Chapter 7: Biological molecules (C1913741)

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Getting started

“I’m on a low carb diet,” Mandy remarked.

“Well, in that case, it’s going to be important to know what carbs are, right?” Jamie replied.

1 Carbohydrates

Carbohydrate is derived from the words carbon and hydrate (meaning water), specifically, a 1:1 (carbon:water) relationship, meaning it has the empirical formula [mathjax]ce{C-H2O}[/mathjax].

An example of a carbohydrate is glucose [mathjax]ce{C6H12O6}[/mathjax], which is an aldehyde ([mathjax]CHO[/mathjax]) with four chiral (handedness, see ) carbons.

Humans can only absorb D-glucose. In a Fischer projection (the open-chain form, discussed ), D-glucose has its 6 carbons numbered from top to bottom, the first being a carbonyl carbon. The next 4 carbons are chiral carbons, the hydroxyl groups for them respectively, are on the right, left, right, and right sides. Carbon 6 is a part of an alcohol group, and as it has two hydrogens attached, is not chiral (handedness).

The diagram  distinguishes between D-glucose and L-glucose, in that: Whereas D [anomer]-glucose has the hydroxyl group towards the right of the highest numbered chiral carbon (carbon 5). In contrast, if the hydroxyl group were on the left [of the highest numbered chiral carbon 5], it would be L [anomer]-glucose. Note that the D- and L- are not related to dextrorotation or levorotation, which is lower case “d-“ and “l-“.

© 2014 MR. SHUM

Like other alcohols, the hydroxyl group on the fifth carbon can act as a nucleophile (love to donate electron pairs), and attack the carbonyl carbon (which because of its slightly positive charge, is a good electron acceptor, and hence electrophile). As the aldehyde and carbonyl carbon tends to undergo nucleophilic addition (discussed ), this will create a hexose (which is six membered ring monosaccharide, with all of its members a carbon, with the exception of one oxygen). The carbons are still named the same way, noting that the anomeric carbon (carbon number 1) is now bonded to two oxygens. The carbonyl carbon (carbon number 1) can have its hydroxyl group in the trans arrangement, facing in the direction against the methyl group [mathjax]ce{CH2OH}[/mathjax] (known as the alpha anomer), and therefore downward; or in the cis arrangement, facing in the direction [of the methyl group] (known as the beta anomer), and therefore upward.

© 2014 MR. SHUM

Glucose can be used to synthesize:

  • Glycogen, which are multi branched chains of glucose, linked by alpha glycosidic linkage. Glycogen is how animals store glucose
  • Starch, which like glycogen contains glucose units, which are again, joined by alpha glycosidic linkage. Plants store glucose as starch
  • Cellulose, which in contrast contain beta glycosidic linkage. Humans have the enzyme to break alpha linkages, but not beta linkages, prohibiting the breakdown of cellulose. This is why humans do not eat grass [which contains cellulose], but cows do. Plant cell walls are made from cellulose
  • Chitin, which again, in contrast contain beta glycosidic linkages. It is found in cell wall of fungi including mushrooms, the exoskeleton of arthropods like insects and lobsters

Enzymes are required to catalyze the hydrolysis (add water, see ) reaction of breaking down glycogen, starch and cellulose.

Formative learning activityMaps to RK7.A
What are carbohydrates?

2 Amino acids, proteins

For nomenclature, the carbonyl carbon is assigned the number 1, the next alpha, then beta, and so forth, until omega. Amino acids are molecules with the alpha carbon [of the amino acid] attached to four groups, including an (1) amine [mathjax]ce{-NH2}[/mathjax] group; (2) carboxylic acid [mathjax]-COOH[/mathjax] group; (3) hydrogen; and (4) a miscellaneous side chain [mathjax]-R[/mathjax] group.

