spontaneous to occur

A

△G

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43
Q

The concentration of H ions (i.e. protons) within biological systems is crucial because most biomolecules can act as…

A

weak acids or bases (i.e. their groups can become ionized)

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44
Q

pH alters the_____ ___ of an amino acid

A

ionization state;

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45
Q

how a molecules is charged, depends on __ of solution

A

pH

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46
Q

how does pH affects the ionization state of nucleotides

A

Need to maintain pH in biological systems
[H+] affects enzyme mechanisms, H-bonding, protein folding
Molecules behavior depends on its ionization state and [H+] affects ionization state

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47
Q

Ionization state

A

whether a molecules is charged or uncharged

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48
Q

pH

A

[H+] is measured as pH
pH = -log[H+]
Scale of 0 -14 with 0 being highly acidic and 14 being strongly basic

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49
Q

what is Kw

A

ionization constant = 1 x 10^14 = [H+][OH-]

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50
Q

Weak acids

A

acid that is not completely ionized in solution
E.g. (acetic acid) CH3COOH ⇌ CH3COO- (acetate) + H+
COOH = acid; COO- = -ate

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51
Q

Strong acids

A

acids that is completely ionized in solution

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52
Q

Acid

A

proton donor

Each acid has its own tendency to lose a proton easily, which is defined by Ka (equilibrium constant)

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53
Q

Henderson-Hasselbalch equation

A

pH = pKa + log([A-]/[HA])
When the pH = pKa, then [HA] = [A-] (pH =pKa =4.76)
When the pH < pKa, then [HA] > [A-]
When the pH > pKa, then [HA] < [A-]
- We can calculate the pH of any solution if the molar ratio of acid to conjugate base and pKa is known through the Henderson-Hasselbalch equation

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54
Q

Base

A

proton acceptor

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55
Q

Titration curve of acetic acid

A

If we titrate a weak acid with a strong base (e.g. NaOH), the acid is releasing protons
If you are adding strong acid, the conjugate base is absorbing the protons
Y-axis = pH
X-axis = OH- added

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56
Q

Titration curve - The curve levels off ->

A

buffer, where the pH does not change very much even though large amounts of base (or acid) are being added
Equal concentration of acid and conjugate base
In this range the pH does not change much
The buffering range is usually +/-1 (for acetic acid: 3.8 - 5.8)

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57
Q

when do Buffers fail

A

Buffers fail when you run out of the acid or conjugate base

In the direction of adding NaoH -> when you run about of acid

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58
Q

buffer

A

Buffer is mixture of acid and conjugate base, resisting changes in pH because both forms are present, and it is most effective when the pH =Pka
Buffers are a storage area for protons

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59
Q

In biological systems, 3 key buffers

A
  1. Carbonate buffer system
  2. Phosphate buffer
  3. Histidine and cysteine can also buffer
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60
Q

Protein characteristics

A

a linear polymer built out of amino acids (ɑɑ)
A protein’s final 3-D shape depends on its sequence of aa
Aa contain a large number of different functional groups allowing for massive diversity
Proteins can interact with each other and other molecules to form complexes
Proteins can be flexible or rigid

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61
Q

The Amino Acids

A

Amino acids contain a Central carbon (alpha carbon) attached to an amino group, a carboxyl group, a single hydrogen group, and a unique side chain “R”
Note that the alpha carbon is chiral
There are 2 enantiomers of each amino acid (except glycine)

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62
Q

Chiral center

A

an atom with its substituents arranged so that the molecule is NOT superimposable on its mirror image
Cannot overlap mirror image

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63
Q

Enantiomer:

A

a pair of molecules each with one or more chiral centers that are mirror images of each other
We can draw each aa in the L or D form

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64
Q

In biological systems, almost all aa exist in the _ form (both free and in proteins)

A

L

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65
Q

L and D form structure

A

In Fischer projections, if you position the carboxyl group above the C-alpha and the R group below, then the amino group will be left of C-alpha in the L designation and right of C-alpha in the D designation

