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BIOSCI 106 > Section 1: Chemistry of Life > Flashcards

Section 1: Chemistry of Life Flashcards

1
Q

When was the universe born

A

Believed to be born 14 billion years ago at the time of the ‘big bang’

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2
Q

Predominant elements in the primordial universe

A

Hydrogen and helium - the smallest elements

Condensed tgt to form first generation of stars

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3
Q

How were C, N and O formed

A

By fusion of hydrogen and helium under heat and pressure in the stars

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4
Q

Supernovas

A

Some of the largest stars became unstable and exploded as supernovas
Dispersed all the elements throughout the universe

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5
Q

What elements are humans primarily made of

A

C, H, O, N
Known as first-tier elements (abundance)
Have strongest tendency to form strong, covalent bonds

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6
Q

Oxygen and hydrogen in living systems

A

Abundant

Explained by presence of water (H2O) everywhere on the planet and within biological systems

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7
Q

Carbon

A

Has an electronic structure that can form up to four very strong and stable bonds with other atoms
Can form single, double and triple bonds, each with diff electronic structures and geometries
Provides versatility, scaffolding and diversity in chemical molecules

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8
Q

Second-tier elements

A

Essential components of biological molecules
Phosphorous and sulfur - forms covalent bonds
Cl, Na, Mg, K, Ca - ionic elements, critical roles in diverse processes

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9
Q

Third and fourth-tier elements

A

Found in trace amounts, but still have critical roles

e.g. transition metals in centre of period table - structural and catalytic elements

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10
Q

Signs of life =

A

Evidence of water or ice

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11
Q

Life on our planet is dependent on ______

A

Water

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12
Q

Primordial earth - water

A

Cooling and condensation of water provided an aqueous environment within which molecules could form

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13
Q

Primordial earth - reducing atmosphere

A

Lack of gaseous oxygen

Supports bond formation

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14
Q

Miller Urey experiment

A

Reproduced primordial “soup” of earth ~4 million years ago

More than 20 amino acids produced, including some not seen in nature

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15
Q

Types of biopolymers

A

DNA - made from nucleotides
Proteins - made from amino acids
Carbohydrates - made from sugars

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16
Q

What are biopolymers made of

A

Simple polymers of smaller organic chemical subunits

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17
Q

How are biopolymers formed

A

Formed from same reaction path of nucleophilic attack coupled with elimination of water for each biopolymer

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18
Q

Why does our body need weak bonds?

A

Signalling molecules need to be turned on and off, so must bind strongly enough for it to change shape, but must still be able to come off

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19
Q

Electronegativity

A

A measure of the tendency of an atom to attract a shared pair of electrons (or electron density)
A difference in electronegativity between 2 atoms in a covalent bonding arrangement results in a bond that is polarised

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20
Q

Polarised bonds

A

Electrons in the bond aren’t shared evenly between the two atoms, and instead are more closely associated with the more electronegative atom

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21
Q

Drawing dipole moments

A

Arrow from high electron density atom to low electron density atom

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22
Q

Charge-charge interactions

A

Dependence of energy on distance: 1/r (strongest)

Between atoms that have full positive and full negative charges

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23
Q

Charge-dipole interactions

A

Dependence of energy on distance: 1/r^2
Related by interparticle distance, so much weaker than charge-charge interactions
Forms a polar molecule with a dipole moment
Between a full positive charge and a partial negative charge (or vice versa)

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24
Q

Dipole-dipole interactions

A

Dependence of energy on distance: 1/r^3

Between atoms with a partial positive and partial negative charge

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25
Q

Non-polar molecules - charge

A

Has neither a net charge nor a permanent dipole moment

But when they are close to charged groups, there is a redistribution of e-; called an induced dipole

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26
Q

Charge-induced dipole interactions

A

Dependence of energy on distance: 1/r^4

Involves inducing a dipole in one non-polar molecule by putting it in close proximity to a full positive/negative atom

