Episode 20: Welcome to the MCAT Podcast series, where Doctor Dan will cover the actual science material required for the MCAT. Starting off with an overview of Biological Sciences topics, we’ll get increasingly more specific as time passes.
Biology for the MCAT
Classes of Organic Molecules
Four major classes of organic molecules found in living organisms are carbohydrates, fats, proteins, and nucleic acids.
Though these classes of molecule have different structure and function, they are built up of many similar building block molecules bonded together. In each case, building block molecules are combined by the removal of water, and this is called “condensation reactions.”
Condensation reactions are reversible. The complex organic molecules can be hydrolyzed into the simpler building blocks molecules with the addition of water. The basic building block molecules of carbohydrates are the simple sugars or monosaccharides.
When two simple sugars are bonded together, a disaccharide is formed. When many simple sugars are bonded together in long chains, a polysaccharide is formed. Starch, glycogen, and cellulose are examples of polysaccharides.
The carbohydrates are an important energy source for all organisms. Lipids, the fats, and fat-like substances tend to be insoluble in water. Fats are made up of two building block molecules – glycerol and fatty acids. Phospholipids are derived from the fats. They are important constituents of cell membranes.
The basic building block molecules of the proteins are amino acids. Amino acids are bonded together to form a protein by condensation reactions. The resulting bond is the peptide bond and the chains produced are polypeptide chains. The primary structure of each protein is the sequence and type of amino acids making up the polypeptide chains.
Because hydrogen bonds form between one amino acid and another, the chain assumes a stable regular shape known as the secondary structure. These regular molecules may in turn be folded into complicated globular shapes by weak attractions between the different R groups within the chain, thus forming the tertiary structure of the protein.
Some globular proteins are made up of two or more polypeptide chains held together by weak bonds. The way these chains fit together determines the ordinary structure. Because the conformation of a protein depends on weak bonds, it is easily altered causing a change in biological function.
The building block unit of nucleic acids is the nucleotide, which is made up of a five carbon sugar attached to a phosphate group and to a nitrogen-containing base. Nucleotide units are joined together through condensation reactions between the sugar of one nucleotide and the phosphate group of the next.
There are four different nucleotides in each nucleic acid. It is the different sequences of the nucleotides that encode their hereditary information. The two types of nucleic acids, DNA and RNA, differ in their basic make up and in the number of strands in the molecule. We will be discussing this in greater detail later.
Free Energy and Enzymes
Chemical reactions that release free energy are exothermic or exergonic. Reactions that require the addition of free energy are endothermic or endergonic. In living systems, an exothermic reaction is usually coupled with an endothermic reaction. Although exothermic reaction proceeds spontaneously, initiating a reaction may require an activation energy.
Chemical reactions can be speeded up by heat, by increasing the concentrations of the reactants, or by providing the appropriate catalyst. In living systems, the catalysts are enzymes. Most enzymes are highly specific and each can interact only with those reactants or substrates that fit spatially and chemically into the active site of the enzyme.
Since the formation of the enzyme, substrate complex requires the enzyme and the substrate to be complementary. Anything that alters the shape of the enzyme will alter its activity. In addition to temperature and pH, many chemical substances can mask, block or alter the shape of the enzyme and its active site.
The Biological Cell
Now, let us discuss cells. The fundamental organizational unit of life is the cell. Most cells are very small and have a large ratio of surface area to volume so they can effectively exchange materials like oxygen, nutrients, and waste with the surrounding environment.
Cells are bounded by a plasma membrane composed of lipids and proteins with many small pores. According to the fluid mosaic model, the plasma membrane consists of a bi-layer of phospholipids with their hydrophilic heads oriented towards the surfaces of the membrane and their hydrophobic tales toward the interior.
The proteins are distributed both on the surfaces and in the interior of the membrane. The pores are thought to be bounded by protein. The distinctive properties of these proteins make the pore selective as to what can move through them. The cell membrane is an active part of the cell. It regulates the movement of materials between the ordered interior of the cell and their outer environment.
