IB Biology Macromolecules | A1.2, B1.1, B1.2

Elements in carbohydrates?

C, H, O. H:O ratio is 2:1 (general formula CH2O; glucose = C6H12O6).

Elements in lipids?

C, H, O only, but far fewer O atoms than carbohydrates. (Phospholipids also contain P.)

Elements in proteins?

C, H, O, N and usually S (in addition to C, H, O).

Elements in nucleic acids?

C, H, O, N, P.

C
H
O
N
P
S
Carb & Lipid = First 4 Letters
Proteins = First 5 letters (and sometimes S)
Nucleic Acid = First 5 letters

Which element is ONLY in proteins and which is ONLY in nucleic acids (in a phage)?

Sulfur (S) only in protein; phosphorus (P) only in DNA. This is why Hershey and Chase labeled S and P.

Is glycerol a fatty acid? A sugar?

Neither. Glycerol is an alcohol (3 hydroxyl groups); its C:H:O is not 1:2:1 like sugars.

Why can carbon form so many different compounds?

It has 4 electrons in its outer shell, so it forms four strong, stable covalent bonds (with C, H, O, N, S) giving chains, branched chains and rings; can also form double bonds.

Organic vs inorganic compounds

Organic: carbon-based compounds found in living things (urea, proteins, sugars, lipids). CO2, carbonic acid and hydrogencarbonate are NOT organic. Inorganic = all others (e.g. water).

Define macromolecule

Very large organic molecule: protein, nucleic acid or polysaccharide.

The 4 types of organic compound in living things and their monomers

Carbohydrates (monosaccharides), lipids (fatty acids + glycerol), proteins (amino acids), nucleic acids (nucleotides).

Functional groups: hydroxyl, carboxyl, amine

Hydroxyl -OH; carboxyl -COOH; amine -NH2.

Define covalent bond

Bond formed when two atoms share a pair of outer electrons. Strongest bond in biological molecules; only broken in specific reactions.

Define condensation reaction

Reaction that joins two molecules and removes a small molecule (usually water). A new covalent bond forms. Needs an enzyme and energy.

COndensation = COmbining together + water Exit
joins molecule together & removes water

Define hydrolysis reaction

'Splitting by water.' Water is split into -H and -OH which are added to a large molecule, breaking it into smaller molecules. Enzyme-catalyzed.

Another name for condensation

Dehydration synthesis.

Condensation word equation: two monosaccharides

Monosaccharide + monosaccharide → disaccharide + water (forms a glycosidic bond).

Condensation word equation: two amino acids

Amino acid + amino acid → dipeptide + water (forms a peptide bond).

Condensation word equation: fats

Glycerol + 3 fatty acids → triglyceride + 3 water (forms 3 ester bonds).

Hydrolysis word equation: disaccharide

Disaccharide + water → 2 monosaccharides.

Bond formed in polysaccharides / polypeptides / triglycerides / nucleic acids

Glycosidic / peptide (peptide linkage) / ester / phosphodiester.

Define polymer and monomer

Polymer: large molecule made of repeating subunits. Monomer: the repeating subunit.

Where does condensation of amino acids occur?

At the ribosome (peptidyl transferase joins the amine group of one amino acid to the carboxyl group of the next).

Define monosaccharide

Simplest sugar; cannot be hydrolyzed to a simpler sugar (e.g. glucose). Small, sweet, soluble in water.

Define disaccharide and give 3 examples with their monosaccharides

Sugar from two monosaccharides. Sucrose = glucose + fructose; maltose = glucose + glucose; lactose = glucose + galactose.

Define polysaccharide

Very large carbohydrate formed by condensation of many monosaccharides (removing water). Examples: starch, glycogen, cellulose.

Pentose vs hexose

Pentose = 5-carbon sugar (ribose, deoxyribose). Hexose = 6-carbon sugar (glucose, fructose, galactose).