© 2014 MR. SHUM

There are twenty amino acids, which differ only due to the R group [with the exception of proline]. The R group can be classified based on polarity and pH. Based on pH, histidine, lysine and arginine are basic; and aspartic acid and glutamic acid are acidic. Based on polarity, the nonpolar amino acids are valine, isoleucine, phenylalanine, methionine, alanine, leucine, tryptophan, proline, cysteine, glycine [which can be memorized with the mnemonic “VIP MALT PC Glycine”]; and the polar amino acids are the remainder. 9 of the 20 amino acids are essential, meaning they cannot be synthesized [de novo] by the body, and so must be supplied in diet.

Alpha amino acids are amino acids that have the amino group ([mathjax]ce{NH2}[/mathjax]) attached to the alpha carbon. Polypeptides are short chains of alpha amino acids, linked by peptide bonds/linkage. Peptide bonds form as a result of dehydration, where an [mathjax]OH[/mathjax] drops from [mathjax]COOH[/mathjax], and [mathjax]H[/mathjax] drops from [mathjax]ce{NH2}[/mathjax]. The amino acid after dehydration (loss of the respective groups) is referred to as a residue.

Proteins are long chains of amino acids. Peptide bonds have partial double bond character, so it is unable to rotate about its axis, which helps to establish the secondary and tertiary structures of the protein. So proteins have four distinct aspects of structure, including:

  • Primary structure, which is the sequence of amino acids
  • Secondary structure, which is the use of hydrogen bonds to link amide and carboxyl group, creating a coiled alpha helix, or folded beta sheet
  • Tertiary structure, which is the folding of a polypeptide into its 3D structure. It is caused by disulfide bonds between cysteine residues, ion-dipole bonds relating to the acidic and basic side chains of amino acids, dipole-dipole bonds relating to the polar and nonpolar side chains of amino acids, and London dispersion forces
  • Quaternary structure, which is the assembly of the tertiary subunits into a larger structure, caused by similar forces to tertiary structure

Although the amino acid is usually drawn in its unionized form, the carboxylic acid is a stronger acid than a protonated amine [see ], so the carboxylic acid is more likely to lose its proton. This will leave a negatively charged carboxylate ([mathjax]-CO_{2}^-[/mathjax]) and positively charged amino group ([mathjax]-NH_{2}^-[/mathjax]), known as a zwitterion (aka dipolar ion). As a result of the zwitterion, an amino acid has high melting point; has large dipole moments, therefore increasing boiling point; is water soluble; and because of the charges, is therefore less acidic than most carboxylic acids, but less basic than most amines.

© 2014 MR. SHUM

Isoelectric point is the pH at which a molecule carries no net charge. For an amino acid, this would be the pH at which the amino acid exists as a zwitterion. For all amino acids except histidine, lysine and arginine, the isoelectric point is below a pH of 7. The isoelectric points of the remaining amino acids is just under a pH of 6, except for aspartic acid and glutamic acid, which have an isoelectric point around a pH of 3. If an amino acid is in a solution with a pH below its isoelectric point [i.e. more acidic], the high concentration of [mathjax]ce{[H+]}[/mathjax] will protonate the carboxylic group [of the amino acid], leaving it with a positive charge. In contrast, if it is in a solution with a pH above its isoelectric point [i.e. more basic], the high concentration of [mathjax]ce{[OH-]}[/mathjax] will deprotonate the amino group [of the amino acid], leaving it with a negative charge. The charges can then be separated out by electrophoresis, which is where the amino acid solution is placed between two oppositely charged electrodes, such that the positively charged amino acids will then migrate towards the negative electrode, and the negatively charged amino acids will migrate towards the positive electrode. The zwitterion amino acids will remain stationary.

Denaturation is the application of heat or a strong chemical to a protein. Denaturation affects quaternary, tertiary and secondary structure. Primary structure is unaffected as covalent peptide bonds are not disrupted by denaturation.

