Chapter 3 MCAT Biology

P3.1 - Proteins are macromolecules.

They function as:

  • Enzymes

  • Hormones

  • Receptors

  • Channels

  • Transporters

  • Antibodies

  • Support structures

Fig 1 - Amino acid structure

All 20 amino acids share a nitrogen-carbon-carbon backbone with a variable R group (sidechain).

3.2 - Protein Structure

P1 - Peptide bonds link amino acids into polypeptides.

P2 - Bonds form between carboxyl and alpha-amino groups, losing water.

Fig 2 - Peptide Bond Formation

P3 - Disulfide bridges between cysteine R-groups, backbone: N-C-C-N-C-C.
Residue - individual amino acid. Amino terminus is first, carboxyl terminus is last.


Q1 - In the oligopeptide Phe-Glu-Gly-Ser-Ala, which residue has a free alpha-amino group, and which residue has a free alpha-carboxyl group?
A1 - The oligopeptide begins with the exposed Phe amino group and ends with the exposed Ala carboxyl group. All other residues are linked together by peptide bonds.

P4 - Hydrolysis of protein by another is proteolysis or proteolytic cleavage; the cutting enzyme is a proteolytic enzyme or protease.

Q2 - If the peptide Ala-Gly-Glu-Lys-Phe-Phe-Lys is cleaved by trypsin, what amino acid will be at the new N-terminus, and how many fragments will result?
A2 - Trypsin cleaves on the carboxyl side of the Lys residue, resulting in Phe being at the N-terminus of the new Phe-Phe-Lys fragment. After trypsin cleavage, there will be two fragments: Phe-Phe-Lys and Ala-Gly-Glu-Lys

P5- Cys with reactive thiol (sulfhydryl, SH)

can form a covalent sulfur-sulfur bond (disulfide bond) with another cysteine's thiol.

may occur within the same or different polypeptide chains.

stabilize tertiary protein structure.

A cysteine residue bonded to another is called cystine.

Fig 5- Formation of the DisulfidE

P6-Three-dimensional structure

improper fold or denature of non-functional protein

level of structure= bond

denaturation -disruption of a protein shape without breaking peptide bonds

proteins denatured by urea which disrupts hydrogen bonding interaction, by extremes of pH, extremes of temperature, and by changes in salt concentration(toxicity)

P7- primary structure, amino acid links to the subsequent polypeptide.

P8- Secondary structure, initial folding of a polypeptide, stabilized by hydrogen bonds between backbone NH, CO groups.

common motifs: alpha helix, beta-pleated sheets.

two types of beta sheets: parallel (same direction), and anti-parallel (opposite direction).

folds back on itself, it forms an antiparallel B-pleated sheet.

direction of the amino acid chain matters: it goes from the N-terminus (start) to the C-terminus (end).

Fig 5- alpha helix

Fig 6- beta-pleated sheet

Q1- if a single polypeptide folds once and forms a B-pleated sheet with itself, would this be a parallel or antiparallel?

A1- antiparallel, as a B-pleated sheet would have a C to N direction, while others would have N to C.

N --> --> --> --> --> C

When it folds back on itself to form a B-pleated sheet, it would look like this:

N --> --> --> --> --> C
C <-- <-- <-- <-- <-- N

P9- Tertiary Structure, interaction between distantly located amino acid residues.

folding of secondary structures, like α-helices, lead into higher-order tertiary structures, driven by R-group interactions and solvent.

hydrophobic R-groups fold into the interior

hydrophilic R-groups exposed to the surface.

under right conditions → hydrophobic avoidance of water, hydrogen bonding → polypeptide folds spontaneously into lowest energy conformation

Fig 7- Globular Protein in Aqueous Solution

Q2- Which of the following may be considered an example of tertiary protein structure?

A2- van der Waals interactions be considered an example of tertiary protein structure; Convalent disulfide bonds between Cys residues located far apart on a polypeptide

P 10- Quaternary Structure

highest level of protein structure → interactions between polypeptide subunits

subunit → single polypeptide chain in a multisubunit complex

example → mammalian RNA polymerase 2 contains 12 different subunits

subunit interactions → instrumental in protein function, e.g., cooperative binding of oxygen in hemoglobin

stabilizing forces → non-covalent interactions, Van der Waals forces, hydrogen bonds, disulfide bonds, electrostatic interactions

exception → peptide bond not involved, defines primary structure sequence

Q3- What is the difference between a disulfide bride involved in the quaternary structure and one involved in tertiary structure?

A3- Quaternary form between chains, not linked by peptide bonds. Tertiary disulphide forms between residues in the same polypeptide.