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27
Q

Dipole-induced dipole interactions

A

Dependence of energy on distance: 1/r^5

Between a dipole and an induced dipole

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28
Q

Van der Waals (dispersion forces)

A

Dependence of energy on distance: 1/r^6 (weakest)
Numerous
Between paired non-polar molecules
Only becomes significant when atoms approach each other very closely
Distribution of e- within a molecule is always fluctuating, so when two non-polar molecules approach closely, the fluctuations tend to localise in an area of +ve charge on one molecule next to a region of partial -ve charge on the second molecule

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29
Q

Aromatic rings - stacking

A

Fairly strong interaction, made of van der Waals interactions
Rings interact through their pi-orbitals above and below the ring surfaces, where e- are loosely held
Gives rise to mutually attractive induced dipoles

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30
Q

Van der Waals - biopolymers

A

Though weak in energy, the great numbers of interactions produce a very large stabilising force
e.g. base-pair stacking of DNA, where aromatic bases in DNA stack directly on top of each other as the helix winds around

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31
Q

Base pairs - distance

A

3.4 Å

The closest distance 2 Cs can make with each other

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32
Q

Hydrogen bonds

A

Between two electronegative atoms - one ‘donates’ a H to the bond
Between a partial positive charge on the H (donor) and a partial -ve charge on the electronegative acceptor atom
N-H-O-C
Bond length is fixed - rigid

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33
Q

Hydrogen bonds - unique features

A

Directionality (optimal angle 180 degrees, 90 degrees is possible but v weak)
Partial covalent bond character

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34
Q

Hydrogen bonds - function

A

Determines structure and properties of biopolymers

Predominant feature of base pairing in DNA - holds molecules tgt and provides means of DNA replication

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35
Q

Non-polar covalent bond

A

Bonding e- shared equally between two atoms

No charges on atoms

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36
Q

Polar covalent bond

A

Bonding e- shared unequally between two atoms
Partial charges on atoms
One atom has a stronger tendency to pull e- towards it than the other

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37
Q

Ionic bond

A

Complete transfer of one or more valence e-

Full charges on resulting ions

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38
Q

Intramolecular and intermolecular forces

A

Dominated by weak, non-covalent interactions

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39
Q

Hydrogen bonds - O lone pairs

A

If lone pairs are directed towards H, then the bond is very strong

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40
Q

Hydrogen bonds - distance from O to H

A

Sum H + O vdW radii: 2.6 Å (the closest we would expect a H and O to approach each other
Actual H-O distance: 1.9 Å
Discrepancy: 0.7 Å

Due to element of e- being shared and partial covalent behaviour

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41
Q

nm to Å

A

1 nm = 10 Å

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42
Q

Unique properties of water

A

Hydrogen bonding ability

Polar nature

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43
Q

Water - hydrogen bonding ability

A

Can form 4 H bonds with other molecules, particularly other water molecules by its 2 H atoms and 2 sets of lone pairs of e-
Provides water with a high bpt and heat of vapourisation

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44
Q

Predominant state of water

A

Liquid

Similar sized molecules are gaseous molecules

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45
Q

Water - heat capacity

A

Very high
Affords a nearly constant temp in large bodies of water
In essence, acts as a temperature buffer

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46
Q

Water is the _______ of life

A

Universal solvent

Allows molecules to move around and interact in a common medium

47
Q

Water - ionic compounds

A

Cations and anions dissociate from their salt crystal and become hydrated by ‘shells’ of water molecules
Polarity of water molecule allows them to surround and coordinate +vely and -vely charged species and shields them from re-associating into an ionic crystal

48
Q

Water and hydrophilic molecules / functional groups

A

Dissolve readily because of their charge / polarity in the highly polar water solvent
Forms H bonds to water molecules

49
Q

Water and hydrophobic molecules

A

Non-polar, non-ionic and can’t form H bonds –> limited solubility in water
When they do dissolve, they don’t attract hydration shells, and instead water cages / clathrate structures form around the hydrophobic molecule