This type of molecular passage from one side of a membrane to another requires no external energy. This is governed by charge and osmolality balance, which are intrinsic properties of solutions.
The general rule is that the net movement of particles of a particular substance is from regions of higher concentration to regions of lower concentration of that substance. This movement of particles is called “diffusion.” The plasma membrane is differentially permeable. It allows particles of some substances to pass through while excluding others.
The movement of water through a plasma membrane is called “osmosis.” Cell membranes are relatively permeable to water and to certain simple sugars, amino acids and lipid soluble substances. They are relatively impermeable to polysaccharides, proteins and other very large particles. Their permeability to small particles varies.
The bilipid layer presents a barrier to substances insoluble in lipids. For such substances, some protein components of the membrane function as carrier molecules called “permeases.” In facilitated diffusion or passive transport, the substances being carried move with the concentration gradient and no energy is required.
In active transport, substances are moved against a concentration gradient; hence, the cell must expend energy. Sometimes substances are taken into the cell by an active process called “endocytosis.” The reverse sequence is called “exocytosis.” The cell membrane cannot completely regulate the exchange of materials.
A cell in a medium that is hypertonic, meaning higher osmotic concentration, relative to it tends to loose water and shrinks. Conversely, a cell in a hypotonic medium lower osmotic concentration relative to it tends to gain water and swell and may even burst. A cell in an isotonic medium, osmotic concentrations in balance neither gains nor looses appreciable water.
Fungi and bacteria have cell walls made not of cellulose but of other complex polysaccharide molecules.
Most animal cells have a cell coat of carbohydrates covalently bonded to protein or lipid molecules in the plasma membrane. This coat is called a “glycocalyx.” Eukaryotic cells have membrane-bound nucleus; whereas, prokaryotic cells – for example, bacteria – lack a membrane-bound nucleus.
The nucleus contains the chromosomes which contain the genes. It can therefore direct the cell’s life processes. Separating the nucleus from the cytoplasm is a double nuclear membrane interrupted by pores.
The nuclear membrane is continuous at places with the endoplasmic reticulum. The endoplasmic reticulum forms a system of interconnected membrane enclosed spaces. Sometimes the membranes of the endoplasmic reticulum are rough with ribosomes on their outer surfaces. When no ribosomes are present, the endoplasmic reticulum is smooth. Ribosomes are sites of protein synthesis.
The endoplasmic reticulum functions both as a passageway for intracellular transportation and as a manufacturing surface. The Golgi apparatus consists of stocks of membrane-bound vesicles that function in the storage, modification, and packaging of secretory products.
Located within the cytoplasm are many other organelles. The mitochondria are the power houses of the cell. Chemical reactions within the mitochondria provide energy for the activities of the cell.
Lysosomes are membranous sacs that function as storage vesicles for powerful digestive enzymes. They may act as the cell’s digestive system, hydrolyzing materials taken in by endocytosis.
Microtubules and microfilaments appear to function in intracellular movement and cell support. Microtubules also form the spindle of dividing cells and are the essential components of centrioles, cilia, and flagella.
Cellular metabolism is a general term embracing the myriad of enzyme-mediated reactions of a living cell. It can be divided into two phases: anabolism – the building up phase – and catabolism – the breaking down phase.
Before the potential energy is stored in complex organic compounds, it can be used by the cell to do work. The compounds must be broken down in a series of chemical reactions and the energy transferred to ATP.
The first series of reactions in the degradation of glucose is termed glycolysis. It is the breakdown of glucose to two molecules of Pyruvic acid with the production of two molecules of NADH, a net gain of two ATP molecules. This process common to all living cells is anaerobic, meaning oxygen is not needed.
The fate of the Pyruvic acid depends on the oxygen supply. In the absence of sufficient oxygen, the Pyruvic acid maybe reduced by NADH to form carbon dioxide and ethyl alcohol or lactic acid in a process called “fermentation.” NAD molecules, thus formed, are available to be reused in glycolysis.