3.3 Carbohydrates

P1- oxidation→ breaks down CO2 (burning/combustion)

release large amounts of energy→ primary source cellular metabolism

P2- monosaccharide → simple sugar (CnH2nOn)

Fig 8- Monosaccharide

P3-2 monosaccharides → disaccharide (few oligosaccharides, many polysaccharides)

bond → glycosidic linkage (covalent bond formed in the dehydration reaction, requires enzymatic catalysis)

common examples → sucrose, lactose, maltose, cellobiose

Fig 9- Dissaccharides and a- or b-glycosidic bonds

P4-Polymers→ disaccharides

glycogen→ energy store carbohydrate in animals, 1000 glucose units

starch→ energy stores in plants

cellulose→ polymer of cellobiose

cellobiose does not exist freely in nature, only in polymerized, cellulose form

Fig 10-polysaccharide glycogen

3.4- Lipids are oily or fatty substances → 3 physiological roles:

  1. adipose cells → triglycerides → store energy

  2. cellular membranes → phospholipids → barrier between environments

  3. cholesterol → building block for hydrophobic steroid hormones

P1- hydrophobicity, lipophobic

P2- Fatty Acid Structure

fatty acids → long unsubstituted alkanes, end in carboxylic acid

chain length → 14 to 18 carbons

synthesis → 2 carbons at a time from acetate → only even-numbered fatty acids in humans

saturated fatty acids → no carbon-carbon double bonds, max hydrogens bound

unsaturated fatty acids → one or more double bonds in tail

Q1- How does the shape of an unsaturated fatty acid differ from that of a sturated fatty acid?
A1-unsaturated fatty acid is bent at the double bond. saturated is not.

Q2- If the fatty acid are mixed into water, how are they likely to associate with each other?

A2- minimal contact, exposing the charged carboxyl group to aqueous environment

Fig 12- FA micelle

P3 - Triglycerols

composed of 3 fatty acids esterified to glycerol

glycerol → 3-carbon triol, formula: HOCH2-CHOH-CH2OH

3-hydroxyl groups → can be esterified to fatty acids

storage → fatty acids in inert form of fat (free fatty acids are reactive)

lipases → enzymes that hydrolyze fat

triglycerols → stored in fat cells as energy source

fats vs. carbohydrates → more efficient energy storage due to:

  1. packing → hydrophobicity allows closer packing than carbohydrates

  2. energy content → fat stores more energy than carbohydrates, carbon for carbon

P4- Diacylglyercol phosphate

minimize interaction with water → orderly structure

Fig 15- lipid bilayer membrane

Q3- Would a saturated or an unsaturated fatty acid residue have more van der Waals interactions with neighbouring alkyl chains in a bilayer membrane?

A3- Saturated will make a solid membrane, whereas the unsaturated has less contact to form van der Waals due to the bent shape.

P5- Terpenes, isoprene units (C5H8),linear or cyclic

Fig 16- structure

Fig 17- Terpene structure

P6- Squalene→ triterpene, six isoprene units, a component of earwax

Fig 18- Squalene St.

P7-Vitamin A→ terpenoid (functionalized terpenes)

Fig 19-Vitamin st.

P8- Steroids, hydrophobicity, tetracyclic ring system

steroid cholesterol, a component of lipid bilayer→ both obtained from diet and synthesized in the liver→ carried into blood packaged with fats and proteins→ lipoproteins

atherosclerotic vascular diease→ builds up cholesterol “plaque” on the inside of blood vessels

Fig 20- Cholesterol-derived hormones

2 types→ testosterone (an androgen/male sex h.), estradiol (an estrogen/female sex h.)

3.5 Phosphorus-Containing compound

P1-Phosphoric acid→ inorganic, lacks carbons, potential to donate 3 protons, dissociated, largely in anionic forms.

Fig 21- PA dissociation

P2- Phosphate→ orthophosphate

2 orthophosphate bound together →anhydride linkage → form pyrophosphate

P-O-P bound in pyrophosphate → high energy phosphate bond→ name due to the hydrolysis of pyrophosphate is extremely favourable.

3 reasons phosphate anhydride bonds store energy:

  1. linked phosphates → strong negative charge repulsion

  2. orthophosphate → more resonance forms, lower free energy than linked phosphate

  3. orthophosphate → more favorable interaction with (biological solvents)water than linked phosphate

P3-Nucleotides, building blocks of nucleic acids (RNA and DNA)

each nucleotide → ribose or deoxyribose sugar

a purine or pyrimidine base → joined to carbon one of ribose; 1, 2, 3 phosphates → joined to carbon 5 fig23-ATP

ATP → role in cellular metabolism, a universal short-form energy molecule

energy → extracted from food oxidation, stored in phosphoanhydride bond of ATP

energy usage → powers cellular processes synthesizes glucose or fats for long-term storage

applies to all living organisms, including bacteria and humans; some viruses carry ATP outside host cells.