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66
Q

Zwitterionic aa

A

has both positive and negative charge
Positive amino; negative carboxyl
the predominant form of aa in biological systems (neutral pH 7)
Assume pH 7 when not noted

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67
Q

There are __ common key aa and these (or slight modification are used in all living things)

A

20

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68
Q

Nonpolar, aliphatic R groups

A 
Hydrocarbon side chains that are open or nonaromatic ring
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine  (Ile, I)
Methionine (Met, M)
Proline (Pro, P)
Glycine  (Gly, G)
LIMP VAG
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69
Q

Aliphatic

A

compound with open-chain structure (alkane)

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70
Q

Glycine (Gly, G)

A

not really hydrophilic or hydrophobic, not really anything but hydrophobic aa are the best fit
Simplest aa
R = Hydrogen
Only achiral aa

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71
Q

Alanine (Ala, A)

A

Contains a methyl group CH3

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72
Q

Valine (Val, V)

A

peace sign/V with CH, and two CH3

Hydrocarbon side chain

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73
Q

Leucine (Leu, L)

A

Y shape with CH2-CH-(two)CH3

Hydrocarbon side chain

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74
Q

Isoleucine (Ile, I)

A

has a second chiral center only one form though

Hydrocarbon side chain

75
Q

Methionine (Met, M)

A

the start aa when synthesizing protein (unless cut off)

Hydrocarbon sidechain, except it has a nonpolar thioether (CH2-CH2-S-CH3)

76
Q

Proline (Pro, P)

A

R group bound to amino group (formed a 5 membered group)
The steric hindrance causes (both cis and trans occur)kinks in the chain
Aliphatic side chain but with a twist, the end of the R group is bonded to the Nitrogen in the amino group
The ring structure makes it more restrained - not that flexible (cannot twist)
often introduces kinks into aa chains i.e. polypeptides

77
Q

All of the above are hydrophobic and will tend to cluster together -> effect on R groups

A

Different sized R groups allow for close packing
Often found in the center of proteins (away from water)
Not reactive (more structural roles or binding)

78
Q

Aromatic amino acids

A

Contain aromatic rings (e.g. phenyl rings)
Also participates in hydrophobic interactions
Tend to find clustered inside away from water
Phenylalanine (Phe, F)
Tyrosine (Tyr, Y)
Tryptophan (Trp, W)
FYW: Fuck you want

79
Q

Phenylalanine (Phe, F)

A

Alanine with a hydrophobic phenyl group

80
Q

Tyrosine (Tyr, Y)

A

Like F, but has a reactive -OH group attached to phenol ring that can form H-bonds
has polar groups; more towards the surface near water
The ring makes them predominantly hydrophobic
Typically pKa 10.9

81
Q

Tryptophan (Trp, W)

A

5 membered wing and 6 membered ring
5 membered ring has NH on the right that does not lose H easily
Contains an indole group, which are 2 fused rings with an NH group
Reactivity: F < W < Y
Less hydrophobic than Phe

82
Q

Positively charged Basic R groups aa

A

Lysine (Lys, K):
Arginine (Arg, R)
Histidine (His, H)
Kiss Right Here

83
Q

Lysine (Lys, K):

A

Lysine discovered when they watched cells die and saw lysate come out
Assigned K because, L was taken and they went 1 letter back
4 CH2 then attached to NH3+ at the end
Amino group pKa is high -> greater than 10.8
Stays positively charged at pH 7
Does not like to give up proton -> basic
Contain long chains with ionizable groups (amino group)

84
Q

Arginine (Arg, R)

A

pKa above 12
Contain long chains with ionizable groups (quandinium group)
Positively charged at pH 7

85
Q

Histidine (His, H)

