Lesson 1 of 5Biochemistry

Unit 1 · Lesson 1 of 5

The Chemistry of Life: Bonds, Water and Functional Groups

Atoms, isotopes and radioisotope tracers, ionic and covalent bonds, electronegativity, hydrogen bonds and the properties of water, pH and buffers, the six functional groups of biological molecules, and the four reaction types that cells run: condensation, hydrolysis, redox and neutralization.

8 min read10 practice questionsAsk AI about this →

Key things to remember

1 $Δ EN$ < about 0.5: nonpolar covalent; about 0.5–1.7: polar covalent; > about 1.7: ionic.
2A hydrogen bond is an attraction between a $δ^{+}$ H (on O or N) and a $δ^{-}$ O or N elsewhere; it is weak alone but powerful in large numbers.
3 $pH = - lo g [H^{+}]$ ; each pH unit is a tenfold change in $[H^{+}]$ . Blood is buffered at 7.35–7.45 by $H_{2} CO_{3} / HCO_{3}^{-}$ .
4Functional groups: hydroxyl –OH, carbonyl C=O, carboxyl –COOH (acid), amino –NH₂ (base), phosphate –OPO₃²⁻, sulfhydryl –SH (disulfide bridges).
5Condensation releases $H_{2} O$ to join monomers; hydrolysis uses $H_{2} O$ to split them. Joining $n$ monomers releases $n - 1$ water molecules.
6Redox: OIL RIG. The molecule that loses electrons is oxidized; the one that gains them is reduced.

A living cell is a crowded bag of chemicals following the same rules as chemicals in a beaker. The same few elements (carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur make up about 98% of your body's mass) are joined by the same few kinds of bonds. So why does a drop of oil bead up on water while sugar vanishes into it? Why does a protein lose its shape in a fever or in stomach acid? Why can a swimming pool stay cool on a hot afternoon? Every one of these comes down to which atoms are bonded, how evenly they share electrons, and which small groups of atoms hang off a molecule. This topic builds that chemical toolkit. Everything later in the course (enzymes, respiration, DNA, nerve impulses) is explained with it.

Atoms, isotopes and radioisotope tracers

An atom has a nucleus of protons (positive) and neutrons (neutral), surrounded by electrons (negative). The number of protons (the atomic number) fixes the element; the electrons, especially the outermost valence electrons, decide how it bonds. Isotopes are atoms of the same element with different numbers of neutrons, such as carbon-12 and carbon-14. Because isotopes have the same electrons, they react the same way, so a cell cannot tell them apart. Some isotopes have unstable nuclei and decay, giving off radiation; these are radioisotopes. That combination (chemically identical, but detectable) makes radioisotopes perfect tracers: swap a radioactive atom into a molecule, and you can follow where that molecule goes in a cell, an organism or a patient. Each radioisotope decays with a fixed half-life, the time for half of the radioactive atoms to decay. Medical tracers are chosen with short half-lives so they do their job and then fade quickly.

Isotope	Half-life	How it is used
Technetium-99m	about 6.0 h	The most widely used diagnostic tracer. It emits gamma rays that a camera outside the body can detect, and it is attached to carrier molecules that collect in bone, heart muscle or other target tissues.
Fluorine-18	about 110 min	Built into fluorodeoxyglucose (FDG) for PET scans. Cancer cells take up glucose quickly, so tumours show up as bright spots.
Iodine-131	about 8.0 days	The thyroid gland absorbs iodine to make thyroid hormones, so swallowed I-131 concentrates there and destroys overactive or cancerous thyroid tissue.
Cobalt-60	about 5.3 years	External radiation source for cancer therapy; cobalt-60 radiotherapy units were pioneered in Canada in 1951.
Carbon-14	about 5730 years	Research tracer (Melvin Calvin followed carbon-14 from $CO_{2}$ into sugars to map the Calvin cycle) and radiocarbon dating of once-living material.
Phosphorus-32 and sulfur-35	about 14 days and 87 days	Hershey and Chase (1952) labelled viral DNA with phosphorus-32 and viral protein with sulfur-35 to show that DNA is the genetic material.

Radioisotopes behave chemically like their stable isotopes, so cells process them normally while detectors track them.

Electronegativity, bond types and hydrogen bonds

Electronegativity (EN) is how strongly an atom pulls on the electrons in a bond. Oxygen (3.44) and nitrogen (3.04) are greedy; carbon (2.55) and hydrogen (2.20) are close to each other. The difference, $Δ EN$ , decides the bond type. In a nonpolar covalent bond electrons are shared about equally. In a polar covalent bond they are shared unequally, so the more electronegative atom gets a partial negative charge ( $δ^{-}$ ) and the other a partial positive charge ( $δ^{+}$ ). In an ionic bond the difference is so large that an electron is effectively transferred, forming oppositely charged ions that attract. A hydrogen bond is not a bond inside a molecule; it is the attraction between a $δ^{+}$ hydrogen (attached to O or N) on one molecule and a $δ^{-}$ O or N on another molecule or another part of the same large molecule. Each is only about one-twentieth as strong as a covalent bond, but there are enormous numbers of them. They hold water together, zip DNA's two strands, and fold proteins.

