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PMP 102 > Biological molecules > Flashcards

Biological molecules Flashcards

1
Q

what are macromolecules?

A

composed of molecular subunits

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2
Q

what are supramolecular complexes?

A

assembly of macromolecules

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3
Q

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

A

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

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4
Q

what are some characteristics of biomacromolecules?

A

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

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5
Q

what is the monosaccharide molecular formula?

A

Cm(H2O)n

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6
Q

what is the empirical formula?

A

C(H2O)

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7
Q

what are monosaccharides?

A

carbohydrates that cannot be hydrolysed to more simple compounds

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8
Q

what are disaccharides?

A

sugar that can be hydrolysed to two monosacharides

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9
Q

what are polysaccharides?

A

carbohydrates that can be hydrolysed to many monosaccharides

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10
Q

what are the monosaccharides classifications?

A
  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)
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11
Q

what are epimers?

A

diastereomers that differ only in the stereochemistry at a single carbon

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12
Q

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

A
  • 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
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13
Q

what is an aldohexoses?

A

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

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14
Q

what are anomers?

A

diastereomeric products

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15
Q

what are the reactions of carbohydrates?

A
  1. reduction
  2. oxidation
  3. glycoside formation
  4. alkylation to give ethers and acylation to give esters
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16
Q

what linkage does maltose have?

A

alpha-1,4’ glucosidic linkage

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17
Q

what linkage does cellobiose have?

A

bet-1,4’ glucosidic linkage

18
Q

what linkage does lactose have?

A

beta-1,4’ galactosidic linkage

19
Q

what linkage does gentiobiose have?

A

beta-1,6’ glucosidic linkage

20
Q

what are oligosaccharides?

A

smaller polysaccharides, containing about 3-10 monosacharide units

21
Q

what is the charge of amino acids?

A

at physiological pH (around 7.4)

22
Q

what is the only amino acid that is not chiral?

A

glycine

23
Q

why is gly a special amino acid?

A

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

24
Q

why is cys a special acid amino?

A

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

25
Q

why is pro a special amino acids?

A

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

26
Q

what amino acids are essential in the diet?

A

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

27
Q

what are the acid-base properties of amino acids?

A

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

28
Q

what is an isoelectric point pI?

A

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

29
Q

what is the formula for isoelectric point pI?

A

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

30
Q

what are the ways of synthesis of amino acids?

A
  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
31
Q

what are the reactions of amino acids?

A
  1. Esterification of the carboxyl group (in acidic conditions)
  2. Acylation of the amino group: formation of amides
32
Q

how to form a peptide bond?

A

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

33
Q

what is a peptide?

A

compound containing two or more amino acids linked by amide bonds

34
Q

what are the features of the peptide bond?

A

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

35
Q

what are the different structures of protein?

A
  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
36
Q

what are the characteristics of complex lipids?

A

-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

37
Q

what are the characteristics of simple lipids?

A

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

38
Q

what are glyceides?

A

simple fatty acid esters of the trio glycerol

39
Q

what are triglycerides?

A

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

40
Q

what are phospholipids?

A

lipids that contain groups derived from phsphoric acid

41
Q

what are phosphoglycerides?

A

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

42
Q

what are phosphatidic acids?

A

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

PMP 102 (29 decks)

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