Glucose properties linked to its function

Soluble (transported in blood), chemically stable, and releases lots of energy when oxidized in cell respiration. Also the building block of starch, glycogen, cellulose.

Difference between alpha and beta glucose

Only the -OH on carbon 1: alpha = OH points DOWN, beta = OH points UP. (They are isomers/anomers.)

ABBA: Alpha Below, Beta Above

Which glucose builds starch/glycogen and which builds cellulose?

Alpha glucose → starch and glycogen. Beta glucose → cellulose.
Alpha Animal store Glycogen
Beta builds a better wall

Amylose: structure

Unbranched chain of alpha-glucose with 1,4 glycosidic links; coils into a helix stabilized by hydrogen bonds.

Amylopectin: structure

Alpha-glucose chains with 1,4 links plus 1,6 links at branch points (branched).

Glycogen: structure and location

Alpha-glucose like amylopectin but larger and more highly branched. Animal energy store in liver and muscle cells (brain does not store it).

Why are starch and glycogen good energy stores?

Compact (coiling and branching); insoluble (no osmotic effect); branching lets enzymes hydrolyze many ends quickly; alpha-glucose easily added by condensation or removed by hydrolysis.

Starch: where and what?

Main plant energy store, laid down in plastids. Mixture of amylose and amylopectin.

Cellulose: structure

Beta-glucose with 1,4 links; every other glucose is rotated 180 degrees, giving straight, unbranched, uncoiled chains that H-bond to each other to form microfibrils/fibers.

Cellulose: function

Structural support and mechanical strength in plant cell walls (most abundant carbohydrate).

Starch/glycogen vs cellulose: why different function?

Different glucose isomer and bonding orientation → starch/glycogen coiled or branched (energy storage); cellulose straight (structure).

Glycoprotein

Membrane protein with carbohydrate chain (glycocalyx) attached, on the OUTER surface of the cell membrane; used in cell-cell recognition (e.g. ABO antigens).

Roles of glycocalyx

Cell-cell recognition (self vs non-self); receptor sites for chemical signals like hormones; helps cells bind to form tissues.

Define lipid

Substance in living organisms that dissolves in non-polar solvents but is only sparingly soluble in water. Includes fats, oils, waxes and steroids. Hydrophobic.

Generalized structure of a fatty acid

Carboxyl group (-COOH) at one end + a long hydrocarbon chain (typically 16 to 18 C). Carboxyl reacts with glycerol -OH to form an ester bond.

Define saturated fat / fatty acid

Fatty acid with no C=C double bonds (fully hydrogenated carbon chain). Straight chain, packs tightly, solid at room temp (butter, animal fat).

Saturated = Solid at room temperature. Saturated is bad for you.

Define unsaturated fatty acid

Has one or more C=C double bonds, so one fewer H on each double-bonded carbon. Double bond bends the chain.

Unsaturated = Un-Solid at room temperature. Good for you.

Monounsaturated vs polyunsaturated

Mono = one C=C double bond. Poly = two or more C=C double bonds.

Why are unsaturated fats liquid at room temperature?

Double bonds bend (kink) the chain so tails cannot pack closely; lower melting point. Plant oils (e.g. olive, avocado).

Cis fatty acid

H atoms on the SAME side of the C=C double bond; chain is bent. Natural; liquid oil.
Cis = “C” Same

Trans fatty acid

H atoms on OPPOSITE sides of the C=C double bond; chain stays straight. Made in the lab (partially hydrogenated); serious health risk.
Trans = Transportation ACROSS

Where is unsaturated vs saturated fat used for energy storage?

Unsaturated (oils): plants and cold-blooded animals. Saturated (fats): warm-blooded animals (endotherms).

Define triglyceride

Ester formed from 1 glycerol + 3 fatty acids by condensation (3 water removed, 3 ester bonds). Non-polar, insoluble.

Class notes: monomer and polymer of fats?

Monomer = fatty acid; polymer = triglyceride (as given in class notes; technically lipids are not true polymers).