A

Uncharged at pH 7
pKa is 6 -> close to 7
Can act as a buffer
Has ionizable group (imidazole ring)
It can either be charged or uncharged depending on its location in a proteins
Often found in the active site of enzymes when it can act as a hydrogen donor or acceptor
Easy to manipulate histidine as it is close to 7
Depending on the location change pH -> true for all aa
Charged (groups basic and acidic amino acids) are often found on the surface of proteins (interacting with water and away from hydrophobic aa)

86
Q

Acidic Negatively charged R groups

A

Contain carboxylic acids (carboxyl groups) in the R group
Negatively charged at pH 7 (pKa < 4)
Aspartate (Asp, D)
Glutamate (Glu, E)

87
Q

Polar uncharged R groups

A 
Reactive and capable of h-bonding
Not charged
More hydrophilic
More reactive
Serine (Ser, S)
Theranine (Thr, T)
Cysteine (Cys, C)
Asparagine (asn, N)
Glutamine (Gln, Q)
Queen Can Never Shit Today
88
Q

Serine (Ser, S)

A 
-CH2OH
Contain alipathic (open chain) hydroxyl groups
89
Q

Theranine (Thr, T)

A

Contain alipathic hydroxyl groups

90
Q

Cysteine (Cys, C)

A

Polar; Can weakly H-bond
Contains sulfidyl (thiol) -SH group
-CH2-SH
Two cysteine comes together -> disulfide bonds
Can link two chains or two parts of the same chain together
Done by oxidation (loss of electrons) of 2 cysteines to a single nonpolar cysteine
Disulfide bond is a covalent bond
E.g. primary structure of insulin
pKa 8.3

91
Q

Asparagine (asn, N)

A

Resembles aspartate except instead of -OH it has a H2N
Derivative of aspartate with Nitrogen attached
Cannot ionize the group
Contain terminal carboxyamid instead of carboxyl group
Terminal NH2 is not charged and will not lose its Hydrogen

92
Q

Glutamine (Gln, Q)

A

Derivative of glutamate with NH2
Terminal NH2 is not charged and will not lose its Hydrogen
Contain terminal carboxy amid instead of carboxyl group

93
Q

Terminal alpha carbonyl group typical pKa

A

3.1

94
Q

Aspartate (asp, D)

A

-CH2 - COO-
Acidic: low pKa
aspartic acid pKa 4.1

95
Q

Glutamate (Glu, E)

A

-CH2 - CH2- COO-
Acidic: low pKa
Glutamic acid pKa 4.1

96
Q

Terminal alpha amino group typical pKa

A

8.0

97
Q

Protein structure

A

Primary structure 1° -> secondary structure 2° -> tertiary structure 3° -> quaternary structure 4°

98
Q

Primary structure

A

linear sequence of aa linked by peptide bonds to form a protein

99
Q

Protein synthesis in ribosome

A

condensation reaction
Spontaneity wise -> formation of protein is not favourable
Must add energy to for it to form
High activation energy required to break peptide bond
Peptide bond is polar -> polypeptide is polar

100
Q

Peptide bond

A

linkage of an alpha carbonyl of on aa to the amino group of another aa with the loss of water
Not energetically favourable but once formed is stable

101
Q

Polypeptide

A 
series of aa residues linked by peptide bonds
Polar -> have 2 different ends
Free amino end (-NH3+) -> N terminal end
Left side
Involved in ionic interaction
Free carboxyl end (-COO-) -> C terminal end
Right side
Involved in ionic interaction
102
Q

backbone

A

(repeating unit N-C(a)-C) and unique R group
Backbone is hydrophilic and can form H-bond with each group capable of doing one H-bond
All the carbonyls and N-H groups in the backbone can hydrogen bond (The C=O and N-H can each form 1 hydrogen bond
Important for forming 3D structures)
Exception: proline

103
Q

why does proline have limited H-bonding

A

the R group is connected to the N of the amino group so there is no H attached to the N

104
Q

Residue

A

aa unit in a polypeptide

105
Q

Daltons (Da)

A

Weight of proteins is expressed in Daltons (Da) or more commonly kDa
Same as molecular weight
1 Da = mass of H atom ~ 1g/mole

