Metals Flashcards
Whats a Stromatolite?
- A single celled organism
- Colonies of small bacteria
- They produce oxygen
Whats a Cyanobacteria?
A phylum consisting of free-living bacertai and the endosymbiotic plasmids
When do Cyanobacteria increase in abundance?
In the Proterozoic
Whats the Proterozoic?
A geological eon spanning the time from appearamce of oxygen in the earths atmosphere to just before the proliferation of complex life on earth
Whats are Diblastic organisms?
animals with a body wall composed of only 2 layers; ectoderm and endoderm
What are Trilobites?
A group of extinct marine arachnomorph arthropods
whats the burgess shale ?
A fossil bearing deposit exposed in the canadian rocks of the british columbia, Canada
What was the atmospheric oxygen % before animals?
When dinosaurs were present?
When humans were present?
Before animals: 35%
Jurassic period: 25%
Human presence (today): 21%
In the early phases of the earths history, how was oxygen consumed?
Through chemical weathering and oxidation of surfaces
When did Stromatolites-layeres cyanobacteria- start producing oxygen?
In the Proterozoic period (2.5 Ga)
What does evolution of the chlorophyll allow?
How does this lead to the production of oxygen?
Photosynthesis
Now water and sunlight can be used to form organic compounds from carbon dioxide, which leads to the production of oxygen
In the early history, what compounds were there an abundance of?
What was being produced?
There was an abundance of: CO2, H2S and Fe2+
There was a production of organic compounds
What period did photosynthesis start?
Proterozoic period (2.5 Ga)
Why is high amounts of oxygen not good for Fe (II) ?
It gets oxidised which forms Fe (III)
Tell me the main features of the 2.8-2.0 Ga period?
- 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
This image shows the change in atmospheric and ocean compounds over history…
What are the two forms of the iron-sulphur clusters?
In the iron-sulphur clusters, does the Fe molecules ever touch one another?
no
What does the abundance of Fe allow in the iron-sulphur clusters?
Varying oxidation states
What amino acid is attached to the iron-sulphur clusted?
How?
why?
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
How are the variable oxidation states achieved in the clusters?
Electrons shuffle in and out of the cluster
What type of environment is required for radical chemistry?
An anaerobic environment
What shell element it iron?
A d shell element
This shows the scale of E’ for ease of redox…
Draw a standard electrode and its conditions
What do redox reactions allow ?
- 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
Define Bioavailability
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.
Whats the name for Fe(II) and Fe(III)?
Fe (II): Ferrous
Fe (III): Ferric
Draw the redox reaction between Ferrous and ferric
What colour solids are Fe2+ and Fe3+?
Fe2+ : black solid
Fe3+: red solid
Whats a Pourbaix diagram?
Whats labels are on the axis?
A map of conditions under which species are stable in water
X axis: Proton transfer (pH)
Y axis: Electron transfer (E/V)
Here is a Pourbaxi diagram of iron
Tell me the properties of Ferric
Tell me the properties of Ferrous
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
What are the two types of Siderophore?
1. Siderophore ferrichrome
2. Siderophore enterobactin
Tell me about Siderophore ferrichrome
Identify the hydroxamate group on the image
- Siderophores based on Hydroxamate
- Ferrichrome is a Hexa-peptide: 3x Glycine, 3x N-hydroxyl-I-ornithine
Tell me about Siderophore enterobactin
- 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)
Draw the structures for:
Phenolates
Catecholate
What is used to transport iron in the blood plasma?
Transferrin
Tell me about the structure of Transferrin
- 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-)
When iron is taken up whats used to help do this?
Sideophores
Whats Ferritin?
- A storage protein
- stores iron
Name an organ which can store iron
the liver
Whats the iron cycle…
Tell me about the structure of Ferritin?
- Priniciple non-heme iron form
- Mineral core contains:
up to 4500 Fe atoms
Hydrates Fe (III) oxide, similar to Ferrihydrite (5Fe2O3•9H2O)
Can iron be excreted in the human body?
no
Name a disease that leads to too much iron being present in the blood
What race is this usually found in?
