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BIOL1021 > Metals > Flashcards

Metals Flashcards

1
Q

Whats a Stromatolite?

A
  • A single celled organism
  • Colonies of small bacteria
  • They produce oxygen
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2
Q

Whats a Cyanobacteria?

A

A phylum consisting of free-living bacertai and the endosymbiotic plasmids

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3
Q

When do Cyanobacteria increase in abundance?

A

In the Proterozoic

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4
Q

Whats the Proterozoic?

A

A geological eon spanning the time from appearamce of oxygen in the earths atmosphere to just before the proliferation of complex life on earth

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5
Q

Whats are Diblastic organisms?

A

animals with a body wall composed of only 2 layers; ectoderm and endoderm

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6
Q

What are Trilobites?

A

A group of extinct marine arachnomorph arthropods

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7
Q

whats the burgess shale ?

A

A fossil bearing deposit exposed in the canadian rocks of the british columbia, Canada

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8
Q

What was the atmospheric oxygen % before animals?

When dinosaurs were present?

When humans were present?

A

Before animals: 35%

Jurassic period: 25%

Human presence (today): 21%

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9
Q

In the early phases of the earths history, how was oxygen consumed?

A

Through chemical weathering and oxidation of surfaces

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10
Q

When did Stromatolites-layeres cyanobacteria- start producing oxygen?

A

In the Proterozoic period (2.5 Ga)

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11
Q

What does evolution of the chlorophyll allow?

How does this lead to the production of oxygen?

A

Photosynthesis

Now water and sunlight can be used to form organic compounds from carbon dioxide, which leads to the production of oxygen

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12
Q

In the early history, what compounds were there an abundance of?

What was being produced?

A

There was an abundance of: CO2, H2S and Fe2+

There was a production of organic compounds

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13
Q

What period did photosynthesis start?

A

Proterozoic period (2.5 Ga)

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14
Q

Why is high amounts of oxygen not good for Fe (II) ?

A

It gets oxidised which forms Fe (III)

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15
Q

Tell me the main features of the 2.8-2.0 Ga period?

A
  • Deep water deposits of iron-rich and iron-poor layers which are deposited in Banded Iron formation (BIF)
  • contains Magnetite (Fe3O4) with a higher iron-to-oxygen ratio than todays deposits
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16
Q

This image shows the change in atmospheric and ocean compounds over history…

A
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17
Q

What are the two forms of the iron-sulphur clusters?

A
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18
Q

In the iron-sulphur clusters, does the Fe molecules ever touch one another?

A

no

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19
Q

What does the abundance of Fe allow in the iron-sulphur clusters?

A

Varying oxidation states

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20
Q

What amino acid is attached to the iron-sulphur clusted?

How?

why?

A

Cysteine is the residue attached to the cluster

4 Cys bind [4Fe-4S]

it adds additional coordinating sulphurs and keeps the cluster held to the protein

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21
Q

How are the variable oxidation states achieved in the clusters?

A

Electrons shuffle in and out of the cluster

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22
Q

What type of environment is required for radical chemistry?

A

An anaerobic environment

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23
Q

What shell element it iron?

A

A d shell element

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24
Q

This shows the scale of E’ for ease of redox…

A
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25
Q

Draw a standard electrode and its conditions

A
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26
Q

What do redox reactions allow ?

A
  • sort different metals according to their redox potential
  • sort Fe oxidation states according to their redox potential
  • look at different oxidation states and their solubility
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27
Q

Define Bioavailability

A

the proportion of a drug or other substance which enters the circulation when introduced into the body and so is able to have an active effect.

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28
Q

Whats the name for Fe(II) and Fe(III)?

A

Fe (II): Ferrous

Fe (III): Ferric

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29
Q

Draw the redox reaction between Ferrous and ferric

A
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30
Q

What colour solids are Fe2+ and Fe3+?

A

Fe2+ : black solid

Fe3+: red solid

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31
Q

Whats a Pourbaix diagram?

Whats labels are on the axis?