106
Q

Note about nomenclature
A point mutation is usually written as original aa location and new aa
D 614 C =

A

D 614 C = aspartate at position 614 has been replaced by cysteine

107
Q

Knowing the 1° aa sequence should help us to

A
  1. Determine shape: 3D shape of protein depends on its sequence of aa
  2. Understand function
  3. Understand disease (e.g. within aa are binding to covid)
  4. Understand evolutionary history (compare sequences of protein and see how they changed over time)
108
Q

explain how proteins are flexible but conformationally restrained

A

Backbone of a polypeptide is restrained due to double bond characteristics of the peptide bond
Because of resonance between the peptide bond and the carbonyl group
Result: peptide bond is planar and locks a series of atoms into a plane
There is no rotation about the peptide bond
The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charged, setting up a small electric dipole

109
Q

configuration about the peptide bond

A

Peptide bonds could technically exist in cis or trans as the peptide bond acts as a double bond
Virtually all peptide bonds in proteins occur in the trans configuration
except X (aa)-pro (proline) (both cis and trans occur)
Cis configuration has steric hinderance
More correct in zigzag fashion -> trans configuration

110
Q

dihedral angle (aka torsion angle)

A

We can measure the amount of rotation about the bond
Ranges from -180° to +180°
The bond between N-C and the bond between C-C=O are free to rotate
This provides flexibility allowing the protein to fold in many different ways
Dihedral angles
The N-C(a) dihedral angle = ɸ(phi)
The C(a)-C=O dihedral angle = Ѱ (psi)
Not all combinations of angles of Ѱ and ɸ are permissible
due to steric hindrance
Further limits the number of structures a protein can adopt

111
Q

Ramachandran plot

A

combinations of dihedral angles that are permissible are shown in this plot
This plots is the same for 18 of the aa (different from proline and glycine)
Proline considered alpha helix wrecker
Areas of dark blue are favourable
Areas of light blue are borderline
Note that ¾ of all angle combinations are not possible (white)

112
Q

Large molecules that can freely rotate among many bonds will adopt ____ ___(i.e. a mixture of many different structures)

A

random coils

113
Q

They can often spontaneously fold into a single structure under ______ ____

A

physiological conditions

114
Q

Secondary structure (2°)

A

the spatial arrangement of aa residues that are close to each other in a linear sequence
Alpha ɑ helix:
Beta 𝛃 sheet

115
Q

Alpha ɑ helix:

A

polypeptide backbone forms the inner part of a right-handed helix, with the side chains (i.e. R) sticking outwards
The helix is stabilized by intrastrand hydrogen bonds between the NH and C=O groups of the backbone (N-C-C repeated)
Intrastrand H-bond = H-bonding with itself which helps hold the helix together

116
Q

is there space in the centre of the helix?

A

No space in the centre of the helix -> everything is packed together

117
Q

The helix is stabilized by intrastrand hydrogen bonds between which groups and how many residues away

A

The carbonyl of residue (i) forms a H-bond with the N-H 4 residues further down the chain- closer to C-terminal (i.e. residue i + 4)

118
Q

Alpha helices have ideal dihedral angles of

A

Ѱ= -45 and ɸ = -60

119
Q

R groups i, i+1, i+2 are pointing

A

R groups i, i+1, i+2 are pointing away from each other
The different R groups in this proximity a hydrophobic and hydrophilic groups that point away from each other -> amphipathic

120
Q

R groups i, i+3, i+4 are pointing

A

R groups i, i+3, i+4 are pointing in a similar direction

121
Q

Each amino acid residue in the helix increases the helix length by

A

1.5 Å (i.e. we say the helix rises by 1.5Å)

122
Q

Left-handed helices

A

left hand helices are permitted but rare as they are not as stable due to the fact that the amino acids are in L

