Molecules in Medicine


Biochemistry is the study of the proteins, lipids, nucleic acids and other small molecules that comprise every cell in our bodies and permit them to grow, divide, assemble into organs and tissues, respond to (or generate) hormonal or electrical signals, allow us to think and smell and taste and feel and be human.

The diagnosis of every disease is facilitated by monitoring the biochemical changes that accompany it; the molecular basis of every disease will help all of us find the corresponding cures.

Only by understanding how normal proteins, lipids, and nucleic acids function, can we truly understand and appreciate human physiology in both health and disease.


In his course we will cover aspects of protein structure, function, regulation, and localization. We will also review the central pathways of energy metabolism, because these pathways are essential to our understanding of a number of disease states and they serve as examples of a variety of themes used by cells to accomplish diverse and essential processes.


Energy metabolism in our daily lives

Metabolism comprises the biochemical processes by which our bodies store energy from dietary constituents and utilize that energy to synthesize cellular constituents. As you will hear in forthcoming lectures, these processes are closely inter-related and regulated by circulating hormones.

Our bodies require energy to enable muscles to perform mechanical work, to enable cells to pump ions, and to assemble macromolecules from smaller precursor subunits. The energy donor in most energy requiring reactions is adenosine triphosphate or ATP, a molecule you will be hearing much more about in subsequent lectures.

Humans have evolved to store ingested calories from food. It is only in very recent time on an evolutionary scale that humans did not need to withstand long periods of fasting or famine.

Each day, an average, sedentary individual meets his or her energy requirement of 1600-2400 kilocalories by consuming:

Dietary constituent

Energy Yield

200-300 g carbohydrate

(4 kcal/gm = 800-1200 kcal)

70-100g protein

(4 kcal/gm = 280-400 kcal)

60-90g fat

(9 kcal/gm = 540-810 kcal)

Our diets of carbohydrate, protein and fat yield molecules that we convert into ATP. Much of the course will present the detailed enzymatic reactions by which this takes place.


Food molecules are broken down in several stages to form ATP.


1. Proteins, starches and fats are broken down into smaller units (starches into sugars, proteins into dipeptides, etc.) in the stomach, small intestine, and intracellular degradative compartments.

2. Glycolysis is a central ATP-producing pathway which takes place in the cytosol and converts glucose into two molecules of pyruvate. This process yields two moles of ATP and two moles of NADH. Pyruvate is then converted into Acetyl CoA + CO2. Fat and certain amino acids are broken down into Acetyl CoA in mitochondria, as well.

3. The citric acid cycle generates the reduced electron carriers, NADH and FADH2, by oxidizing Acetyl groups in acetyl CoA to CO2 + H2O. The electrons from NADH and FADH2 are passed along an electron-transport chain within the mitochondrial inner membrane; the energy released by their transfer is used to drive a process that drives ATP production and consumes molecular oxygen (O2). It is these final processes that yield most of the cell's ATP. Oxidative phosphorylation drives the majority of ATP synthesis in most cells: about 30 molecules of ATP are generated from the complete oxidation of glucose to H2O and CO2.


Different tissues have different energy requirements

Brain. Glucose is virtually the sole fuel for brain, except during prolonged starvation. The brain requires 120g daily; in the resting state, this represents 60% of the entire body's glucose utilization. In starvation, ketone bodies (generated by a process called fatty acid oxidation) can be used; fatty acids (an important energy source in resting skeletal muscle and heart) are bound to a plasma protein called albumin, and cannot cross the blood brain barrier.

Muscle. Muscle has a large store of glycogen (1200 kcal or 3/4 of all the glycogen in our bodies). In actively contracting skeletal muscle, glycolysis far exceeds the citric acid cycle rates; this generates lactate, which is reconverted to glucose in the liver. In resting skeletal muscle, fatty acids are the major fuel; glucose is preferred during exertion. Ketone bodies are the preferred fuel for heart muscle.