Hereditary Hemochromatosis (HFE)
common in Northern European ancestry (in particular Celtic)
What organs are affected by iron overload?
- Pituitary glans
- Adrenal gland
- Liver
- Testis
- Ovary
- Pancreas
- Heart and circulation
- Thyroid and parathyroid glans
Whats the main function of iron in heme?
Cytochrome C: Heme containing protein involved in electron transfer- respiration, energy transduction
Whats Porphyrin?
Without a metal-ion in its cavity is a free base.
Some iron containing porphyrins are called hemes
How many bonds does the heme (iron in a porphyrin) contains?
What amino acid is present?
5 bonds, 3 of which are coordinate bonds
Histidine residue is also present
What does the heme; porphyrin need Fe2+ to be?
The Fe2+ needs to be on the plane in order for oxygen to be able to bind
What are the rules to follow when choosing which metal is best to use for something?
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
What colour is the rock crab, Cancer productus, blood?
What is this colouring caused by?
The blood is a purple colour
this colouring is due to Hemocyanin
What organisms is Hemocyanin found in?
Arthropods and Molluscs
Tell me about the structure of Hemocyanin?
Contains 2 Copper ions coordinated by Histidines
Identify the Metals/ Metalloids and Non-metals
In biological systems, what are the several non-metals which are required?
H, C, N and O
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 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
Whats a Micronutrient?
Something that’s not required in large amounts in the diet
There are 12 main micronutrients in the body. What are they and name which are metals/ non-metals
Micronutrients:
Non-metals: F, I and Se
Metals: V, Cr, Mn, Co, Ni, Cu, Zn, Mo and Sn
Some organisms require further micronutrients what are these and identify their group e.g. metals/ non-metals/ metalloids
Non-metals: Br
Metalloids: B, As
Metals: Sr, Ba, W, Cd
All the previous micro and macronutrients are the 25 essential elements
Name the non-metal and metal elements which are found in ALL biological systems
Non-metal: H, C, O and N
Metals: Na, K, Mg and Ca
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?
there’s 1.5% of Ca2+ in the body and its important for biological function
What are the reasons for organisms to utilise specific metals?
- 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
For an element to be of use to an organism, what must it be?
- available in the local environment
- abundant
- must be accessible/ extractable to the biological organism
When getting the metal thats needed what is this referred to as?
bioavailability
Whats the main function of K+, Ca2+ and Mg2+
to serve as a structural and catalytic role in proteins
Na+ and K+ are group 1 metals. what are they used for?
they are used in cell communication- nerve cells
Ca2+ and Mg2+ are group 2 metals, what are they used for?
Bio-minerals and cell signalling, muscle and nucleotide chemistry
Out of the group 1 metals of Na+ and K+, whats is the radius of each in Å?
Na+: 1.02 Å
K+: 1.38 Å
Out of the group 2 metals of Mg2+ and Ca2+, what is the radius of each in Å?
Mg2+: 0.72 Å
Ca2+: 1.00 Å
Tell me about the distribution of Na+, K+, Mg2+ and Ca2+ intracellularly and extracelluarly?
Na+ and K+ are reversed in the concentrations inside/outside cells
Big difference with Ca2+ inside/outside cells
What is 1Å in nm?
1 Å = 0.1 nm
Tell me about generation if action potentials and how this is linked with Na+ and K+ gates?
Are outer S- electrons easily lost?
What does this mean that there is remaining?
outer S-electrons are easily lost which means that there no unpaired electrons
Tell me about some states/ properties of S-metals?
The metals are in ionic state and are highly soluble
Ionic bonds predominate as they are poor complexes, what is the exception to this?
Ca2+
What two things can Ca2+ be?
It can be an ion and a complex forming metal
Tell me some other properties of S-metals?
- Diamagnetic
- colourless
Tell me properties of hard metals?
- small
- high charge
- strong lewis acid/ base
Tell me properties of soft metals ?
- Large
- low charge
- weak lewis acid/ bases
Tell me some examples of strong lewis bases?