123
Q

Alpha helices are depicted as

A

twisted ribbons or a rod

124
Q

Usually the maximum length of a helix are ___ or less

A

45 Å or less

125
Q

keratin structure

A

keratin are 2 alpha-helices can intertwine into coiled coils

126
Q

Beta barrels are depicted as _______ _____

A

twisted arrows

127
Q

in a parallel B sheet, each aa residue extends a B-strand by ____ Å

A

3.25

128
Q

Tertiary Structure (3°)

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
IMPORTANT because 3° is the 3D structure

129
Q

myoglobin

A 
O2 storage protein in mammalian muscles
Red in steak is not blood (hemoglobin) -> myoglobin (O2) capacity
Globular protein with no symmetry
Very few voids (i.e. holes in the core)
Single polypeptide chain of 153 aa
130
Q

what does the heme group in myglobin do?

A

heme group (ison in a protoporphyrin ring)
Where the O2 binds
In myoglobin the O2 binds tightly and is only released when [O2] is low

131
Q

how many a-helices in myoglobin

A

70% of the chain is in a-helices (8 a-helices)

Most of the rest is in loops and turns

132
Q

The core of the myoglobin protein is almost exclusively composed of

A

The core of the protein is almost exclusively composed of hydrophobic residues (Except for 2 His which are needed at the O2 binding site)

133
Q

structural domains

A

Some proteins can have multiple regions called structural domains lined by flexible sections of the polypeptide (often with no defined structure)

134
Q

In most tertiary structure, the dihedral angle for each residue - Ramachandran plot

A

In most tertiary structure, the dihedral angle for each residue in the protein falls into the permissive area in a Ramachanran plot

135
Q

Quaternary structure (4°)

A

Folded on its own
The spatial arrangement of multiple subunits (polypeptides) and the nature of their interactions
Some proteins are composed of more than one polypeptide chain
Some proteins must be multimers (protein with quaternary structure) in order to function

136
Q

homomers

A 
Quaternary structure (4°)
Chains can be identical
137
Q

Heteromers

A 
Quaternary structure (4°)
Chains can be different
138
Q

Hemoglobin (H6)

A

O2 transporter in mammals
Hemoglobin can only do its just as a tetramer (composed of 4 subunits: 2 a-subunits and 2-B-subunits)
It is the interactions between the subunits that are critical for function, hemoglobin can’t function unless it is a tetramer

139
Q

quaternary structure example: the capsid of viruses (in this case, minute virus of mice)

A

Composed of 9 VP1 and 51 VP2 protein subunits to form an isohedral (polygon with many sides) capsid (complex quaternary structure) with just enough room the fit the viral DNA

140
Q

how many structures can a protein adopt

A

Even with limitations on the backbone of a polypeptide, there are trillions of structures it could adopt and it would take forever for a protein to try each one
But, most proteins fold into just one structure in less than a second

141
Q

Alphafold2 and riseltafold

A

Up until 2 years ago, we could not predict a protein’s 3D structure based on primary sequence but nature could
Now, computer AI programs such as Alphafold2 and riseltafold

142
Q

what is folding driven by

A

Folding is driven by thermodynamics (i.e. finding the most stable complex - most negative △G)
The free energy change between folded and unfolded proteins is small (20-60kJ difference)
This is partly driven by entropy, ie the hydrophobic residues are excluded from water in the core while the hydrophilic residues are on the surface

143
Q

Many B-sheets and a-helices are ______

A

amphipathic

144
Q

In order to bury the backbone of a polypeptide in the core, it needs to _____

A

H-bond

145
Q

what can destabilize structures

A

Unpaired charged or polar groups in the core can destabilize structures

146
Q

Can a portion of the primary sequence be used to define secondary structure?