A

A map of conditions under which species are stable in water

X axis: Proton transfer (pH)

Y axis: Electron transfer (E/V)

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32
Q

Here is a Pourbaxi diagram of iron

Tell me the properties of Ferric

Tell me the properties of Ferrous

A

Ferric

  • Ferric: iron with an oxidation number +3 i.e. Fe (III) or Fe3+
  • Ferric is insoluble (soluble in pH<3 waters under oxidising conditions)
  • Fe3+ couldn’t be found in diet as is completely insoluble in pH in body

Ferrous

  • Ferrous: iron with an oxidation number 2+ i.e. Fe (II) or Fe2+
  • Ferrous only soluble under strong reducing conditions
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33
Q

What are the two types of Siderophore?

A

1. Siderophore ferrichrome

2. Siderophore enterobactin

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34
Q

Tell me about Siderophore ferrichrome

Identify the hydroxamate group on the image

A
  • Siderophores based on Hydroxamate
  • Ferrichrome is a Hexa-peptide: 3x Glycine, 3x N-hydroxyl-I-ornithine
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35
Q

Tell me about Siderophore enterobactin

A
  • Siderophores based on: Phenolates and Catecholate
  • Affinity for Fe (III), Ka ~ 1050. This means that bacteria can erode steel constructions
  • Siderophores have a low affiniy for Fe (II)
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36
Q

Draw the structures for:

Phenolates

Catecholate

A
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37
Q

What is used to transport iron in the blood plasma?

A

Transferrin

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38
Q

Tell me about the structure of Transferrin

A
  • Has 2 Fe molecules per protein
  • ASP and TYR provide a -ve charge each, which allow the Fe3+ to bind
  • Binds Fe (II) and carbonic acid (HCO3-)
  • The Fe (III) transferring complex contains carbonate (CO3-)
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39
Q

When iron is taken up whats used to help do this?

A

Sideophores

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40
Q

Whats Ferritin?

A
  • A storage protein
  • stores iron
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41
Q

Name an organ which can store iron

A

the liver

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42
Q

Whats the iron cycle…

A
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43
Q

Tell me about the structure of Ferritin?

A
  • Priniciple non-heme iron form
  • Mineral core contains:

up to 4500 Fe atoms

Hydrates Fe (III) oxide, similar to Ferrihydrite (5Fe2O3•9H2O)

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44
Q

Can iron be excreted in the human body?

A

no

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45
Q

Name a disease that leads to too much iron being present in the blood

What race is this usually found in?

A

Hereditary Hemochromatosis (HFE)

common in Northern European ancestry (in particular Celtic)

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46
Q

What organs are affected by iron overload?

A
  • Pituitary glans
  • Adrenal gland
  • Liver
  • Testis
  • Ovary
  • Pancreas
  • Heart and circulation
  • Thyroid and parathyroid glans
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47
Q

Whats the main function of iron in heme?

A

Cytochrome C: Heme containing protein involved in electron transfer- respiration, energy transduction

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48
Q

Whats Porphyrin?

A

Without a metal-ion in its cavity is a free base.

Some iron containing porphyrins are called hemes

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49
Q

How many bonds does the heme (iron in a porphyrin) contains?

What amino acid is present?

A

5 bonds, 3 of which are coordinate bonds

Histidine residue is also present

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50
Q

What does the heme; porphyrin need Fe2+ to be?

A

The Fe2+ needs to be on the plane in order for oxygen to be able to bind

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51
Q

What are the rules to follow when choosing which metal is best to use for something?

A

Rule 1: Rule of Abundance

When a function can be accomplished equivalently by two or more entities or elements then organisms will utilise the more abundant, readily available and accessible one (example: SrSO4 biominerals)

Rule 2: Rule of Efficiency

The rule of efficiency asserts that organisms will choose the more efficient entity as long as it is readily available (FeS cluster RedOx)

Rule 3: Rule of Basic Fitness

The rule of basic fitness asserts that for an element to be selected it should have a basic ability or potential to carry out the desired function - it should inherently fit to a particular function (Co in B12)

Rule 4: Rule of Evolutionary Improvements

Rule of basic fitness dictates which element is suitable for a specific purpose. However, although it may be able to do its job it may be unspecific, slow or have deleterious effects

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52
Q

What colour is the rock crab, Cancer productus, blood?

