Biochemistry Flashcards
How do electrons exist?
In a probability density - they belong in a certain possibility within
How are shells and sub shells arranged?
By energy level
Why are electrons added to 4s before 3d?
4s is at a lower energy level than 3d
What causes electron shielding and what does electron shielding cause?
Filled up shells and sub shells - it weakens the nuclear charge to outer electrons
Definition of a mole?
Amount of any substance that contains as many elementary entities as there are atoms in 12 grams of pure carbon-12
What does periodicity refer to?
Patterns of physical and chemical properties within the periodic table
What happens to the atomic radius as you go down a group?
Down a group - atomic radius increases
What happens to the atomic radius when you go across a period and why?
Atomic radius decreases. This is because as you go across a period, more electrons are being added to the sub shells but they’re not increasing in energy levels so theres no extra shielding. However, you’re adding more protons which increases the nuclear charge and draws more electrons closer to the nucleus
Definition of ionisation energy?
The energy required to remove one mole of electrons from one mole of gaseous atoms
Why do noble gases have a high ionisation energy?
Have a full outer shell of electrons
Why do group one elements have a low ionisation energy?
Theres only one electron in their outermost shell so theres low level of nuclear charge
What gives a higher level of stability in an atom?
When a sub shell if filled or half filled
Across a period, what is the general pattern of ionisation energy?
Increases
Down a group, what is the general pattern of ionisation energy?
Decreases
What is electronegativity?
A measure of the tendency of an atom to attract a pair of bonding electrons via Pauling scale. Fluorine is most electronegative (4.0) and Cs and Fr are least electronegative (0.7)
Across a period, what is the general patter of electronegativity and why?
Electronegativity increases across a period as there is a lower atomic radius so the nuclear charge exerts a higher level of control over outer shells of electrons
Down a group, what is the general patter of electronegativity and why?
Electronegativity decreases down a group as theres increased levels of shielding due to more filled shells so less attractive forces from the nucleus to pull outer electrons closer
What is orbital hybridisation?
A theory/model that explains how elements form bonds when their electron structure is unfavourable - carbon is the biggest example of this
Why is carbon a good example of orbital hybridisation?
There are only 2 electrons in carbons outer shell but it needs 4 to share - it hybridises the outer electrons (making one large sub shell out of two) so 2p becomes 2sp^3. Each become half filled. The structure changes too and electrons spread as far as possible (trigonal pyramidal - 109.47º)
What is an ionic bond?
A chemical link between two oppositely charged ions, caused by the electrostatic force between oppositely charged ions in an ionic compound - always between metals and non-metals
Properties of ionic compounds
- High melting and boiling points
- Water soluble
What is a covalent bond?
A chemical link formed when two atoms share electron pairs - always between non-metals
How are carbon-carbon sigma bonds formed?
Through sp^3 hybridisation
How are carbon-carbon double bonds (pi bonds) formed?
Formed through sp^2 hybridisation using a sigma and pi bond. There’s an electron dense area surround the bonds
Properties of covalent compounds?
-Lower melting and boiling points due to fewer intermolecular interactions, though there are strong intramolecular. Water has a slightly higher mpt and bpt due to intramolecular interactions (hydrogen bonds)
What is co-ordinate bonding?
A co-ordinate covalent bond is a covalent link between two atoms, but in which both of the shared electrons comes from one of the bonding partners.
Frequently involves O, N, Cl due to unpaired/lone electrons
Most commonly found in transition metals
What is hydrogen bonding?
A weak electrostatic attraction that forms between polar molecules and occurs when. hydrogen atom bonds to.a highly electronegative atom (O-H, F-H, N-H, Cl-H)
Strength of hydrogen bonds
A hydrogen bond individually is very weak but if theres lots of them together in a structure, they’re strong e.g. in proteins, peptide bonds hold amino acids together but hydrogen bonds join amino acids together at different points
Definition of stereoisomer?
A form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms but differ in 3D orientations of their atoms in space
What are the 2 enantiomers of stereoisomers and which is in all human proteins?
L and D
L-amino acids is in all proteins in humans
What are the 5 classifications of amino acids by R group?
1) Non-polar, aliphatic R groups
2) Polar, uncharged R groups
3) Aromatic R groups
4) Positively charged R groups
5) Negatively charged R groups
Explain non-polar, aliphatic classification and some amino acid examples
Non-polar - Side chains cannot form hydrogen bonds/non-soluble in water (hydrophobic)
Aliphatic - A chain of carbons and hydrogens
Glycine - Simplest and only non-chiral amino acid as it doesn’t have 4 different groups
Proline - an IMINO acid, side chain forms a bond with nitrogen in amine group
Methionine - contains unreactive sulphur
Explain polar, uncharged classification and some amino acid examples.
Soluble in water, contains atoms that can form hydrogen bonds
Serine and threonine - contain hydroxyl groups that can be phosphorylated to control the activity of metabolic pathways
Cysteine - SH which forms hydrogen bonds and another amino acid can protect from oxygen free radicals (oxidative stress)
Explain aromatic classification
Benzene ring - relatively big - highly hydrophobic - tend to be found in the centre of water soluble proteins/outside of proteins in membranes (intact with hydrophobic fatty acids)
-Only 3 amino acids (proteinogenic) that can absorb UV light
Explain positively charged classification and AA examples
- Referred to as basic amino acids (lysine and arginine)
- Side chains are positively charged - electrostatic interactions (salt bridges)
Explain negatively charged classification and AA examples
- Each has COO- in side chain (aspartate and glutamate)
- Can form electrostatic interaction with positively charged R groups
- Can interact with metal ions
In humans, which amino acid is found at highest levels in the blood in its free form (not part of protein)?
Glutamine
Which pathways are important for amino acid synthesis?
Glycolysis, pentose phosphate pathway and TCA cycle (Krebs cycle)
What are essential amino acids?
We can’t make them, they have to come through the diet
What are non-essential amino acids?
We can make using one of more essential amino acid
What are conditionally essential amino acids?
Not required in healthy adults but are in young people and some diseased people. Its essential for them because they can’t generate enough themselves
Whats an electrophile?
reactive molecule thats attracted to areas rich in electrons - usually something with a negative charge or double bond (positively charged ions)
Features of alkanes
- Non-polar, few intermolecular bonds
- Small hydrocarbons have very low mpt and bpt, tend to be gases at room temp
- As chain increases, carbon chains wrap around each other and interacting, increasing bpt
Features of alkenes
-Unsaturated, have at least one pi bond
-More reactive than alkanes
-Less flexible than alkanes
-Found in unsaturated fatty acids
-Low mpt bpt
Non polar
