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Must-know facts

24 facts

1Living and non-living matter contain the same elements; living matter has relatively far more carbon and hydrogen.
2Tissue ground in trichloroacetic acid and filtered gives the acid-soluble pool (filtrate) and the acid-insoluble fraction (retentate).
3Wet weight, then dry weight after removing water, then ash after burning; ash holds inorganic elements such as calcium and magnesium.
4Alpha-amino acids: H, COOH, NH2 and an R group on the alpha carbon; 20 types in proteins; glycine (R = H), alanine (methyl), serine (hydroxy methyl).
5Acidic glutamic acid, basic lysine, neutral valine; aromatic tyrosine, phenylalanine, tryptophan; zwitterion depends on pH.
6Palmitic acid 16 C, arachidonic acid 20 C; glycerol is trihydroxy propane; lecithin is a membrane phospholipid.
7Nucleoside = base + sugar; nucleotide = base + sugar + phosphate.
8Adenine and guanine are purines; cytosine, thymine and uracil are pyrimidines.
9Acid-soluble pool: 18 to about 800 Da. Macromolecules except lipids: 10,000 Da and above. Micromolecules: under 1000 Da.
10Lipids come down in the insoluble fraction as membrane vesicles; they are not strictly macromolecules.
11Water is the most abundant chemical in cells (70–90% of cell mass); proteins 10–15%.
12Proteins are heteropolymers joined by peptide bonds; cellulose is a homopolymer of glucose; inulin is a polymer of fructose.
13Collagen is the most abundant protein in animals; RuBisCO is the most abundant in the biosphere.
14Starch helices hold iodine (blue); cellulose cannot. Glycogen is branched, reducing end on the right.
15Chitin of arthropod exoskeletons is a complex polysaccharide of amino-sugars.
16Four levels of protein structure; only right-handed helices; adult haemoglobin = 2 alpha + 2 beta subunits.
17Ribozymes are nucleic acids that act as enzymes.
18Most enzymes are damaged above about 40°C; thermophile enzymes stay active up to 80–90°C.
19Carbonic anhydrase: about 200 molecules of H2CO3 an hour without it, about 600,000 a second with it (about 10 million times faster).
20Enzymes lower activation energy; E + S ⇌ ES → EP → E + P.
21Velocity rises with substrate and plateaus at Vmax when all enzyme is occupied.
22Malonate competitively inhibits succinic dehydrogenase by resembling succinate.
23Six enzyme classes: oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases.
24Co-factors: prosthetic group (haem in peroxidase and catalase), co-enzyme (NAD, NADP contain niacin), metal ion (zinc in carboxypeptidase).

Common traps

Where marks are lost

Putting lipids among the true macromolecules because they sit in the acid-insoluble fraction.

Lipids are small (never above 800 Da). They separate with the insoluble fraction only because broken membranes form insoluble vesicles. The true macromolecules are proteins, nucleic acids and polysaccharides.

Calling a nucleoside a nucleotide, or the reverse.

Nucleoside = base + sugar (adenosine). Add a phosphate esterified to the sugar and it becomes a nucleotide (adenylic acid).

Listing uracil or cytosine as purines.

Only adenine and guanine are purines. Cytosine, thymine and uracil are pyrimidines.

Naming RuBisCO as the most abundant protein in animals, or collagen as the most abundant in the biosphere.

Collagen: most abundant in the animal world. RuBisCO: most abundant in the whole biosphere.

Saying an enzyme changes the energy of the substrate or product, or makes an endothermic reaction exothermic.

An enzyme lowers only the activation energy, the climb to the transition state. The levels of S and P, and whether the reaction releases energy, stay the same.

Thinking low temperature destroys enzymes the way high temperature does.

Low temperature makes an enzyme temporarily inactive; high temperature denatures the protein and destroys activity.

Expecting velocity to keep rising in step with substrate concentration.

Velocity levels off at Vmax once every enzyme molecule is busy; adding more substrate then has no effect.

Mixing up the co-factor examples.

Haem is a prosthetic group (peroxidase, catalase); NAD and NADP are co-enzymes containing niacin; zinc is the metal ion of carboxypeptidase.

Calling a protein a homopolymer, or cellulose a heteropolymer.

A protein uses many types of amino acid, so it is a heteropolymer. Cellulose repeats only glucose, so it is a homopolymer.

Key terms

23 terms

Acid-soluble pool: The filtrate left when tissue ground in trichloroacetic acid is strained; it holds the small molecules.
Acid-insoluble fraction: The retentate from the same filtration; it holds proteins, nucleic acids, polysaccharides and membrane lipids.
Ash: What remains after dried tissue is fully burnt; it contains inorganic elements such as calcium and magnesium.
Alpha-amino acid: An amino acid whose amino and carboxyl groups are on the same carbon, the alpha carbon.
Zwitterion: The form of an amino acid that carries both a positive and a negative charge at a particular pH.
Triglyceride: Glycerol with three fatty acids esterified to it; a fat or an oil.
Phospholipid: A lipid containing phosphorus and a phosphorylated organic compound, found in cell membranes; lecithin is one.
Nucleoside: A nitrogen base attached to a sugar.
Nucleotide: A nucleoside with a phosphate esterified to its sugar; the building block of nucleic acids.
Secondary metabolite: A compound of plants, fungi or microbes, such as an alkaloid or pigment, whose role in its host is often not fully known.
Heteropolymer: A polymer built from more than one type of monomer, such as a protein.
Homopolymer: A polymer of one type of monomer repeated many times, such as cellulose.
Primary structure: The sequence of amino acids in a protein, from the N-terminal to the C-terminal.
Tertiary structure: The folding of a whole protein chain on itself into a three-dimensional shape.
Quaternary structure: The arrangement of two or more folded polypeptide subunits relative to one another.
Ribozyme: A nucleic acid that acts as an enzyme.
Active site: The crevice or pocket in an enzyme into which the substrate fits.
Activation energy: The difference in energy between the substrate and the transition state; enzymes lower it.
Vmax: The maximum velocity of an enzyme reaction, reached when all enzyme molecules are occupied by substrate.
Competitive inhibitor: A substance resembling the substrate that competes for the active site, like malonate for succinic dehydrogenase.
Apoenzyme: The protein part of an enzyme that needs a co-factor to be active.
Prosthetic group: An organic co-factor tightly bound to the apoenzyme, such as haem in catalase.
Co-enzyme: An organic co-factor that binds only briefly during catalysis and serves many enzymes, such as NAD.

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