A

Yes and no. certain aa residues are more likely or less likely to be found in and stabilized or unstabilized a-helices and B-sheets
The more positive the delta G value, the more destabilized
aa acids such as Pro and Gly destabilize a-helices
Experiments have shown that the exact same protein sequence in 2 different proteins can adopt 2 different secondary structures
We can’t always determine secondary structure by looking at a portion of a primary structure
Tertiary structure influences 2ndary structure

147
Q

Protein folding process

A

Folding is an all or none process, either protein is folded or it is not

148
Q

what does it mean that proteins can breathe

A

proteins can breathe: i.e. they can flex and open and close

149
Q

what does it mean that “Folding is thought to be cooperative”

A

There may not be just one pathway that a protein follows to fold
I.e. as one one protein of the protein folds (for example, an a-helix) , it will influence how another protein folds - a protein doesn’t have sample every possible structure
There might be multiple pathways to the folded state

150
Q

Not all proteins have a single proteins structure

A

Some might only form a structure when bound to another protein
Some proteins exist in an equilibrium between 2 structures

151
Q

Modifications of aa in proteins (4)

A

aa can be post translationally (after synthesis of protein) covalently modified

  1. phosphorylation
  2. glycosylation
  3. hydroxylation
  4. carboxylation
152
Q

Proteins can also be cleaved and trimmed after synthesis

A

(in fact most are)
E.g. fibrinogen (inactive) -cut-> fibron (active)
Many viruses make super long polypeptides that are then cut into small functional proteins

153
Q

Enzyme

A

biological macromolecule that acts as a catalyst for biochemical reactions - usually proteins
Enzymes are very specific, they will only catalyse are specific set of reactions

154
Q

Catalyst

A

a chemical that increases the rate of the reaction without being consumed
Enzymes speed up the rate of reaction - they are essential for biological synthesis
Rate can be read as molecules of substrate coverted per second (per molecule of enzyme if it is present)

155
Q

proteolytic enzymes (i.e. proteases)

A

cleave peptide bonds

156
Q

Trypsin

A

cleaves only the peptide bond on the carboxyl side of Lys and Arg

157
Q

Thrombin

A

cleaves only Arg-gly protein bond

158
Q

Specificity is based on

A

a series of weak interactions between the substrate and the enzyme, especially in the active site

159
Q

The shape of the enzyme (Especially at the active site) determines (2)

A

specificity and function

160
Q

Active site

A

the region of the enzyme that bonds the substrate

It contains the residues that directly participate in the reaction

161
Q

Characteristics of active sites

A

Tends to be a cleft or open hollow part for substrate to come in
The residues in an active site can be far apart in the primary sequence and fold to come close together
Cleft in the enzyme made up of residues from all over the primary aa sequence
They take up a small volume of the enzyme
Water is usually excluded from the active site, changing the behaviour of the residues -> hydrophobic effect
The substrate is bound to the active site by a series of weak interactions

162
Q

is the substrate and enzyme complementary

A

The substrate and the enzyme must be complementary, otherwise the substrate cannot bind and catalysis cannot occur
The active site is not a perfect complementary fit to the substrate

163
Q

lock and key

A

(rare) complementary match to the substrate

too specific and hard for the product to let go of substrate

164
Q

Induced fit

A

binding of the substrate causes the active site to assume matching shape
enzyme does have a perfect fit but the enzyme changes shape

165
Q

Cofactor

A

an inorganic ion or small organic compound (often referred to as a coenzyme) required for enzymatic activity
The heme requires Fe2+ as cofactor

166
Q

Prosthetic group

A

A cofactor that is tightly bound to an enzyme

E.g. myoglobin (tertiary structure) has a heme prosthetic group

167
Q

FAD and NAD as cofactors

A

FAD (more like a cofactor than NAD, though both are cofactors) fits more perfectly to enzyme

168
Q

Apoenzyme

A

An enzyme without its cofactor

169
Q

Holoenzyme

A

an enzyme with its cofactor

170
Q

Enzyme thermodynamics

A
  1. Enzymes do not alter the final equilibrium of products to reactants
  2. Enzymes do not alter △Grxn -> they obey the laws of thermodynamics
    I.e. they can’t change the spontaneity of reaction
    If △G of a reaction is (+), its is a nonspontaneous and adding enzyme will NOT change that
  3. Enzymes speed up the rate of reaction
171
Q

enzymes accelerate reaction by

A

decreasing the activation energy (△G‡) by facilitating the formation of transition state (X‡)
Imagine substrate being converted to a product
In order to form the products, the substrate goes through a transition state (X‡)
The transition state has the highest G (Gibb’s free energy) in the reaction and the lowest concentration

172
Q

how does the activation energy controls the reaction rate?