50
Q

Water and amphipathic molecules

A

Produces monolayers, micelles, bilayers, and vesicles

51
Q

Ka

A

Acid dissociation constant

52
Q

pKa

A

Describes the propensity of a functional group (any weak acid) to dissociate at a specific pH (often pH ~7)

53
Q

pH and pKa

A

If pH < pKa, functional group will most likely be in acid form (protonated)
If pH > pKa, functional group will most likely be in base form (deprotonated)
If pH = pKa, side chain has an equal probability of being in the protonated or deprotonated form

54
Q

pH in human body

A

Varies between 2 and 8

Often very tightly controlled by buffering systems

55
Q

Buffer system

A

Resists changes in pH when an acid or base is added

56
Q

Systems maintaining pH in human blood

A

Renal system
Respiratory system
Chemical buffering system

All interplay to keep blood pH tightly regulated

57
Q

Chemical buffers in blood

A

Bicarbonate (dominant)
Phosphate
Protein

58
Q

Dissolution of CO2 in water

A

Catalysed by enzyme carbonic anhydrase

Produces carbonic acid (weak acid) –> dissociates to produce bicarbonate (conjugate base) and H+

59
Q

CO2 in water - equilibrium

A

Addition of acid or base, or changes in bicarbonate (renal system) or carbon dioxide (respiratory system) conc in blood, pertubates the chemical equilibrium
Equilibrium shifts so pH is maintained in range 7.35-7.45

60
Q

pH of blood at lungs

A

Tends towards a higher pH (less acidic) than at the tissues that are more acidic
Promotes release of oxygen at the tissues

61
Q

Assembly of higher order structures of α-keratin

A
  1. Monomer - composed of an α-helical domain (amphipathic) and a globular domain. Every 4 amino acids is hydrophobic.
  2. Dimer (made of 2 monomers) - coiled-coil. Hydrophobic effect (hydrophobic regions inside coil) and vdW interactions
  3. Protofilament (made of 2 dimers) - join tgt by various weak interactions
  4. Protofibril (made of 2 protofilament) - join tgt by various weak interactions
62
Q

α-keratin and water

A

Water molecules can get in between the protofibrils, which disrupts weak interactions causing it to slide freely
Once dry again, it is set in place of where the interactions were

63
Q

α-keratin - disulphide bonds

A

2 cysteine -SH chains = -S-S- bond

Can use a reducing agent to break the disulphide bond back into their -SH groups

64
Q

α-keratin and hair

A

More disulphide bonds between cysteines = stronger and curlier hair
Burnt hair smells sulfurous

Perms use a reducing agent to break disulphide bonds, which are then rearranged and neutralised –> stays in place

65
Q

What is required to change the state of water

A

To make water into ice or vapour requires energy, because the default state of H2O on this planet is liquid

66
Q

pKa and Ka equations

A 
pKa = -log10 (Ka)
Ka = { [A-][H+] } / [HA]
67
Q

Adding strong acid or base into a buffer system

A

Protons combine with conjugate base to produce more weak acid
Strong base takes proton from weak acid to produce more weak acid

68
Q

CO2 pathway - bicarbonate system

A

CO2 –> CO2 + H2O –eq arrow– H2CO3 –eq arrow– HCO3- + H+

Production of H+ causes pH to drop, therefore blood pH changes during exercise

69
Q

Interplay between buffer, respiratory and renal systems

A

During exercise, cell metabolism increases and produces more CO2 –>
More CO2 dissolves in blood, forming carbonic acid which lowers blood pH slightly –>
Receptors in brain sense the drop in pH and send nerve signals to increase breathing rate –>
Increased breathing rate quickly moves more CO2 from blood. Blood pH rises slightly, returning to normal –>
Homeostasis CO2 level in body

70
Q

Prion proteins

A

Mis-shapen / disease forms of ‘normal’ brain proteins
Can interact with normal versions of same protein and convert them in a chain reaction –> forms amyloid fibres (toxic)
Appear to be infectious
Very stable - can’t boil, radiate etc
Normal form: α-helix, disease form: β-pleated sheet –> assembled into long structures

