Biomolecules flash cards

1. 1.What is the aim of analysing the chemical composition of living tissue, and what are the two broad fractions obtained?

   Grind a tissue in acid (e.g. trichloroacetic acid) and filter. The filtrate = acid-soluble pool (small molecules, micromolecules); the retentate = acid-insoluble fraction (macromolecules).

   Hint: Trichloroacetic acid slurry filtered into two pools.

2. 2.Define biomolecules.

   All the carbon compounds obtained from living tissues are called biomolecules. They range from small (micro) molecules to large macromolecules.

   Hint: Carbon compounds of living matter.

3. 3.What is the molecular-weight cutoff used to separate micromolecules from macromolecules?

   Molecules with molecular weight less than ~1000 Da are micromolecules (acid-soluble); those greater than ~1000 Da (e.g. proteins, nucleic acids, polysaccharides) are macromolecules (acid-insoluble).

   Hint: ~1000 dalton boundary.

4. 4.Which biomolecule class is the MOST abundant in living organisms overall?

   Water (about 70–90% of the cell) is the most abundant molecule. Among the dry-weight organic macromolecules, proteins are the most abundant.

   Hint: Water overall; proteins among dry-weight organics.

5. 5.List the acid-soluble pool components.

   Amino acids, monosaccharides (sugars), nucleotides, nucleosides, fatty acids, glycerol, organic acids, vitamins, and other small metabolites.

   Hint: The building blocks and small metabolites.

6. 6.Which biomacromolecule is surprisingly found in the acid-SOLUBLE pool rather than the insoluble one, and why?

   Lipids. Though lipids can be large aggregates, individual lipid molecular weights do not exceed ~800 Da, so they come into the acid-soluble pool (they are part of membranes that break up on grinding).

   Hint: Lipids are technically not true macromolecules.

7. 7.QUESTION: In the acid-insoluble fraction of a tissue, name the four main classes of macromolecules found.

   Proteins, nucleic acids, polysaccharides, and lipids (lipids get carried into the insoluble fraction as part of membrane fragments, even though individual molecules are small).

   Hint: The four big biomacromolecule classes.

8. 8.Distinguish primary metabolites from secondary metabolites.

   Primary metabolites have identifiable functions in normal physiological processes (e.g. amino acids, sugars). Secondary metabolites have no obvious/direct role in the host's basic metabolism but are useful ecologically or to humans.

   Hint: Primary = essential physiology; secondary = 'extra'.

9. 9.Give examples of secondary metabolites and their categories.

   Alkaloids (morphine, codeine), terpenoids, essential oils, flavonoids, rubber, gums, drugs, pigments (carotenoids, anthocyanins), lectins, toxins, antibiotics.

   Hint: Alkaloids, pigments, rubber, antibiotics, toxins.

10. 10.In which organisms are secondary metabolites most commonly found?

    Mainly in plants, fungi, and microbes. Many have roles in defence, and many are of medicinal or commercial importance to humans.

    Hint: Plants/fungi/microbes — ecological & human uses.

11. 11.What are biomacromolecules, and which biomolecule class is excluded from the true polymer definition?

    Biomacromolecules are polymers (molecular weight > 1000 Da) with a defined arrangement of repeating units in the acid-insoluble fraction. Lipids are excluded — they are not true polymers/macromolecules despite appearing in that fraction.

    Hint: Polymers of MW >1000; lipids are the exception.

12. 12.Define carbohydrates and give their general empirical formula.

    Carbohydrates are polyhydroxy aldehydes or ketones (or compounds yielding them on hydrolysis). General formula: $(CH_2O)_n$ — hence 'hydrates of carbon'.

    Hint: Polyhydroxy aldehyde/ketone; $C_n(H_2O)_n$.

13. 13.Classify carbohydrates into three groups by degree of polymerisation.

    Monosaccharides (single sugar, e.g. glucose, fructose, ribose), oligosaccharides (2–10 units, e.g. sucrose, maltose, lactose), and polysaccharides (many units, e.g. starch, cellulose, glycogen).

    Hint: Mono / oligo / poly.

14. 14.Give the molecular formula of glucose and state its ring form.

    Glucose = $C_6H_{12}O_6$, an aldohexose. In solution it forms a six-membered pyranose ring (glucopyranose).

    Hint: Aldohexose, pyranose ring.

15. 15.What monosaccharide units make up sucrose, lactose, and maltose?

    Sucrose = glucose + fructose; Lactose = glucose + galactose; Maltose = glucose + glucose.