What is this colouring caused by?

A

The blood is a purple colour

this colouring is due to Hemocyanin

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53
Q

What organisms is Hemocyanin found in?

A

Arthropods and Molluscs

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54
Q

Tell me about the structure of Hemocyanin?

A

Contains 2 Copper ions coordinated by Histidines

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55
Q

Identify the Metals/ Metalloids and Non-metals

A
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56
Q

In biological systems, what are the several non-metals which are required?

A

H, C, N and O

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57
Q

The following nine elements are required in significant amounts, and are called Macronutients?

What does this term mean?

What are the nine elements which are macronutrients and identify which are the non-metals, metals and metalloids?

A

A Macronutrient is something that is required in large quantities in the diet

Macronutrients: S, P, Cl, Si, Na, K, Mg, Ca and Fe

non-metals: S, P and Cl

Metalloids: Si

Metals: Na, K, Mg, Ca and Fe

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58
Q

Whats a Micronutrient?

A

Something that’s not required in large amounts in the diet

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59
Q

There are 12 main micronutrients in the body. What are they and name which are metals/ non-metals

A

Micronutrients:

Non-metals: F, I and Se

Metals: V, Cr, Mn, Co, Ni, Cu, Zn, Mo and Sn

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60
Q

Some organisms require further micronutrients what are these and identify their group e.g. metals/ non-metals/ metalloids

A

Non-metals: Br

Metalloids: B, As

Metals: Sr, Ba, W, Cd

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61
Q

All the previous micro and macronutrients are the 25 essential elements

A
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62
Q

Name the non-metal and metal elements which are found in ALL biological systems

A

Non-metal: H, C, O and N

Metals: Na, K, Mg and Ca

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63
Q

Metals of the S-group are found in all biological system and are also the one with the highest incidence in humans. What is the element of the highest % and what is this?

A

there’s 1.5% of Ca2+ in the body and its important for biological function

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64
Q

What are the reasons for organisms to utilise specific metals?

A
  • chemical suitability of the element for the particular function
  • Choice is based in current availability
  • choice is also based on availiability in the evolutionary past
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65
Q

For an element to be of use to an organism, what must it be?

A
  1. available in the local environment
  2. abundant
  3. must be accessible/ extractable to the biological organism
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66
Q

When getting the metal thats needed what is this referred to as?

A

bioavailability

67
Q

Whats the main function of K+, Ca2+ and Mg2+

A

to serve as a structural and catalytic role in proteins

68
Q

Na+ and K+ are group 1 metals. what are they used for?

A

they are used in cell communication- nerve cells

69
Q

Ca2+ and Mg2+ are group 2 metals, what are they used for?

A

Bio-minerals and cell signalling, muscle and nucleotide chemistry

70
Q

Out of the group 1 metals of Na+ and K+, whats is the radius of each in Å?

A

Na+: 1.02 Å

K+: 1.38 Å

71
Q

Out of the group 2 metals of Mg2+ and Ca2+, what is the radius of each in Å?

A

Mg2+: 0.72 Å

Ca2+: 1.00 Å

72
Q

Tell me about the distribution of Na+, K+, Mg2+ and Ca2+ intracellularly and extracelluarly?

A

Na+ and K+ are reversed in the concentrations inside/outside cells

Big difference with Ca2+ inside/outside cells

73
Q

What is 1Å in nm?

A

1 Å = 0.1 nm

74
Q

Tell me about generation if action potentials and how this is linked with Na+ and K+ gates?

A
75
Q

Are outer S- electrons easily lost?

What does this mean that there is remaining?

A

outer S-electrons are easily lost which means that there no unpaired electrons

76
Q

Tell me about some states/ properties of S-metals?

A

The metals are in ionic state and are highly soluble

77
Q

Ionic bonds predominate as they are poor complexes, what is the exception to this?

