Biological molecules

Question 1

what are macromolecules?

Answer 1

composed of molecular subunits

Question 2

what are supramolecular complexes?

Answer 2

assembly of macromolecules

Question 3

what are the 4 main tyoes of monomeric subunits (building blocks)?

Answer 3

amino acids –> proteins
fatty acids –> phospholipids
carbohydrates –> polysaccharides
nucleobases –> nucleic acids

Question 4

what are some characteristics of biomacromolecules?

Answer 4

Most of their constituents (natural building blocks) are chiral molecules which exist as
single enantiomers

Interactions between bio(macro)molecules are stereospecific: they require specific
configurations in the interacting molecules

The environment in which bio(macro)molecules interact is mainly constituted by
water: water is the solvent of all biochemical processes, and it often acts also as a
reactant in biochemical reactions

Question 5

what is the monosaccharide molecular formula?

Answer 5

Cm(H2O)n

Question 6

what is the empirical formula?

Answer 6

C(H2O)

Question 7

what are monosaccharides?

Answer 7

carbohydrates that cannot be hydrolysed to more simple compounds

Question 8

what are disaccharides?

Answer 8

sugar that can be hydrolysed to two monosacharides

Question 9

what are polysaccharides?

Answer 9

carbohydrates that can be hydrolysed to many monosaccharides

Question 10

what are the monosaccharides classifications?

Answer 10

1. the number of carbon atoms in the carbon chain
2. whether the sugar contains a ketone or an aldehyde group
3. the stereochemical configuration of the asymettrical carbon atom farthest from the carbonyl group (D= right, L=left)

Question 11

what are epimers?

Answer 11

diastereomers that differ only in the stereochemistry at a single carbon

Question 12

what are the steps of the functional group interconcersion (FGI) of aldehyde to hemiacetal?

Answer 12

• Step 1: Protonation of the carbonyl group
• Step 2: The OH group acts as a nucleophile
• Step 3: Deprotonation gives a cyclic hemiacetal
• Note: 5- and 6-membered cyclic hemiacetals are stable

Question 13

what is an aldohexoses?

Answer 13

glucose
the equilibrium favours six-membered rings with a hemiacetal linkage between the aldehyde carbon and the hydroxy group on C5

Question 14

what are anomers?

Answer 14

diastereomeric products

Question 15

what are the reactions of carbohydrates?

Answer 15

1. reduction
2. oxidation
3. glycoside formation
4. alkylation to give ethers and acylation to give esters

Question 16

what linkage does maltose have?

Answer 16

alpha-1,4’ glucosidic linkage

Question 17

what linkage does cellobiose have?

Answer 17

bet-1,4’ glucosidic linkage

Question 18

what linkage does lactose have?

Answer 18

beta-1,4’ galactosidic linkage

Question 19

what linkage does gentiobiose have?

Answer 19

beta-1,6’ glucosidic linkage

Question 20

what are oligosaccharides?

Answer 20

smaller polysaccharides, containing about 3-10 monosacharide units

Question 21

what is the charge of amino acids?

Answer 21

at physiological pH (around 7.4)

Question 22

what is the only amino acid that is not chiral?

Answer 22

glycine

Question 23

why is gly a special amino acid?

Answer 23

smallest r group
no contribution to hydrophobic effect
found in flexible protein regions

Question 24

why is cys a special acid amino?

Answer 24

the –SH group makes it polar. If at an appropriate distance, 2 cysteine residues can react (oxidise) to form a disulphide bond. These bonds are very important to strengthen protein 3-D structures. Although covalent, they are reversible upon reduction

Question 25

why is pro a special amino acids?

Answer 25

cyclic secondary amine (imino acid): rigid conformation, reduces the flexibility of the protein region. Often found at bends in protein secondary structures

Question 26

what amino acids are essential in the diet?

Answer 26

Arg, Val, His, Met, Leu, Thr, Lys, Phe, Trp, Iso

Question 27

what are the acid-base properties of amino acids?

Answer 27

1.High melting points, generally over 200 °C 2.More soluble in water than they are in other common organic solvents 3.Less acidic than most carboxylic acids and less basic than most amines. In fact, the acidic part of the amino acid molecule is the -NH3+ group, not a -COOH group. The basic part is the -COO- group, and not a free -NH2 group Amphoteric: having both acidic (NH3+) and basic (COO-) properties

Question 28

what is an isoelectric point pI?

Answer 28

pH at which concentration of the zwitterion is maximum. pH at which the concentrations ofcationic and anionic forms are equal

Question 29

what is the formula for isoelectric point pI?

Answer 29

pI: pKa2 (before) + pKa3 (after) /2

Question 30

what are the ways of synthesis of amino acids?

Answer 30

1. Naturally occurring amino acids: hydrolysis proteins and separation of the amino acid mixture 2. Reductive amination: biomimetic (“mimicking the biological process”) synthesis 3. Biological synthesis (biosynthesis) of amino acids 4. Transmission (biosynthesis, enzyme transaminase) 5. amination of an alpha-halo acid 6. the strecker synthesis

Question 31

what are the reactions of amino acids?

Answer 31

1. Esterification of the carboxyl group (in acidic conditions) 2. Acylation of the amino group: formation of amides

Question 32

how to form a peptide bond?

Answer 32

amines and acids condense, with the loss of H2O, to form amides

Question 33

what is a peptide?

Answer 33

compound containing two or more amino acids linked by amide bonds

Question 34

what are the features of the peptide bond?

Answer 34

Peptide bonds are rigid and planar: due to resonance, both the C-O and C-N bonds have partial double bond nature (electrons delocalised): big role in the 3-D structure of peptides and proteins (“protein folding”) Restrict rotation around the C-N bond: it cannot rotate freely. Rotation is instead permitted around the N-Cαand C-Cαbonds

Question 35

what are the different structures of protein?

Answer 35

1. the covalent-bonded structure (Amino acid linear sequence) 2. the hydrogen-bonded local 3-D arrangement into an a-helix or a pleated sheet 3. the complete 3-D conformation (Global arrangement of polypeptide chain) 4. the association of two or more peptide units in the active protein (Arrangement of multiple subunits into complexes)Protein Structure

Question 36

what are the characteristics of complex lipids?

Answer 36

-easily hydrolysed to simpler constituents -esters of long-chain carboxylic acids called fatty acids -two major groups of fatty acid esters are waxes and glycerides -waxes: esters of long-chain alcohols -glycerides: esters of glycerol

Question 37

what are the characteristics of simple lipids?

Answer 37

not easily hydrolysed by aqueous acid or base -steroids, prostaglandins and terpenes

Question 38

what are glyceides?

Answer 38

simple fatty acid esters of the trio glycerol

Question 39

what are triglycerides?

Answer 39

all three of the glycerol OH have been esterified by fatty acids

Question 40

what are phospholipids?

Answer 40

lipids that contain groups derived from phsphoric acid

Question 41

what are phosphoglycerides?

Answer 41

phosphoric acid group in place of one of the fatty acids of a triglyceride

Question 42

what are phosphatidic acids?

Answer 42

simplest class of phosphoglucerides. These consist of glycerol esterified by two fatty acids and one phosphoric acid group.