    Hint: Table sugar, milk sugar, malt sugar.

16. 16.Which sugars are the pentoses in nucleic acids, and how do they differ?

    Ribose (in RNA) has $-OH$ at the 2' carbon; deoxyribose (in DNA) has $-H$ at 2' (one oxygen less).

    Hint: 2'-OH vs 2'-H.

17. 17.Compare the structure and function of starch, glycogen, and cellulose.

    Starch = plant storage (amylose + amylopectin, $\alpha$-1,4 & $\alpha$-1,6 links), forms helix, gives blue with iodine. Glycogen = animal storage, highly branched. Cellulose = plant structural, $\beta$-1,4 links, straight fibres, no helix, not stained by iodine.

    Hint: Storage α (starch/glycogen) vs structural β (cellulose).

18. 18.Why can humans digest starch but not cellulose?

    Humans have $\alpha$-amylase to break $\alpha$-1,4 glycosidic bonds of starch but lack the enzyme (cellulase) to hydrolyse the $\beta$-1,4 bonds of cellulose.

    Hint: No cellulase for β-linkages.

19. 19.How does starch hold iodine to give the blue colour?

    The helical secondary structure of amylose traps iodine molecules within its coils, giving the characteristic blue-black colour. Cellulose, being non-helical, does not do this.

    Hint: Iodine sits inside the starch helix.

20. 20.Name some structurally complex/modified carbohydrates in living tissue.

    Aminosugars (e.g. glucosamine, N-acetyl galactosamine), chitin (exoskeletons of arthropods), and constituents of cell walls.

    Hint: Aminosugars and chitin.

21. 21.Define proteins and their monomer.

    Proteins are polymers of amino acids (polypeptides). They are the most abundant biomacromolecule and carry out most cellular functions.

    Hint: Polypeptides = amino-acid polymers.

22. 22.How many amino acids are commonly found in proteins, and how many are essential for humans?

    20 standard (proteinogenic) amino acids build proteins. Of these, ~9–10 are essential (must be obtained from the diet as the body cannot synthesise them).

    Hint: 20 standard; ~9 essential.

23. 23.Draw the general structure of an amino acid.

    A central $\alpha$-carbon bearing: an amino group $-NH_2$, a carboxyl group $-COOH$, a hydrogen $-H$, and a variable R (side chain) group. Substituted methanes.

    Hint: NH2, COOH, H and R on the α-carbon.

24. 24.On what basis are amino acids classified as acidic, basic, or neutral?

    On the nature of the R group: acidic (extra $-COOH$, e.g. glutamic acid), basic (extra $-NH_2$, e.g. lysine), or neutral (e.g. valine). Aromatic R groups also exist (e.g. tyrosine).

    Hint: Charge/nature of the side chain R.

25. 25.What is the ionizable/zwitterionic nature of amino acids?

    Amino acids exist in different ionized forms depending on pH. At a particular pH (the isoelectric point), they exist as a zwitterion ($-NH_3^+$ and $-COO^-$ simultaneously) with net zero charge.

    Hint: Zwitterion at isoelectric pH.

26. 26.Which bond links amino acids in a protein, and how is it formed?

    The peptide bond ($-CO-NH-$), formed by a dehydration (condensation) reaction between the $-COOH$ of one amino acid and the $-NH_2$ of the next, with loss of water.

    Hint: Peptide (amide) bond by condensation.

27. 27.Define the primary structure of a protein.

    The linear sequence of amino acids in a polypeptide chain, joined by peptide bonds. It has a left end (N-terminus, free amino group) and a right end (C-terminus, free carboxyl group).

    Hint: The amino-acid sequence, N→C.

28. 28.Which end of a polypeptide is written first (left), and what defines it?

    The N-terminus (amino terminal) is the first/left amino acid with a free $-NH_2$ group. The last/right is the C-terminus with a free $-COOH$.

    Hint: N-terminal on the left, C-terminal on the right.

29. 29.What is the secondary structure of a protein?

    Regular local folding of the polypeptide backbone stabilised by hydrogen bonds — forming $\alpha$-helix (right-handed helix) and $\beta$-pleated sheet patterns.

    Hint: α-helix and β-pleated sheet, H-bonded.

30. 30.Describe the tertiary structure of a protein and why it matters.

    The overall three-dimensional folding of the whole polypeptide into a compact shape (hollow, globular etc.). It is essential for the biological activity of the protein.

    Hint: The full 3-D shape; needed for function.

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