A

Ca2+

78
Q

What two things can Ca2+ be?

A

It can be an ion and a complex forming metal

79
Q

Tell me some other properties of S-metals?

A
  • Diamagnetic
  • colourless
80
Q

Tell me properties of hard metals?

A
  • small
  • high charge
  • strong lewis acid/ base
81
Q

Tell me properties of soft metals ?

A
  • Large
  • low charge
  • weak lewis acid/ bases
82
Q

Tell me some examples of strong lewis bases?

A
  • OH-
  • OR-
  • PO43-
  • NO3-
  • Cl-
  • NH3
83
Q

Tell me some weak lewis bases?

A

the weak lewis bases of N, O and S donors

84
Q

In proteins what 3 ways are ligands made and give examples for each

A
  1. Hard: Glu/Asp, Thr/Ser/Tyr, peptide carbonyl C=O
  2. Borderline: Met/Cys
  3. Soft: peptide C(CO)N
85
Q

Tell me some regulatory actions of Ca2+

A

regulatory Actions:

  • Ca2+ can be passed across cell membranes
  • Ca2+ provides intracellular signals
  • Ca2+ is a famous secondary messenger
  • Ca2+ can switch metabolic reactions on and off
86
Q

Tell me some structural roles of Ca2+?

A
  • Ca2+ is found in bones and in teeth
  • Ca2+ has a structural role in proteins
87
Q

can Ca2+ be synthesised?

A

no

88
Q

Tell me about the structure of Calmodulin?

A
  • A total of 4 Ca2+ ions bind
  • Ca2+ binding results in conformational changes of calmodulin
  • Can change structures independently of Ca2+ levels
89
Q

Is FURA2 found in the body or is it synthesised?

A

its synthesised

90
Q

Is Ca2+ a hard or soft metal?

A

A hard metal

91
Q

Tell me about Ca2+ ligands?

A

They are carboxylates of acidic amino acids (Asp, Glu), Peptide carbnyl (C=O), and water

92
Q

Tell me about a identifiable characteristic of FURA2- Ca2+ complex?

A

it fluoresces

93
Q

What does sperm entry causes to occur during fertilisation?

A

sperm entry causes a Ca2+ wave through the egg

94
Q

What can be used to detect Ca2+?

A

FURA2

95
Q

What does Ca2+ trigger in the egg?

A

Meiosis in the egg

96
Q

Phosphate compounds of Ca2+ are used in teeth and bone. Tell me 2 different structures which can do this?

A

Ca5(PO4)3(OH)

Ca10(PO4)6(OH)3

97
Q

Name and draw 3 Ca2+ phosphate(s) structures

A
98
Q

What is used to make bone?

A
  1. Collagen triple helices: template for crystallization of hydroxyapatite
  2. undifferentiated bone-marrow stem cells bind
  3. cell differentiation to bone-forming osteoblasts
99
Q

What is the structure of the Ca2+ complex which is found in kidney stones and bladder stones

Whats the name of this compound?

A

“staghorn”- Calcium oxalate

100
Q

What does calcium oxalate often form around?

A

The uric acid nucleus

101
Q

How may kidney stones be prevented?

Tell me about certain food which are good/ bad for stone formation?

A

Kidney stones may be prevented with a low oxalate diet and by drinking plenty of fluids

Examples:

Bad:oxalate in spinach is a high

Ok: brussels sprouts are a moderate

Good: cauliflower a low oxalate vegetable.

102
Q

Chalk and eggshells are made from Calcium carbonate. Draw the structure of this?

A
103
Q

What is an egg shell made of?

A

Calcium carbonate embedded in organic compounds

104
Q

Eggshells contain more than 400 different proteins. Give examples of some which are required for

1. Structure

2. Defense

A

Structure

  • Ovalbumin
  • Ovocalyxin

Defense

  • Lysozyme
  • Ovotransferrin
105
Q

Name a Ca2+ carbonate stone/ crystal?

A

Otolith

106
Q

What is otolith comprised of?

