Week 1: Biochemistry, proteins, and membrane dynamics

Reading guide, based on Silverthorn’s human physiology; 8th edition.

Mammalian Physiology requires a basic understanding of cell biology and biochemistry. This has
been covered in previous (introductory) courses and is considered prerequisite knowledge. This
reading guide can be used to review this material using our textbook. There will be a quiz
posted on blackboard in the first week of class (week 1 quiz ) covering this material.

2-4 BIOCHEMISTRY

The study of the functioning of the human body requires basic knowledge of chemistry and
physics. Molecular interactions are essential to understand the principle of homeostasis and
other physiological principles and mechanisms. Most of the material listed below is
introductory chemistry and biology, with a focus on understanding protein function and
biological membranes.

LEARNING OBJECTIVES

29-48 Basic chemistry (a lot of it is covered in fig. 2.1- 2.6, 2.8, 2.9)
Recognize the basic structure of biochemical molecules (fig. 2.1-2.4), define:
 Organic molecules, lipoproteins, glycoproteins, glycolipids
 Polymers (p. 29)
 Functional groups (e.g. phosphate group)
 Lipids
 Fatty acids – saturated vs. unsaturated fatty acids (pay attention to the double bonds)
 Carbohydrates
 Proteins (peptide bonds, amino acids, etc.)
 Nucleotides (nucleid acid, nitrogenous bases, etc.)
Covalent and noncovalent bonds and interaction (fig. 2.5, 2.6, 2.8), define:
 Cations vs anions
 Polar vs nonpolar
 Covalent bonds
 Noncovalent bonds:
o Ionic bonds
o hydrogen bonds
o van der Waals forces
 Hydrophilic vs hydrophobic interactions (or lipophobic vs. lipophilic). See also fig. 2.8
o Pay special attention to phospholipids
 pH (recognize that low pH corresponds to high [H+] in a solution, see fig. 2.9)
 Law of mass action: be able to predict the direction of a chemical reaction when the
equilibrium is disturbed (p. 47, 48, fig. 2.11); concept check 13

46-53 Protein interaction

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Week 1: Biochemistry, proteins, and membrane dynamics

 List and define seven protein categories, most important ones: enzyme, signal
molecules, receptors)
 Define binding/active site, substrate, ligand
 Define affinity, specificity, competition, agonist, competitive antagonist (called inhibitor
in our text) (p. 46-49)
o Recognize that changes in amino acid sequence can alter protein chemistry,
affinity, specificity, etc. (it’s good to know the basic structure of amino acids and
that amino acids vary in the R group)
 Activation and modulation, define allosteric modulation vs. covalent modulation and an
example of each; recognize that physical factors, such as pH can alter protein structure,
chemistry and function (p. 51)
 Define saturation (p. 51)

93-102 Chemical reactions are catalyzed by enzymes

 Define enzymes (p. 98)
 Recognize that enzymes lower the activation energy of reactions (fig. 4.7)
 Recognize that enzymes exhibit all the properties of proteins, including affinity,
specificity, competition, modulation

110-118 Central dogma DNA -> RNA -> amino acid chain
 Distinguish between transcription and translation (fig. 4.18)
 Recognize that proteins can be modified (posttranslational modification, p. 116)

5 MEMBRANE DYNAMICS

Membrane dynamics are important for maintaining the dynamic steady states of the body’s
intracellular and extracellular compartments. Concentration differences drive the movement of
substances, which is often selective depending on the type of membrane proteins expressed
on/in a cell.

LEARNING OBJECTIVES

123-147, 149-153 Osmosis and diffusion

 The textbook makes the concepts of osmolarity a little bit too complicated. Just make
sure you can:
o Define osmolarity, tonicity
o Define hypertonic, hypotonic, isotonic solution
 You should be able to answer questions such as: “When a cell is placed in
a hypotonic solution, it will (a) shrink); or (b) swell and perhaps even
burst. Explain your answer.
 Define pressure gradient and concentration gradients
o Describe bulk flow and recognize that how fluids flow depending on pressure
gradients (p. 131).

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Week 1: Biochemistry, proteins, and membrane dynamics

o Recognize that molecules diffuse down the concentration gradient (p. 132-133).
o Describe the factors that determine the rate of diffusion (fig. 5.7).
 Describe facilitated diffusion (p. 136)
 Describe active transport and contrast it to facilitated diffusion (p. 136)
o Distinguish between primary active transport and secondary active transport (p.
142)

147-149 (Vesicular transport – just a very basic understanding is enough)

 Describe the functions of the plasma membrane including its role in exocytosis and
endocytosis (fig. 5.19)