L1: Charge and Shape in Biological Systems Flashcards
What determines the structure and function of biological molecules, cells, organs, and organisms?
Determined by the interactions of the atoms they are made from
What is it that nature is able to achieve so well and is so remarkable?
Able to produce many different molecules from very few building blocks - use very similar elements
What does the nucleus of an atom consist of?
Protons and neutrons
What mass and charge do protons and neutrons have?
Both has a mass of 1
Protons have a charge of +1
Neutrons have a charge of 0
What property results from the nucleus having both protons and neutrons?
- The nucleus is very dense - most of the mass is concentrated here
- Accounts for very little of the volume
What surrounds the nucleus? How are these arranged?
Cloud of electrons arranged in shells which can contain 2, 8, or 18 electrons
What charge and mass do electrons have?
Mass of 0
Charge of 1/1836
What do all atoms of an element have in common?
All have the same number of protons (same atomic number)
Why are partially filled electron shells not preferable? How is this resolved?
Not as energetically preferable as filled shells
Atoms donate and accept electrons in order to achieve the octet rule, to become more stable
What is a cation?
Atoms which have lost electrons from their outer shell to become positively charged
What is an anion?
Atoms which have gained electrons in their outer shell to become negatively charged
Define ionic bonding
Electrostatic attraction between a metal and non-metal, formed from the transfer of electrons, to form a giant ionic lattice structure
Which is the cation and which is the anion? Why?
Na+ is the cation - loses electron to Cl
Cl- is the anion - gains electron Na
What ion does hydrogen form? How?
- Loses an electron to form H+
- No electrons so is just a proton
What chemical property does H+ cause?
Responsible for acidity - pH is a measure of the concentration of free H+ ions
Define covalent bonding
- Localised electrostatic attraction between a shared pair of electrons and the nuclei of the bonded atoms. There is overlap of the atomic orbitals, where the electrons are shared
- Covalent bonding is very strong
Why is covalent bonding a favourable process?
By sharing electrons this brings the molecule to a lower energy level overall
Why can water form?
- Oxygen has a slight negative charge and hydrogen has a slight positive charge
- Oxygen is more electronegative than hydrogen, meaning the shared pair of electrons are more greatly attracted to oxygen
- This creates a polar bond
What type of bonding can form as a result of water being a polar molecule?
Hydrogen bonding between water molecules
What two types of bonding are found in liquid water? Where?
- Covalent bonds (sharing electrons between oxygen and hydrogen)
- Hydrogen bonds attraction between non-bonding electrons on oxygen and hydrogens on adjacent water molecules)
What is one of the most important functions of hydrogen bonding other than in water?
- Between base pairs in DNA
- Specificity of the base-pairing results from specific hydrogen bonding patterns between A/T and C/G
Why does water have a high latent heat capacity?
Lots of hydrogen bonds in water, means it requires a large amount of kinetic energy to break the hydrogen bonds, which gives water stability
Why can ice float?
- Ice is less dense than water
- Most substances are more dense in a solid form. The hydrogen bonds in the water molecule fix at lower temperatures, causing the polar molecules to move further apart than in the liquid state to form a lattice structure
- This produces a giant covalent structure, which oxygen atoms at the centre of a tetrahedral structure.
Why is ice floating so important?
- Important to evolution
- Allows ice to be an insulator and life to survive underneath, which allowed life to survive and evolve over generations
Why is water being a polar molecule beneficial?
- Makes water a good solvent
- Able to solubilise polar regions of molecules (or polar species like ions)
- Driver of the conformation of biological structures
What can water not solubilise? Why?
- Non-polar molecules
- Because water is polar and repels non-polar molecules so H bonding does not occur
What is meant by hydrophilic/lipophobic?
Areas of molecules with charge, good hydrogen-bonding potential and/or a low proportion of carbon atoms tend to sit in or face water
What is meant by hydrophobic/lipophilic?
Areas of molecules with high proportion of carbons tend to be pushed out of the aqueous phase
What is one of the biggest examples of a structure formed due to differences in polarity?
Phospholipid bilayer - negatively charged polar head which is hydrophilic and a neutrally charged non-polar fatty acid tail which is hydrophobic/lipophilic
What are two other examples of phospholipid structure which are determined by polarity?
Liposome - bilayer of phospholipids in a sphere
Micelle - monolayer of phospholipids in a sphere
Define what an acid is
- Acids are compounds that can lose an H+ ion (proton), in the process they become negatively charged
- Fully dissociate in an aqueous solution but will remain associated as the covalent molecule in a less polar solvent
Name some strong inorganic acids
Hydrochloric acid
Sulphuric acid
Why can equilibrium occur in a weak organic acid?
The energy difference between the two states can be relatively small, allowing a shift in equilibrium between each side of the reaction, and a back and forth between the form, possible in the physiological pH range
What is an example of a weak organic acid?
Any carboxylic acid
Define what a base is
Bases are compounds that can (reversibly) form covalent bonds by taking an H+ ion to become positively charged
Can equilibrium occur in weak bases like with with acids?
- Yes
- At a physiological pH
- Energy difference between the two states is relatively small
Which two acidic amino acids are predominantly ionisable at a physiological pH?
Glutamic acid and aspartic acid
What charge do acidic amino acids have at a physiological pH? What is the pKa value?
Negatively charged
Low pKa - less than 7.4
Which two basic amino acids are predominantly ionisable at a physiological pH?
Lysine and Arginine
What charge do basic amino acids have at a physiological pH? What is the pKa value?
Positively charged
High pKa above 7.4
What property do the acidic and basic amino acids have when charged?
VERY hydrophilic
When something is charged it is very soluble in water
What structure do the backbone amines and carboxylic acids combine to form in peptides?
Amides /amide linkages
Giver an overall equation for the formation of an amide
What property is significant about amides?
Neutral across the physiological pH range, so DO NOT ionise
What groups have an impact on the structure of the protein?
Side/ R-groups
What can influence the side/R-group structures?
The ionisation states on the amino acids
What is the primary structure of a protein?
The order of the amino acids - the polypeptide sequence
How does the primary structure of a protein influence the secondary structure?
- Arrangement of primary structure into defined regions, e.g. alpha helix and beta sheets
- Determined by the shape (conformational preference) of the residues due to their hydrophobicity/hydrophilicity preference (determined by the R groups) and maintained by regular hydrogen bonding pattern
What is the tertiary structure of a protein?
- Higher order of folding from secondary structure which gives the overall shape of a protein
- Conformation of residues influences the structure ( the most common is proline-induced turns)
- More bonding interactions (ionic and H bonding are the most important) and disulfide bridges/bonds between cysteines
How does hydrophilicity play a role in the folding of a protein?
Lipophilic/hydrophobic residues prefer to be at the center of the protein (away from water) and will influence structure
