Biomolecules - Biological Chemistry 1A

Why is ribose less stable than deoxyribose

Extra -OH group destabilises the molecule

Why is ATP a good energy storage molecule?

Bonds between each phosphate group can be individually hydrolysed

When is ATP required in a reaction?

When it is thermodynamically unfavourable

What is sucrose formed from?

D-glucose and D-fructose

Which group on a nucleotide accepts and donates hydride ions?

Nicatinamide

Why is the extra -OH group on ribose in RNA destabilising?

Can undergo side reactions. Can act as a nucleophile, react with the phosphate and break the chain

Which is the acceptor and which is the donator in an A-T base bond?

Donor - Acceptor
Acceptor - Donor

Which is the acceptor and which is the donator in an G-C base bond?

Acceptor - Donor
Donor - Acceptor
Donor - Acceptor

What does 3' or 5' mean in a DNA strand?

Bonded on the 3rd or 5th Carbon in the ring

How is the DNA helix stabilised?

Double bonds sit on top of each other and pi bonds interact

How many DNA base pairs are there per turn?

10 (roughly)

What is the major groove in the DNA double helix?

Backbones further apart

What is the minor groove in the DNA double helix?

Backbones closer together

Which amino acid stereochemical arrangement dominates in nature in amino acids?

R (L configuration)

What does the chiral centre in an amino acid mean for its stereochemistry?

2 different configurations (R or S)

What is an aliphatic side chain?

Hydrocarbon chain

What can proline result in in an amino acid chain?

Kink

What is the only non-chiral amino acid?

Glycine

What are the two acidic amino acids?

Aspartate and glutamate

What do the acidic amino acids have a tendency to do?

Deprotonate to form an O- group

Which two amino acids are amides?

Asparagine and glutamine

Which two amino acids are bases?

Arginine and Lysine

Which alcoholic amino acid can show acidic tendencies?

Tyrosine (phenol group easy to deprotonate)

Which aromatic amino acid is slightly basic?

Histidine (Has an N with a lone pair)

Which two aromatic amino acids are very hydrophobic?

Tryptophan and Phenylalanine

Which amino acids are good for coordinating metals?

Cysteine and methionine

What is the very rare 21st amino acid?

Selenocysteine

What is meant by an essential amino acid?

Required in the diet, cannot be synthesised in the body quickly enough

What is lost when two amino acids are joined together?

Water

What is the bond between two amino acids caused?

Peptide

How can peptide chains be broken down in the lab?

Hydrolysis using strong acid or base

What direction does a protein chain extend in?

C terminus (carboxylic acid group end)

What is formed in the tertiary structure of a protein?

Different domains

How are different domains in a tertiary protein joined?

Short peptide chains

What is the purpose of the different domains in a protein?

Different functionality (bond to different groups)

What are the different sections of a quaternary protein known as?

Subunits

What are subunits in a quaternary protein?

Different proteins with different domains

What does glycine do in a protein chain?

Add flexibility (small)

Where can glycine often be found in a protein chain?

Mobile loops

Where can proline often be found in a protein chain?

Turns at the end of beta sheets

Where are hydrophobic amino acids often found in protein chains?

Protein interiors or spanning membranes

What type of reaction forms a disulfide bond?

Oxidation

What type of reaction breaks a disulfide bond?

Reduction

What is an example of a protein which has disulfide bonds?

Insulin

What forms the bond in a ligand?

Negative lone pair bonds to positive metal

Which group with a lone pair in an amino acid is unlikely to form a ligand bond?

OH group

Which metals can be found in bulk amounts in all cells?

Na, K, Mg and Ca

Which group of metals are found in small amounts in the body?

Transition metals

Which out of Na or K is pumped out of the cells?

Na

What is required for ion pumps to work?

ATP

What is coupled to Na migration into cells?

Sugar transport

What is affected by the concentration of Na and K in cells?

Protein solubility

What is the role of Mg in the body?

Forms complexes
Interacts with ATP

What is the role of Ca in the body?

Signalling
Kinases (e.g. myosin action)

What is the role of Mo in the body?

Nitrogen fixation (requires high E and T industrially)

What is the role of Mn in the body?

Water splitting enzyme

What is the role of Fe in the body?

Electron transfer proteins
Oxygen transport (heme)

What is the role of Cu in the body?

Electron transfer
Oxygen transport (hemocyanin)

Why are Fe and Cu used for electron transfer?

Variable oxidation states

What is the role of Ni in the body?

Hydrogenase

What is the role of Co in the body?

Vitamin B12

What is the role of Zn in the body?

Numerous enzymes (e.g. carbonic anhydrase)

What is the role of carbonic anhydrase?

pH balancing
CO2 transport in blood

Does carbonic anhydrase catalyse the forward or backward reaction?

Both

What allows efficient oxygen uptake and release by haemoglobin and myoglobin?

Cooperativity

What happens as pO2 increases?

Rate and strength of bonding increases

What conformation change takes place in His when oxygen bonds?

T-state to R-state

Does the T-state or R-state in haemoglobin bind to oxygen more strongly?

R-state

What happens when oxygen bonds to haemoglobin?

His moves inwards, protein destabilises. One subunit change induces all to change.

What drives ATP synthesis in the mitochndria?

Proton translocation

Which side of the membrane is acidic in the mitochondria?

Intermembrane space

How many complexes are involved in the electron transport chain during respiration?

4

How many complexes are involved in the electron transport chain during photosynthesis?

2

What reaction does cytochrome C catalyse?

Oxidation and reduction of iron

What makes a fatty acid unsaturated?

Carbon double bond

What is required for a fatty acid to react to form a basic soap?

NaOH

Why do most fatty acids have an even number of carbon atoms?

Synthesised 2 carbons at a time

What does the 18 mean in 18:3(n-3)?

Number of carbons

What does the first 3 mean in 18:3(n-3)?

Number of double bonds

What does the n-3 mean in 18:3(n-3)?

How far into the chain the first double bond is

How is a cis fatty acid changed to a trans fatty acid?

Hydrogenation (H2 gas and catalyst)

Are trans or cis fatty acids unhealthier?

Trans

What do cis double bonds in fatty acids result in?

Curving (worse molecule packing, weaker intermolecular forces, difficult to solidify)

How is energy released by fats in the body?

Hydrolysis of ester bonds

Which amino acid can be used in place of a phosphate group in a phospholipid?

Serine

What is the purpose of cholesterol?

Spaces out phospholipids
Regulates membrane fluidity
Contributes to lipid raft structure

Which type of cholesterol is bad?

LDL (low density lipoprotein)

Are the reactants of photosynthesis or respiration thermodynamically stable (require energy to start reacting)?

Photosynthesis

What forms can sugars be found in?

Aldose or Ketose

Are sugars found in the D or L conformation in nature?

D

Do horizontal lines in Fischer projections go into or out of the plane?

Out

Do vertical lines in Fischer projections go into or out of the plane?

Into

What is the result of a C being bonded to 2xO in a sugar ring?

Less stable and easier to hydrolyse

What is the name for the sugar projection with the sugar in a ring?

Howarth

What is the name for the sugar projection with the sugar in a straight line?

Fischer

What is the name for the sugar form which has a six membered ring?

Pyranose

What are the steps for identifying a sugar from the chair conformer?

1. Identify anomeric C
2. Draw -OH as above/below ring
3. Add the extra C above the ring

What side are -OH groups below the sugar ring shown on in a Fischer projection?

Right

What is the name given to the sugar conformation with a 5 membered ring?

Furanose

Does glucose prefer the pyranose or furanose form?

Pyranose (beta pyranose)