- OH-
- OR-
- PO43-
- NO3-
- Cl-
- NH3
Tell me some weak lewis bases?
the weak lewis bases of N, O and S donors
In proteins what 3 ways are ligands made and give examples for each
- Hard: Glu/Asp, Thr/Ser/Tyr, peptide carbonyl C=O
- Borderline: Met/Cys
- Soft: peptide C(CO)N
Tell me some regulatory actions of Ca2+
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
Tell me some structural roles of Ca2+?
- Ca2+ is found in bones and in teeth
- Ca2+ has a structural role in proteins
can Ca2+ be synthesised?
no
Tell me about the structure of Calmodulin?
- A total of 4 Ca2+ ions bind
- Ca2+ binding results in conformational changes of calmodulin
- Can change structures independently of Ca2+ levels
Is FURA2 found in the body or is it synthesised?
its synthesised
Is Ca2+ a hard or soft metal?
A hard metal
Tell me about Ca2+ ligands?
They are carboxylates of acidic amino acids (Asp, Glu), Peptide carbnyl (C=O), and water
Tell me about a identifiable characteristic of FURA2- Ca2+ complex?
it fluoresces
What does sperm entry causes to occur during fertilisation?
sperm entry causes a Ca2+ wave through the egg
What can be used to detect Ca2+?
FURA2
What does Ca2+ trigger in the egg?
Meiosis in the egg
Phosphate compounds of Ca2+ are used in teeth and bone. Tell me 2 different structures which can do this?
Ca5(PO4)3(OH)
Ca10(PO4)6(OH)3
Name and draw 3 Ca2+ phosphate(s) structures
What is used to make bone?
- Collagen triple helices: template for crystallization of hydroxyapatite
- undifferentiated bone-marrow stem cells bind
- cell differentiation to bone-forming osteoblasts
What is the structure of the Ca2+ complex which is found in kidney stones and bladder stones
Whats the name of this compound?
“staghorn”- Calcium oxalate
What does calcium oxalate often form around?
The uric acid nucleus
How may kidney stones be prevented?
Tell me about certain food which are good/ bad for stone formation?
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.
Chalk and eggshells are made from Calcium carbonate. Draw the structure of this?
What is an egg shell made of?
Calcium carbonate embedded in organic compounds
Eggshells contain more than 400 different proteins. Give examples of some which are required for
1. Structure
2. Defense
Structure
- Ovalbumin
- Ovocalyxin
Defense
- Lysozyme
- Ovotransferrin
Name a Ca2+ carbonate stone/ crystal?
Otolith
What is otolith comprised of?
Tell me what the following Ca2+ compounds are found in:
- Ca2+ oxalate
- Ca2+ carbonate
- Ca2+ phosphate
- Ca2+ oxalate: in stones
- Ca2+ carbonate: on egg/ seashells, otoliths
- Ca2+ phosphate: in bones, teeth
Name an organelle that stores/ releases Ca2+?
The Sarcoplasmic reticulum
Whats required to activate muscles?
Ca2+
How does Ca2+ activate muscles?
- Ca2+ binds to troponin changing its conformation
- this pulls tropomyosin clear of the myosin binding site
- the myosin head can now engage with myosin binding site on actin
As well as ATP, what else is bound to the myosin head and why?
The metal ion Mg2+ as its required to coordinate phosphates
What is myosin?
an ATPase
Why is Mg2+ required in the power stroke?
- Required for catalysis
- it counterbalances the charge that the ATP has
- always attached to nucleic acids
What is Mg2+ usually associated with?
nucleic acids
Mg2+ is required in enzymes to bind nucleotides or nucleic acids; give some examples of this?
- Polymerases
- ATPases / kinases (kinases transfer a phosphate onto something)
- GTPases
What is Mg2+ the cofactor to?
Mg2+ is the metal in chlorophyll
What is Strontium, Sr?
A biomineral that can replace Ca2+
Whats Sr dating?
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
What is Sr found in?
Radiolaria plankton (exoskeleton made of Sr)
Acantharia sp.
SrSO4 crystals
Tell me the most significant, by mass of the S-group metals
Ca++ > K+ > Na+ > Mg++
Whats the most important metal for biomineralisation?
Ca2+
Where is controlled crystallisation found?
in the inner ear
The S-group metals are good for ionic character in signalling, what are the d-group metals good for?