Define phospholipid

1 glycerol + 2 fatty acids + 1 phosphate group (triglyceride with one fatty acid replaced by a phosphate). Major component of cell membranes.

Define amphipathic

Having both a hydrophobic part and a hydrophilic part in the same molecule (phospholipid: hydrophilic phosphate head, hydrophobic fatty acid tails).

Why do phospholipids form a bilayer?

Hydrophilic heads face the water on both sides; hydrophobic tails face each other in the middle away from water.

Define steroid

Group of lipids with four fused carbon rings (cholesterol, estradiol, testosterone). Non-polar.

Why can steroid hormones pass through the phospholipid bilayer?

They are non-polar/hydrophobic, so they dissolve in the hydrophobic core of the bilayer. Examples: estradiol, testosterone.

Triglyceride vs phospholipid vs cholesterol: components

Triglyceride: 3 fatty acids + glycerol. Phospholipid: 2 fatty acids + glycerol + phosphate. Cholesterol: four fused carbon rings, one hydroxyl, one hydrocarbon tail.

Why are fats a better long-term energy store than carbs?

More than twice the energy per gram (9 vs 4 kcal/g); more reduced (more H); compact; insoluble; also thermal insulation, buoyancy, and yields metabolic water.

Adipose tissue: what and why?

Fat cells (adipocytes) storing triglycerides, usually under the skin. Energy store, thermal insulation (limited blood supply), buoyancy (blubber), protection.

Generalized structure of an amino acid

Central alpha carbon bonded to: an amine group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and an R group (side chain).

How many amino acids build proteins?

20 (coded for in the genetic code). Only the R group differs between them.

What does the R group determine?

The properties of the amino acid and the assembled polypeptide. R groups can be hydrophobic or hydrophilic; hydrophilic ones are polar or charged (acidic or basic).

Define peptide linkage / peptide bond

Covalent bond between the carboxyl group of one amino acid and the amine group of the next, formed by condensation (water lost).

Dipeptide vs tripeptide vs polypeptide

Dipeptide = 2 amino acids; tripeptide = 3; polypeptide = long chain of amino acids.

N-terminus vs C-terminus

N-terminus = start of chain (free amine group). C-terminus = end of chain (free carboxyl group).

How many different polypeptides are possible?

20^n for a chain of n amino acids (e.g. 20^5 = 3,200,000). Infinite variety because chains can be any length and any order.

Define essential amino acid

Amino acid that cannot be synthesized by the body and must be obtained from food.

Define non-essential amino acid

Amino acid that the body can make from other amino acids.

Challenge of a vegan diet for amino acids

Plant foods may lack one or more essential amino acids, so a variety of plant foods must be combined to get all essential amino acids.

Primary structure

Linear sequence of amino acids held by peptide bonds. Determined by DNA; determines all higher levels of structure, so shape and function.

Secondary structure

Alpha helices and beta-pleated sheets, stabilized by hydrogen bonds in regular positions along the backbone.

Tertiary structure

Overall 3D shape of one polypeptide from interactions between R groups: hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

Disulfide bridge

Strong covalent bond between the sulfur atoms of two cysteine R groups. Strongest force stabilizing tertiary structure.

How do R groups form ionic bonds?

R groups with a carboxyl group lose H+ (become negative); R groups with an amine group gain H+ (become positive); opposite charges attract.

Hydrophobic interactions in a soluble globular protein

Non-polar (hydrophobic) amino acids fold into the protein's core away from water; polar/hydrophilic ones face the outside.

Common mistake: tertiary structure vs alpha helix bonding

Tertiary structure is determined by interactions between R groups (side chains). Hydrogen bonds between backbone atoms stabilize the alpha helix.

Quaternary structure

Two or more polypeptide chains combined by intermolecular forces (not all proteins have it). Example: hemoglobin.