71
Q

Proteins - folding

A

Amino acid sequence of proteins contain all the info required for it to spontaneously fold up
High cooperative and happens very quickly

72
Q

For spontaneous folding…

A

Gibbs Free Energy must be negative
Energy of folded protein will be lower than that of the unfolded protein
Overall small decrease in energy

73
Q

Folding proteins - cost

A

Folding up a protein costs energy
Energy cost doesn’t favour spontaneous protein folding
But there are also gains made back to lower the overall energy of the system

74
Q

Folding proteins - gains

A

1: Formation of intramolecular non-covalent interactions; salt bridges (charge-charge), H bonding, and vdW interactions add up to a large energy stabilisation overall
Lowering of energy –> -ve value in ΔH

2: Hydrophobic effect; entropy of water system surrounding the protein. As protein folds up, hydrophobic side chains cluster tightly tgt in interior of protein and form vdW interactions
Hydrophilic side chains can form H bonds with water - water molecules themselves aren’t forming cage structures but have full H bonding freedom
System higher in entropy –> more subtracted from equation –> more negative change in energy overall

75
Q

Energy difference between folded and unfolded proteins

A

Small

Only just stable and can be easily unfolded - if too stable, can’t be broken down easily by cell

76
Q

Inherently (or intrinsically) unstructured proteins

A

No defined structure until they interact with other molecules - then they fold into specific 3D shapes
A single protein of undefined structure can bind to multiple binding partners and potentially in multiple conformations

77
Q

Metamorphic proteins

A

Exist as an ensemble of structures that have equal energies and are in equilibrium with each other

78
Q

Amyloid disease

A

Specific proteins can partially unfold or completely change structure (unfold and refold), resulting in inappropriate β-sheet assemblies that deposit/associate in the body as aggregates or fibrils

79
Q

Energy landscape for diseases - fibril structures

A

Low energy species
Drive progression of disease
Change from ‘normal’ protein to disease form involves a switch from intramolecular to intermolecular interactions, resulting lowering in free energy

80
Q

Alzhiemer’s disease

A

Lots of holes in brain

Hard to diagnose as you can’t take out brain tissue, so must look at symptoms

81
Q

Possible ways to end up with sporingforms disease

A

Eating tissue infected with PrP-res
Inherited mutation in gene that codes for PrP-res
PrP-res forms spontaneously

82
Q

Protein sequence - variables

A

Length

Amino acid sequence

83
Q

Protein folding - equilibrium

A

Most proteins are folded up at equilibrium

84
Q

Water and ice density

A

Ice less dense than water, otherwise planet would be covered in ice
Frozen hydrocarbon more dense than liquid

85
Q

Astrocytes

A

Cells that crawl through the brain digesting the dead neurons –> leaves holes in the brain
Amyloid fibres remain in brain

86
Q

Examples of stable proteins

A

GFP - from jellyfish, barrel structure
Antibodies - exquisite specificity for any one of 100 million antigens

Most proteins are only just stable

87
Q

Antibodies (immunoglobulin) - function

A

Bind to foreign molecules (antigens) and neutralise them
Body can produce > 100 million diff antibodies against diff antigens
Must bind with high affinity and selectively

88
Q

Domains

A

Separately folded regions of the same protein

Why?

  • Efficient folding - longer chains in domain of 100-300 amino acids
  • Active sites created in clefts between domains
  • Diff activities combined
  • Allows flexibility - important for function, e.g. domains close over bound substrate
89
Q

Quaternary and oligomeric structure

A

Several separate polypeptide chains cluster tgt

Oligomer = many units (monomer, dimer, trimer, tetramer etc)

90
Q

IgG antibodies (immunoglobulin G)

A 
Multi-domain and multi-chain proteins
Y-shaped molecule
Tetramer:
- 2 heavy chains folded into 4 domains each
- 2 light chains folded into 2 domains each
Flexible hinges between domains
Very stable
Disulphide bonds present
91
Q