A
107
Q

Tell me what the following Ca2+ compounds are found in:

  1. Ca2+ oxalate
  2. Ca2+ carbonate
  3. Ca2+ phosphate
A
  • Ca2+ oxalate: in stones
  • Ca2+ carbonate: on egg/ seashells, otoliths
  • Ca2+ phosphate: in bones, teeth
108
Q

Name an organelle that stores/ releases Ca2+?

A

The Sarcoplasmic reticulum

109
Q

Whats required to activate muscles?

A

Ca2+

110
Q

How does Ca2+ activate muscles?

A
  1. Ca2+ binds to troponin changing its conformation
  2. this pulls tropomyosin clear of the myosin binding site
  3. the myosin head can now engage with myosin binding site on actin
111
Q

As well as ATP, what else is bound to the myosin head and why?

A

The metal ion Mg2+ as its required to coordinate phosphates

112
Q

What is myosin?

A

an ATPase

113
Q

Why is Mg2+ required in the power stroke?

A
  • Required for catalysis
  • it counterbalances the charge that the ATP has
  • always attached to nucleic acids
114
Q

What is Mg2+ usually associated with?

A

nucleic acids

115
Q

Mg2+ is required in enzymes to bind nucleotides or nucleic acids; give some examples of this?

A
  1. Polymerases
  2. ATPases / kinases (kinases transfer a phosphate onto something)
  3. GTPases
116
Q

What is Mg2+ the cofactor to?

A

Mg2+ is the metal in chlorophyll

117
Q

What is Strontium, Sr?

A

A biomineral that can replace Ca2+

118
Q

Whats Sr dating?

A

Sr dating of organisms by looking at Sr content in bones. Something to do with diet and amount of Sr taken up. Look at how populations move around the globe/ where they came from/ helps tackle migration pathways

119
Q

What is Sr found in?

A

Radiolaria plankton (exoskeleton made of Sr)

Acantharia sp.

SrSO4 crystals

120
Q

Tell me the most significant, by mass of the S-group metals

A

Ca++ > K+ > Na+ > Mg++

121
Q

Whats the most important metal for biomineralisation?

A

Ca2+

122
Q

Where is controlled crystallisation found?

A

in the inner ear

123
Q

The S-group metals are good for ionic character in signalling, what are the d-group metals good for?

A

Redox or electron transfer

124
Q

Are the d-group metals radii quite similar?

A

yes they are very similar

125
Q

Tell me about the d-group metals oxidation states?

A

Elements at the end have only one oxidation states.

All the others have at least two positive oxidation numbers

elements close to the centre have the largest range

126
Q

Tell me about repulsion in d-group d-orbitals?

A

Have electrons in different regions in space; hence elections repel each other only weakly

127
Q

Tell me the main reason to the conductivity of metals

A

The electrons are not localised to specific nuclei

The electrons distribute over several nuclei

This is the main reason for conductivity of metals

128
Q

Whats required to form a coordinate/ dative bond?

A

electron pair donors

129
Q

Whats a Lewis base?

A

It donates electron pairs

130
Q

In a dative bond, what does the double arrow represent?

A

It indicates the dative bond (both electrons from the Lewis base)

131
Q

What does the reaction between Lewis acids and Lewis bases form?

A

Lewis acid + Lewis base –> Lewis adducts

132
Q

Give an example of a hard base and a hard acid

A

Hard base: Ammonia

Hard acid: Zn2+ (important function in catalytic reactions)

133
Q

is Zn2+ an enzymatic cofactor ?

A

yes

134
Q

What does Zn2+ accept a free electron pair from?

A

Carbonyls, acids (Lewis bases)

135
Q

Whats a Metalloprotease?

A

Members of a clan of proteases that contain a metal ion at their active site which acts as a catalyst in the hydrolysis of peptide bonds

136
Q

Give 2 examples of a Metalloprotease?