Conjugated protein

Protein combined with a non-protein prosthetic group. Example: hemoglobin (4 chains, each around a heme group containing iron).

Non-conjugated protein

Protein with no prosthetic group. Examples: insulin, collagen.

Fibrous protein

Long, narrow, much-coiled chains; usually insoluble; high tensile strength; structural (collagen, actin/myosin). Insolubility matters: collagen would dissolve otherwise.

Globular protein

Compact, spherical, usually highly soluble in water; enzymes and hormones (insulin, hemoglobin).

Collagen structure

Fibrous, non-conjugated. Three left-handed helices twisted into a right-handed triple helix; repeating Gly-X-Y (every 3rd amino acid is glycine); H bonds between chains.

Insulin structure

Globular, non-conjugated hormone: A chain and B chain linked by disulfide bonds. Regulates blood glucose.

Define denaturation

Change in a protein's 3D structure (loss of its shape) caused by heat or pH change breaking weak bonds; results in loss (usually permanent) of biological function.

Effect of temperature on protein structure (must know)

Heat makes atoms vibrate and disrupts weak intermolecular forces (H bonds, ionic bonds, hydrophobic interactions), changing the shape; the protein denatures.

Effect of pH on protein structure (must know)

pH change alters the charges on R groups, breaking ionic and hydrogen bonds, changing the shape (denaturation).

Carbohydrates: monomer, polymer, bond, elements

Monosaccharide → polysaccharide; glycosidic bond; C, H, O.

Lipids: building blocks, bond, elements

Fatty acids + glycerol (+ phosphate) → triglyceride/phospholipid; ester bond (phosphodiester in phospholipid head); C, H, O (P).

Proteins: monomer, polymer, bond, elements

Amino acid → polypeptide; peptide bond; C, H, O, N, (S).

Nucleic acids: monomer, polymer, bond, elements

Nucleotide → polynucleotide (DNA, RNA); phosphodiester bond; C, H, O, N, P.

Functions of each macromolecule

Carbs: energy, structure, recognition. Lipids: long-term energy, insulation, membranes, hormones. Proteins: enzymes, structure, transport, hormones. Nucleic acids: store and pass on genetic information.

The 3 parts of a nucleotide

Phosphate group, pentose sugar, nitrogenous base (joined by covalent bonds via condensation, catalyzed by enzymes).

How to draw a nucleotide (IB convention)

Circle = phosphate, pentagon = pentose sugar, rectangle = nitrogenous base. Label everything; words horizontal, lines must not cross; spell out bases or give a key.

Where do the phosphate and base attach on the sugar? (must know)

Phosphate on carbon 5 (5'); nitrogenous base on carbon 1 (1'). Free -OH is on carbon 3 (3').

The two pentose sugars

Ribose (RNA) and deoxyribose (DNA). Same pattern; single difference: deoxyribose has H instead of OH on carbon 2.

Names of the 5 nitrogenous bases

Adenine, thymine, cytosine, guanine (DNA); uracil replaces thymine (RNA only).

Purine

Nitrogenous base with a double ring: adenine and guanine.

Pure As Gold
Puine = Adenine Guanine

Pyrimidine

Nitrogenous base with a single ring: cytosine, thymine, uracil.
(Pyrimidine: “CUT" the PY” PY = PYrimidine. CUT = Cytosine, Thymine, Uracil)

(Purine: “Pure as Gold” — Adenine, Guanine)

Complementary base pairing rules

Adenine pairs with thymine (uracil in RNA): 2 hydrogen bonds. Guanine pairs with cytosine: 3 hydrogen bonds. A purine always pairs with a pyrimidine.

Why purine-to-pyrimidine pairing stabilizes DNA

A-T and C-G pairs are equal in length, so the helix has the same 3D structure and width regardless of base sequence.

Define phosphodiester bond

Covalent linkage between the 3' carbon of one sugar and the 5' carbon of the next (through a phosphate group); forms the sugar-phosphate backbone.