A

only a fraction of Substrate will have enough energy to form X‡

173
Q

Activation energy (△G‡) : the energy needed to get to transition state (X‡)

A

△G‡ (s->p) = G(X‡) - G(s)
△G‡ (p->s) = G(X‡) - G(p)
the activation energy is not part of the over △Grxn calculation because the energy put in is returned when the X‡ is converted to products
Consider enzyme converting substrate to product
S +E ⇌ ES ⇌ EP ⇌ E +P
Enzymes interact with the transition state such that the activation energy is lowered
The reaction speeds up as a greater fraction of Substrate has the energy reach X‡

174
Q

Where does the energy come from to lower the activation energy?

A

binding energy (△GB)
Enzymes coming and enzyme binding and stabilizing the transition state
The active site of an enzyme is complementary to the transition state
Binding energy (△GB): the energy derived from the interaction between the enzyme and substrate

175
Q

Beta 𝛃 sheet

A

Beta barrels are depicted as twisted arrows
More common because more stable
2 or more 𝛃 strands (polypeptide strands usually from the same molecule) associated as stack of chains in an extended zigzag form stabilised by interstrand hydrogen bonds
The planarity of the peptide bond means different sections of the sheets are fixed in different planes and the dihedral angle set the angle at which those planes intersect -> forming plates
Do not normally see beta-strand by itself

176
Q

antiparallel beta strands

A

Each aa residue extended the B-strand by 3.8 Å (more spread out than an a-helix)
The R groups of adjacent residues (in a B-strand) point in opposite direction
The strands are arranged into pleated sheet
In an antiparallel sheet, the NH and C=O of one residue on one strand (i) H-bonds to a single residue (j) on the other B-strand
Antiparallel sheets have ɸ= -139 and Ѱ=+135 (idealised angle)

177
Q

Twists and loops - Beta sheets

A

Peptide chains often reverse direction
Can be accomplished by B-turns (have a defined secondary structure or by larger loops (i.e. no common/defined secondary structure)

178
Q

Parallel B-sheet

A

H-bonds are weaker
The NH of one residue (i) in one B-strand H-bonds to a C=O on residue (j) on other B-strand
The C=O of residue i H-bond with the NH two residues further (j+2) on the other B-strand
Parallel B-sheets have ideal angles of ɸ= -119 and Ѱ=+113
in a parallel B sheet, each aa residue extends a B-strand by 3.25 Å

179
Q

Mixed beta sheet

A

Sheets can be twisted
Beta sheets are depicted as broad areas pointing to the carboxyl terminal (i.e. C-terminal)
The distance in primary aa sequence (structure) between beta strands can be small or large
Small: Can be quick hairpin turn and another B-strand
Large: Or there could be 100s of aa forming other structures between B-sheets
B-strands (and thus B-sheets) can be flat or twisted

180
Q

phosphorylation

A

attachment of a phosphate group to the OH of an amino acid (e.g. Ser, Thr, Tyr)
Signal transduction
E,g, phosphoserine

181
Q

Glycosylation

A

attached of one or more sugars to a residue (usually Asn, thr, or ser)
Surface labelling

182
Q

Hydroxylation

A

the addition of an OH group (usually a proline)
Fibre stabilisation
Hydroxyproline -> becomes polar with addition of OH group

183
Q

Carboxylation

A

addition of a carboxyl group to glutamate
E.g. clotting
Carbohydrate-asparagine adduct
Y-carboxyglutamate

BIOC 202 (3 decks)

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