ΔEN	Bond type	Biological example
less than about 0.5	Nonpolar covalent	C–H bonds in fatty acid tails ( $Δ EN = 0.35$ ), which is why fats are hydrophobic
about 0.5 to 1.7	Polar covalent	O–H in water and sugars ( $Δ EN = 1.24$ ); N–H in amino acids ( $Δ EN = 0.84$ )
greater than about 1.7	Ionic	$Na^{+} Cl^{-}$ ( $Δ EN = 2.23$ ); ions such as $Na^{+}$ , $K^{+}$ and $Ca^{2 +}$ drive nerve impulses and muscle contraction

The cut-offs are guidelines, not sharp walls: bond character changes gradually as the EN difference grows.

Fig 1Each water molecule is bent and polar; its slightly negative oxygen attracts the slightly positive hydrogens of neighbouring molecules through hydrogen bonds.

Cohesion, adhesion and surface tension. Water molecules hydrogen bond to each other (cohesion) and to polar surfaces (adhesion). Together these pull water up the narrow xylem vessels of a tall tree and let a water strider stand on a pond.
High specific heat capacity ( $4.18\ \text{J/{(g}\cdot{}^\circ\text{C)}}$ ). Much of the energy added to water goes into breaking hydrogen bonds rather than speeding molecules up, so water's temperature changes slowly. Lakes, oceans and the water inside your cells buffer temperature swings.
High heat of vaporization. Evaporating water must break every hydrogen bond a molecule has, so sweat carries a lot of heat away as it evaporates. That is evaporative cooling.
Ice floats. In ice, hydrogen bonds lock molecules into an open lattice that is less dense than liquid water, so ponds freeze from the top down and the insulating ice lets aquatic life survive winter underneath.
Excellent solvent. Water's partial charges surround ions and polar molecules and pull them into solution. Substances that dissolve are hydrophilic (sugars, salts, amino acids); nonpolar ones that do not are hydrophobic (fats, oils). This split is what makes cell membranes form at all.

pH and buffers in brief

Water splits very slightly into

H^{+}

and

OH^{-}

. An acid releases

H^{+}

into solution; a base removes

H^{+}

(or releases

OH^{-}

). The pH scale measures

H^{+}

concentration:

pH = - lo g [H^{+}]

. Below 7 is acidic, 7 is neutral, above 7 is basic, and because the scale is logarithmic each pH unit is a tenfold change. A buffer is a pair of chemicals (a weak acid and its conjugate base) that soaks up extra

H^{+}

OH^{-}

so the pH barely moves. Human blood stays at pH 7.35–7.45 thanks to the carbonic acid–bicarbonate buffer:

H_{2} CO_{3} ⇌ H^{+} + HCO_{3}^{-}

. Add acid and bicarbonate grabs the

H^{+}

; add base and carbonic acid releases

H^{+}

to neutralize it. Buffers matter because every enzyme only works within a narrow pH range.

Functional groups: the working parts of biological molecules

Fig 2The six functional groups that matter most in biology: hydroxyl, carbonyl, carboxyl, amino, phosphate and sulfhydryl.

Group	Structure	Property	Where it matters
Hydroxyl	–OH	Polar; hydrogen bonds with water	Sugars, glycerol, alcohols; the many –OH groups are why sugars dissolve so easily
Carbonyl	C=O (aldehyde at the chain end, ketone in the middle)	Polar; reactive	Sugars: glucose is an aldehyde sugar (aldose), fructose a ketone sugar (ketose); a free carbonyl end is what Benedict's reagent detects (in the hot alkaline reagent fructose's ketone rearranges into an aldehyde, so it tests positive too)
Carboxyl	–COOH	Acidic: releases $H^{+}$ to become –COO⁻	Amino acids and fatty acids (that is why they are called acids)
Amino	–NH₂	Basic: accepts $H^{+}$ to become –NH₃⁺	Amino acids; the nitrogenous bases of DNA and RNA
Phosphate	–OPO₃²⁻	Negatively charged, hydrophilic; links between phosphates store transferable energy	ATP, the DNA and RNA backbone, phospholipid heads; adding a phosphate (phosphorylation) switches many proteins on or off
Sulfhydryl	–SH	Two –SH groups can join into a covalent disulfide bridge (–S–S–)	The amino acid cysteine; disulfide bridges lock proteins such as keratin (hair) into shape

A bare carbon-hydrogen skeleton is nonpolar and fairly unreactive. Functional groups are small clusters of atoms attached to it that behave the same way whatever molecule they sit on, so knowing these six lets you predict whether a molecule dissolves, acts as an acid or a base, and which bonds it can form.