Fat cells. Triacylglycerols are an enormous reservoir of stored fuel. Liver is the major site of fatty acid synthesis; fat cells esterify these and store them. Glucose levels in adipocytes control whether fatty acids will be re-esterified or released to the liver for oxidation. For energy needs, fatty acids are preferred.

Liver. Liver acts to buffer glucose levels in our bloodstream: it can take up glucose and convert it to glycogen, or it can release this glucose into the bloodstream when needed. Lactate and alanine from muscle are glucose precursors, as are certain amino acids from the diet. The liver is central in lipid metabolism.


Every morning before breakfast, our circulating blood glucose level is 80-90 mg/dl blood. During the first hour or so after a meal, this rises to 120-140 mg/dl, but glucose returns to resting levels within two hours of the last ingestion of carbohydrate.

When blood glucose rises during and after a meal, the peptide hormone, insulin is secreted by the pancreas and serves as a key regulator of glucose utilization. Insulin increases the ability of cells throughout the body to take up circulating glucose and store it for future use. When available glucose exceeds our energy needs, it is stored as a polymer termed glycogen. After glycogen stores are filled, the glucose is converted to fat which is stored in adipose tissue.


Hormonal Regulation



Signals the fed state

Stimulates glycogen synthesis in muscle and liver

Stimulates glucose entry into fat cells which turns on triacylglycerol storage



Secreted in response to low blood sugar in the fasting state

Signals glycogen breakdown

Lead to increase in glucose release from liver



The "Well Fed State"



Illustration #1


Beginning about four hours after a meal:



Illustration #2



Twelve hours after a meal


Illustration #3


A typical 70kg individual has the following energy reserves:


Stored Fuel


Fuel Reserve


Fuel Reserve











Body Fluids











[Although we rely upon stored fat during starvation, the starved state triggers hormonal changes that also decrease our metabolic rate. When we then eat a large meal after a fast, we immediately store the calories, since our bodies are preparing for what may be another fast. Because of changes in enzyme levels, fasting is not a good way to lose weight in the long term. A better way to lose weight is to eat fewer calories overall, on a regular schedule, and engage in aerobic exercise which requires efficient usage of fat stores (see below). This combination keeps the metabolic enzymes active while slowly depleting excess fat stores.]


The selection of fuels during exercise illustrates many important aspects of energy generation. Myosin, the muscle force-generating protein, uses ATP for contraction, but muscle has little ATP. Creatine phosphate can rapidly convert its energy into ATP, but muscle has only a limited creatine phosphate store. A slower source is conversion of muscle glycogen to lactate, and complete oxidation to CO2 is still higher yield but slower rate. Fatty acid breakdown in adipose tissue can yield large quantities of energy, but this is even slower.

Fuel Source

ATP synthesis rate

(maximum mmol/s)

Total ~P available


Muscle ATP


Creatine Phosphate



Muscle glycogen -->lactate



Muscle glycogen -->CO2



Liver glycogen -->CO2



Fat cell fatty acids -->CO2



See Stryer, Chapter 30


In a 10 second, 100 meter sprint, ATP, creatine phosphate and anaerobic glycolysis are energy sources.

Muscle ATP: 5.2 --ð 3.7mM

creatine phosphate: 9.1 --ð 2.6mM, store gone in 6 seconds

blood lactate: 1.6 --ð 8.3mM, due to anaerobic glycolysis


In a 1000 meter run, ATP must come from oxidative phosphorylation because creatine phosphate would be depleted in a few seconds, and glycogen would be used up in 3 minutes if only converted to lactate; Muscle stores of glycogen provide 83 minutes if oxidized to CO2. With fat utilization, longer events (marathons) can be run. In runners, low blood sugar leads to a high glucagon/insulin ratio, mobilizing fatty acid utilization. Fatty acids enter muscle and are converted to acetyl CoA and CO2.


A marathon requires 150 mol of ATP. In a marathon runner, the efficient generation of fat breakdown products (acetyl CoA) enhances the balanced metabolism of glucose and fats.