Biological molecules Flashcards
what are macromolecules?
composed of molecular subunits
what are supramolecular complexes?
assembly of macromolecules
what are the 4 main tyoes of monomeric subunits (building blocks)?
amino acids –> proteins
fatty acids –> phospholipids
carbohydrates –> polysaccharides
nucleobases –> nucleic acids
what are some characteristics of biomacromolecules?
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
what is the monosaccharide molecular formula?
Cm(H2O)n
what is the empirical formula?
C(H2O)
what are monosaccharides?
carbohydrates that cannot be hydrolysed to more simple compounds
what are disaccharides?
sugar that can be hydrolysed to two monosacharides
what are polysaccharides?
carbohydrates that can be hydrolysed to many monosaccharides
what are the monosaccharides classifications?
- the number of carbon atoms in the carbon chain
- whether the sugar contains a ketone or an aldehyde group
- the stereochemical configuration of the asymettrical carbon atom farthest from the carbonyl group (D= right, L=left)
what are epimers?
diastereomers that differ only in the stereochemistry at a single carbon
what are the steps of the functional group interconcersion (FGI) of aldehyde to hemiacetal?
- 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
what is an aldohexoses?
glucose
the equilibrium favours six-membered rings with a hemiacetal linkage between the aldehyde carbon and the hydroxy group on C5
what are anomers?
diastereomeric products
what are the reactions of carbohydrates?
- reduction
- oxidation
- glycoside formation
- alkylation to give ethers and acylation to give esters
what linkage does maltose have?
alpha-1,4’ glucosidic linkage
what linkage does cellobiose have?
bet-1,4’ glucosidic linkage
what linkage does lactose have?
beta-1,4’ galactosidic linkage
what linkage does gentiobiose have?
beta-1,6’ glucosidic linkage
what are oligosaccharides?
smaller polysaccharides, containing about 3-10 monosacharide units
what is the charge of amino acids?
at physiological pH (around 7.4)
what is the only amino acid that is not chiral?
glycine
why is gly a special amino acid?
smallest r group
no contribution to hydrophobic effect
found in flexible protein regions
why is cys a special acid amino?
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
why is pro a special amino acids?
cyclic secondary amine (imino acid): rigid conformation, reduces the flexibility of the
protein region. Often found at bends in protein
secondary structures
what amino acids are essential in the diet?
Arg, Val, His, Met, Leu, Thr, Lys, Phe, Trp, Iso
what are the acid-base properties of amino acids?
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
what is an isoelectric point pI?
pH at which concentration of the zwitterion is maximum. pH at which the concentrations ofcationic and anionic forms are equal
what is the formula for isoelectric point pI?
pI: pKa2 (before) + pKa3 (after) /2
what are the ways of synthesis of amino acids?
- Naturally occurring amino acids: hydrolysis proteins and separation of the
amino acid mixture - Reductive amination: biomimetic (“mimicking the biological process”) synthesis
- Biological synthesis (biosynthesis) of amino acids
- Transmission (biosynthesis, enzyme transaminase)
- amination of an alpha-halo acid
- the strecker synthesis
what are the reactions of amino acids?
- Esterification of the carboxyl group (in acidic conditions)
- Acylation of the amino group: formation of amides
how to form a peptide bond?
amines and acids condense, with the loss of H2O, to form amides
what is a peptide?
compound containing two or more amino acids linked by amide bonds
what are the features of the peptide bond?
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
what are the different structures of protein?
- the covalent-bonded structure (Amino acid linear sequence)
- the hydrogen-bonded local 3-D arrangement into an a-helix or a pleated sheet
- the complete 3-D conformation (Global arrangement of polypeptide chain)
- the association of two or more peptide units in the active protein
(Arrangement of multiple subunits into complexes)Protein Structure
what are the characteristics of complex lipids?
-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
what are the characteristics of simple lipids?
not easily hydrolysed by aqueous acid or base
-steroids, prostaglandins and terpenes
what are glyceides?
simple fatty acid esters of the trio glycerol
what are triglycerides?
all three of the glycerol OH have been esterified by fatty acids
what are phospholipids?
lipids that contain groups derived from phsphoric acid
what are phosphoglycerides?
phosphoric acid group in place of one of the fatty acids of a triglyceride
what are phosphatidic acids?
simplest class of phosphoglucerides. These consist of glycerol esterified by two fatty acids and one phosphoric acid group.