Amino acids can react with itself to form a dipeptide, which is two amino acids linked by a single peptide bond. The amine ([mathjax]-NH_{2}[/mathjax]) on one amino acid acts as a nucleophile (likes to donate electron pairs, discussed ), reacting with, and substituting the hydroxyl group on the carboxylic acid (which with a carbonyl, is a good electrophile, liking to accept electron pairs) of the other amino acid.

Glycoprotein are proteins that contain carbohydrate chains attached. Proteoglycans are a type of glycoprotein, with extra carbohydrate chains. Conjugated proteins are proteins with non-protein groups, for example, cytochrome found in blood.

Formative learning activityMaps to RK7.B
What are amino acids? What are proteins, and how do they relate to amino acids?

3 Lipids

Lipids are molecules that have low water solubility. Because of the rule like dissolves like, lipids thus are or have nonpolar components. Lipids can be divided into:

  • Fatty acids, which are a carboxylic acid with a long fatty chain. Fatty means nonpolar carbon chain. Thus, fatty acids are amphipathic, as they have a polar carboxylic acid head, and a nonpolar carbon chain tail. The longer the carbon chain, the more nonpolar the molecule in its entirety is. Fatty acids can be further divided into saturated fatty acids, where all carbon bonds are single; and unsaturated fatty acids, where there is at least one non-single bonds. Saturated fatty acids are able to pack more closely as it is more orderly structured, therefore remain as a solid for longer, and hence have higher melting points. As they have increased London dispersion forces, they have higher boiling points. Fatty acids have three functions in the body, including (1) hormones (such as the 20 carbon fatty acid prostaglandin, containing a 5-carbon ring); (2) is a component of phospholipid and glycolipid; and (3) can act as fuel for the body. The [mathjax]pK_{a}[/mathjax] of most fatty acids is around 4.5, which is weakly acidic. Therefore, in the cytosol which has a slightly basic pH of around 7.2, most fatty acids would exist in their anion form. Fatty acids are stored in the body in the form of triglyceride (discussed ), which are found in adipose tissue
  • Triglycerides, which are a three carbon glycerol backbone, attached to three fatty acids via ester bonds. In the ester reaction, the acid is the carboxylic acid, and the alcohol is glycerol. The reaction can be reversed by hydrolysis, which is the addition of water, in a reaction known as lipolysis. High blood levels of the hormones: epinephrine, norepinephrine, glucagon, and ACTH (adrenocorticotropic hormone), stimulate lipolysis in adipose tissue. Prostaglandin inhibits lipolysis. Free fatty acids are released into the blood, bound to [the water-soluble transport protein] albumin, and exported to surrounding tissue, to enter the Krebs cycle (discussed ).Fat (9 calories per gram) contains more than twice the energy per gram, when compared with glucose or protein (4 calories per gram)
  • Phospholipids, which are like triglycerides, but only have two fatty acids, with the third one replaced with a phosphate group. Phospholipids are thus amphipathic, as the phosphate group is polar. Phospholipids are the major component of all cell membrane, known as the lipid bilayer, which has two layers of phospholipids, the polar region facing inside and outside the cell, and the nonpolar region against each other
  • Glycolipids, which are like phospholipids, but have the phosphate group replaced with a carbohydrate
  • Steroids, which are four ring structures
  • Terpenes, which notably include Vitamin A. Vitamin A, along with Vitamins D, E, K, are the fat soluble vitamins. This can be memorized with the mnemonic “a fat cat lived in the ADEK

Although lipids are hydrophobic, they can move through blood via lipoproteins, which is a phospholipid and protein shell that emulsifies fats. Examples of lipoproteins which enable fats to be carried in the bloodstream, include high-density (HDL) and low-density (LDL) lipoproteins.

Formative learning activityMaps to RK7.C
What are lipids?

4 Phosphorus compounds

Phosphorus compounds are compounds containing phosphorus. The majority of phosphorus compounds are fertilizers.

Formative learning activityMaps to RK7.D
What are phosphorous compounds?




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Chapter 7: Biological molecules - Organic chemistry - Pre-med science - MR. SHUM'S CLASSROOM