IgG antibodies - loops

A

Each variable domain has 3 hypervariable loops –> 6 at each site –> 12 per antibody
Loops which have diff sequences depending on which antigen they bind to

92
Q

IgG antibodies - flexibility

A

Flexible linkers
Y-shaped arms can open and close
Allows a single antibody to bind 2 antigens at the same time with adjustable distance –> strongest binding to a foreign body

93
Q

How does antibody recognise antigen

A 
Molecular recognition by:
Shape
Size
Charge
Polar/non-polar character
94
Q

Blood sugar levels

A

Varies throughout the way

95
Q

How is blood sugar regulated

A

Pancreas secretes insulin and glucagon
If blood sugar high, insulin helps cells absorb glucose –> reduces blood sugar and provides glucose for energy
If blood sugar low, glucagon instructs liver to release stored glucose –> raises blood sugar

96
Q

Glucagon shape

A

α-helix

97
Q

Glucagon receptor mainly recognises…

A

Shape
Size/length
Weak interactions (chemically), most of which found in side chains of protein

98
Q

Glucagon - examples of pockets

A 
Non-polar surrounded by non-polar
Opposite charges attracting
H-bonds forming (if bond is short)
Site 18 (ARG) causes pi-stacking - a special case of charge-induced dipole
99
Q

Oxyanion site

A

Where 2 Hs with +ve charges balance out the very -ve O

In glucagon receptor, NOT an oxyanion site, but in an enzyme might be

100
Q

Zoonotic diseases in human populations - pathway

A
  1. Virus emerges
  2. Animal reservoir (Primary host)
    - longevity
    - low virulence
    - asymptomatic
  3. Intermediate host
  4. Human disease
    - transmission to humans
    - mutation and adaptation to humans
    - transmission between humans (may have decreased virulence, but easier to spread)
  5. Dissemination
101
Q

Cytokine storm

A

Highly virulent strains of viruses that kill healthy young individuals through an overreaction of the immune system

102
Q

What two surface proteins are required for entry and exit of virus from our cells

A

Hemagglutinin
Neuraminidase (aka sialidase)

Both recognise sialic acid molecules on glycosylated receptor proteins

103
Q

Why is it difficult for humans to directly catch influenza strains from wild birds

A

Because the way sialic acid is ‘presented’ on the host cell surface (i.e. its shape) in bird and human receptors are different
16 types of HA: H1-16
9 types of NA: N1-9
Only 3 types have adapted to infect humans so far; H1N1, H2N2 and H3N2

104
Q

Life cycle of influenza virus - 2 steps

A
  1. Hemagglutinin molecular recognition of sialic acid

2. Neuraminidase molecular recognition of sialic acid and cleaves it away from receptor

105
Q

Sialic acid linkage - birds vs humans

A

Human: α-2,6 linkage
Bird: α-2,3 linkage (straight line)

106
Q

Pigs, birds and humans - catching and spreading viruses

A

Humans have α-2,6 receptors near mouth (closer to outside) and α-2,3 receptors in lungs (harder to reach)
Birds only have α-2,3 receptors, so less likely to reach humans
Pigs have both α-2,3 and α2,6 outside, so can catch the virus from both humans and birds, and can give the virus to humans as well

107
Q

Enzyme active sites are meant to…

A

Stabilise transition states

108
Q

Intermediate hosts - mechanisms/causes

A 
Land use / encroachment
Domestication
Farming practices
Trade/travel
Consumption / bush meat
Climate
Pop changes
109
Q

Sialic acid ring

A

In initial binding event, it changes conformation from chair to boat
Boat conformer is higher energy –> promotes catalysis through a higher energy transition state

110
Q

α-helices

A

Usually right-handed

111
Q

How are α-helices and β-sheets defined

A

By their backbone H-bonding

112
Q

Globular proteins

A

Driven to fold by hydrophobic effect

113
Q

Sialic acid recognised by hemagglutinin

A

Located at the top of a carbohydrate chain attached to a host cell membrane protein

BIOSCI 106 (6 decks)

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