A
  1. Termolysin; bacterial protease
  2. Matrix-Metalloproteases (MMP)
137
Q

Give some examples of Metallo-enzymes-catalysis

A
  • Iron
  • Magnesium
  • Zinc
  • Coper
  • Manganese
  • Nickel
138
Q

Tell me about the structure of Carbonic anhydrase

A
  • 3 x His
  • substrate H2O
  • substrate CO2

Theee His side chains coordinate Zn2+

139
Q

Tell me the products of the reaction between carbon dioxide and water ?

A

CO2 + H2O –> HCO3- + H+

140
Q

Common reactions of carbonic anhydrase to learn/ be aware of

A
141
Q

Provide some examples of how Zinc is used in enzyme catalysis

A

Example 1: Zn2+ is a Lewis acid catalyst in carboxy-peptidases, thermolysin, matrix-metalloproteinases

Example 2: carbonic anhydrase

conversion of CO2 and H2O to bicarbonate HCO3- and H+

essential to regulate blood pH

Example 3: beta-lactamase (cleaves penicillin)

142
Q

Why is Zn2+ a well-suited metal for catalysis ?

A

it can exchnage ligands quickly and is redox inactive

143
Q

Tell me about the uses of Mg2+ in metallo-enzymes?

A

Example 1: ribulose-1,5-bisphosphate carboxylase/oxygenase or RuBisCO

Add CO2 to ribulose 1,5-bisphosphate to form two glycerol 3-phosphates (C5 sugar + C1 give 2x C3 sugars)

Example 2: ATPases (kinases)

Example 3: Polymerases

144
Q

What does Rubisco contain?

A

catalytic Mg2+

145
Q

How many coodinate bonds can Mg2+ have bound to it in Rubisco?

What can the ligands be?

A

six

the ligands can be amino acids, water or substrate

146
Q

What has IUPAC decided a transition metal is?

A

a transition metal is an element that has an incomplete d-shell either in its neutral state or its ions

147
Q

Is Zn a transition metal?

A

No

148
Q

Tell me a structural role for Zn?

A

The zinc finger motif

(A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold)

149
Q

Whats a Zinc fingers biotechnological tool?

A

Directing endonucleases to their targets

150
Q

Tell me a rare cofactor thats found in the body?

A

Molybdopterin cofactor

0.0001% of the mass of the human body

151
Q

In the Molybdopterin cofactor, draw the bonding around the Mo but not the rest of the structure

A
152
Q

What is MoCo required in and give examples of this

A

its required in redox biology

Examples:

  • Sulfite oxidase, SO3 produces sulphate SO4
    *
153
Q

Tell me about the members in the ring system when Cobalt is in Vitamin B12

A

Co is bound to corrin: 15 membered ring system

154
Q

Tell me what 3 oxidation states Co can undertake?

A

Co (I)

Co (II)

Co (III)

155
Q

the electronic structure of Cobalamin is crucial for what?

A

The function of B12

156
Q

Tell me what oxidation state Co is in Methyl-cobalamin and what does this lead to Co having as an oxidation state ?

A

homocysteine → methionine

methyl-cobalamin is the Co (III) state

leads to formation of the Co(I) cobalamin state

157
Q

How is Methyl-cobalamin formed?

A

formed by the conversion of methyl-tetrahydrofolate (methyl-THF) to tetrahydrofolate (THF)

158
Q

How many cycles can Methionine synthase go through?

A

it can go through 2000 cycles

159
Q

what can oxidative stress generate?

A

Co (II)

160
Q

What does Methionine synthase reductase do?

A

comes to rescue the Co (II) state and restores Co (III)

161
Q

Heres a flow diagram for methionine synthase

A
162
Q

Out of the following, identify the macronutrients and micronutrients;

  • Mg
  • Fe
  • Mo
  • Co
A

Macronutrients

Mg

Fe

Micronutrients

Mo

Co

163
Q

Chlorophyll and heme are built on the same porphyrin ring system but carry different metal center’s, what are these centres?

A

Heme: Fe2+

Chlorophyll: Mg2+

164
Q

Why is Ni selected against as the metal to use?

A

It would poison many enzymes

BIOL1021 (12 decks)

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