The four main types of biochemical reaction

Fig 3Condensation (dehydration synthesis) joins monomers and releases a water molecule; hydrolysis uses a water molecule to split the bond again.

Reaction	What happens	Biological example
Condensation (dehydration synthesis)	Two molecules join by a covalent bond; an –OH from one and an –H from the other leave as $H_{2} O$ . Needs an energy input.	Glucose + glucose $\to$ maltose + $H_{2} O$ ; amino acids joining into a protein
Hydrolysis	Water is added across a bond and splits it: –H goes to one piece and –OH to the other. Usually releases energy.	Digestion of starch, proteins and fats; $ATP + H_{2} O \to ADP + P_{i}$
Oxidation–reduction (redox)	Electrons move from one molecule to another. The one that loses electrons is oxidized; the one that gains them is reduced. In cells, electrons often travel with hydrogen atoms.	$NAD^{+} + 2 e^{-} + H^{+} \to NADH$ ; in respiration glucose is oxidized to $CO_{2}$ and $O_{2}$ is reduced to $H_{2} O$
Neutralization	An acid and a base react to form water and a salt, moving the pH toward 7.	$HCl + NaOH \to NaCl + H_{2} O$ ; bicarbonate from the pancreas neutralizes stomach acid entering the small intestine

Remember redox as OIL RIG: Oxidation Is Loss, Reduction Is Gain (of electrons).

Worked examples

Reveal one step at a time and try to beat it to the next line.

Example 1

Use electronegativities (O 3.44, H 2.20, C 2.55, Na 0.93, Cl 3.16) to classify the O–H bond in water, the C–H bond in a fatty acid tail and the bond in sodium chloride. Then explain why table salt dissolves in water but cooking oil does not.

Example 2

A patient receives 800 MBq of technetium-99m (half-life 6.0 h) for a bone scan. How much activity remains 24 h later, and what percentage of the original is that?

Example 3

Starch is a chain of glucose units made by condensation. (a) How many water molecules are released when 5 glucose molecules are joined into a straight chain? (b) How many water molecules are needed to digest the chain back to glucose? (c) Name the reaction type in each direction.

Where marks get lost

Calling the O–H bond inside a water molecule a hydrogen bond. That bond is polar covalent; a hydrogen bond is the weaker attraction between separate molecules (or distant parts of one large molecule).
Mixing up hydrolysis and dehydration synthesis. Hydro-lysis means water-splitting: water is used to break a bond. Dehydration synthesis removes water to make a bond.
Thinking pH 4 is twice as acidic as pH 8. The scale is logarithmic, so a 4-unit difference is $1 0^{4} = 10000$ times more $H^{+}$ .
Confusing carbonyl (C=O) with carboxyl (–COOH). A carboxyl contains a carbonyl plus an –OH on the same carbon, and that combination makes it acidic.
Thinking oxidation always means adding oxygen. In biology it means losing electrons, often by losing hydrogen atoms, as when glucose is oxidized and $NAD^{+}$ is reduced to NADH.

Flashcards 9

Isotope

Radioisotope tracer

Electronegativity

Hydrogen bond

+ 5 more

Practice

Nitrogen has an electronegativity of 3.04 and hydrogen 2.20. Calculate

Δ EN

for an N–H bond in an amino group. Give two decimal places.

Which property of water best explains why coastal cities have milder temperature swings than inland cities?

How many kilojoules are needed to warm 250 g of water by 10.0 °C? Use

c = 4.18\ \text{J/{(g}\cdot{}^\circ\text{C)}}

and give three significant figures.

Gastric juice has a pH of about 2 and pure water a pH of 7. How many times greater is

[H^{+}]

in gastric juice?

times

Match each functional group to what it contributes.

Hydroxyl (–OH)

Carboxyl (–COOH)

Amino (–NH₂)

Phosphate (–OPO₃²⁻)

Sulfhydryl (–SH)

Which reaction is an example of hydrolysis?

Sort these from most acidic (lowest pH) to most basic (highest pH).

1Household ammonia (pH about 11.5)
2Human blood (pH about 7.4)
3Pure water (pH 7)
4Gastric juice (pH about 2)
5Black coffee (pH about 5)

What is the name of the weak attraction between a slightly positive hydrogen on one water molecule and the slightly negative oxygen of a neighbouring water molecule?

A doctor wants to destroy an overactive thyroid gland with minimal surgery. Why is iodine-131 a good choice?

In cellular respiration, glucose loses electrons and oxygen gains them. What is the process called when a molecule gains electrons?

Spot a mistake on this page? Let us know