Redox or electron transfer
Are the d-group metals radii quite similar?
yes they are very similar
Tell me about the d-group metals oxidation states?
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
Tell me about repulsion in d-group d-orbitals?
Have electrons in different regions in space; hence elections repel each other only weakly
Tell me the main reason to the conductivity of metals
The electrons are not localised to specific nuclei
The electrons distribute over several nuclei
This is the main reason for conductivity of metals
Whats required to form a coordinate/ dative bond?
electron pair donors
Whats a Lewis base?
It donates electron pairs
In a dative bond, what does the double arrow represent?
It indicates the dative bond (both electrons from the Lewis base)
What does the reaction between Lewis acids and Lewis bases form?
Lewis acid + Lewis base –> Lewis adducts
Give an example of a hard base and a hard acid
Hard base: Ammonia
Hard acid: Zn2+ (important function in catalytic reactions)
is Zn2+ an enzymatic cofactor ?
yes
What does Zn2+ accept a free electron pair from?
Carbonyls, acids (Lewis bases)
Whats a Metalloprotease?
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
Give 2 examples of a Metalloprotease?
- Termolysin; bacterial protease
- Matrix-Metalloproteases (MMP)
Give some examples of Metallo-enzymes-catalysis
- Iron
- Magnesium
- Zinc
- Coper
- Manganese
- Nickel
Tell me about the structure of Carbonic anhydrase
- 3 x His
- substrate H2O
- substrate CO2
Theee His side chains coordinate Zn2+
Tell me the products of the reaction between carbon dioxide and water ?
CO2 + H2O –> HCO3- + H+
Common reactions of carbonic anhydrase to learn/ be aware of
Provide some examples of how Zinc is used in enzyme catalysis
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)
Why is Zn2+ a well-suited metal for catalysis ?
it can exchnage ligands quickly and is redox inactive
Tell me about the uses of Mg2+ in metallo-enzymes?
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
What does Rubisco contain?
catalytic Mg2+
How many coodinate bonds can Mg2+ have bound to it in Rubisco?
What can the ligands be?
six
the ligands can be amino acids, water or substrate
What has IUPAC decided a transition metal is?
a transition metal is an element that has an incomplete d-shell either in its neutral state or its ions
Is Zn a transition metal?
No
Tell me a structural role for Zn?
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)
Whats a Zinc fingers biotechnological tool?
Directing endonucleases to their targets
Tell me a rare cofactor thats found in the body?
Molybdopterin cofactor
0.0001% of the mass of the human body
In the Molybdopterin cofactor, draw the bonding around the Mo but not the rest of the structure
What is MoCo required in and give examples of this
its required in redox biology
Examples:
- Sulfite oxidase, SO3 produces sulphate SO4
*
Tell me about the members in the ring system when Cobalt is in Vitamin B12
Co is bound to corrin: 15 membered ring system
Tell me what 3 oxidation states Co can undertake?
Co (I)
Co (II)
Co (III)
the electronic structure of Cobalamin is crucial for what?
The function of B12
Tell me what oxidation state Co is in Methyl-cobalamin and what does this lead to Co having as an oxidation state ?
homocysteine → methionine
methyl-cobalamin is the Co (III) state
leads to formation of the Co(I) cobalamin state
How is Methyl-cobalamin formed?
formed by the conversion of methyl-tetrahydrofolate (methyl-THF) to tetrahydrofolate (THF)
How many cycles can Methionine synthase go through?
it can go through 2000 cycles
what can oxidative stress generate?
Co (II)
What does Methionine synthase reductase do?
comes to rescue the Co (II) state and restores Co (III)
Heres a flow diagram for methionine synthase
Out of the following, identify the macronutrients and micronutrients;
- Mg
- Fe
- Mo
- Co
Macronutrients
Mg
Fe
Micronutrients
Mo
Co
Chlorophyll and heme are built on the same porphyrin ring system but carry different metal center’s, what are these centres?
Heme: Fe2+
Chlorophyll: Mg2+
Why is Ni selected against as the metal to use?
It would poison many enzymes