Under aerobic conditions, the Pyruvic acid can be further oxidized with the accompanying synthesis of ATP. This process is called cellular respiration.
The process begins with the breakdown of two Pyruvic acid molecules to form two molecules each of acetyl coenzyme-A, carbon dioxide, and NADH. The acetyl coenzyme-A is fed into the Krebs’ citric acid cycle. In the course of this cycle, two carbons are lost as carbon dioxide, a molecule of ATP is synthesized, and eight hydrogens are removed and picked up by carrier compounds forming three molecules of NADH and one of FADH too.
Since one molecule of glucose gives rise to two molecule of acetyl coenzyme-A, two turns of the cycle occur for each molecule of glucose oxidized. The final stage of respiration involves the passage of the hydrogen electrons from the carrier molecules down a respiratory chain of electron transport molecules down to oxygen with which the electrons and hydrogen ions from the medium combine to form water.
As the electrons are lowered step-by-step down the energy grade end, energy is released and some of it is used to make ATP. This process is called “oxidative phosphorylation.” The total number of new ATP molecules produced by the complete metabolic breakdown of glucose is usually 36 :
- 2 from glycosis
- 2 from the Krebs cycle
- 32 from the electron transport chain.
Cellular respiration captures about 38% of the energy of glucose and converts it into ATP. The rest of the energy is released mostly as heat. Most animals turned “poikilothermic” and all plants promptly lose most of this heat to their environment.
The body temperature and metabolic rate of poikilotherms fluctuates with the environmental temperature. A few animals, homoeothermic maintain a constant high-body temperature. Their metabolic rate can accordingly be maintained at a uniformly high level.
Humans are examples of homeotherms. We will now examine circulatory and lymphatic systems. The closed circulatory system of the human is composed of a heart, arteries, veins, and capillaries. The actual exchange of materials between blood and other tissues takes place in the capillaries. The human heart is a double pump. Each side divided into two chambers—an upper atrium, which receives blood and pumps it into the lower chamber; and the lower ventricle which then pumps the blood away from the heart.
The Human Circulatory System
The right heart receives deoxygenated blood from all over the body and pumps it via the pulmonary arteries to the lungs where it picks up oxygen and gives up carbon dioxide. The oxygenated blood then returns to the left atrium by the pulmonary veins. This portion of the circulatory system is called the “pulmonary circulation”. The left ventricle pumps the blood into the aorta and its numerous branches from which it moves into capillaries where the exchange of materials takes place, then into veins and finally back via the superior or inferior vena cava to the right side of the heart.
This portion of the circulatory system is called the “systemic circulation.” The heartbeat is initiated when a wave of contraction spreads out from the SA node to the AV node, which sends excitatory impulses down the Bundle of HIS stimulating both ventricles to contract. During systole, the blood is forced out of the heart and into the arteries under high-pressure.
During diastole, the blood pressure in the arteries falls. One-way valves and skeletal muscle action aid in moving blood in the veins. When you hear that someone has a blood pressure of 120/80, which is normal – 120 represent the pressure in the arteries during systole in millimeters of mercury.
The 80 in 120/80 represents diastole, the blood pressure during diastole in millimeters of mercury. The movement of materials into and out of capillaries is governed by the balance between hydrostatic blood pressure and osmotic pressure. The lymphatic system helps maintain the osmotic balance of the body fluids by returning excess tissue fluid and proteins to the blood.
Lymph nodes act to filter up particles and also a site of formation/maturation of some white blood cells. Blood consists of plasma, the liquid portion and formed elements, which are the red blood cells, white blood cells, and platelets. Blood clotting is initiated when damage tissue and disintegrating platelets release thromboplastin, which converts the plasma protein, prothrombin into thrombin.
The thrombin then converts fibrinogen into fibrin which forms the clot; thus fibrin forms the clot. The erythrocytes contain the oxygen-carrying pigment hemoglobin, which transports oxygen from the lungs to the tissues.
Most carbon dioxide is carried in the form of the bicarbonate ion HCO3-. The leukocytes defend the body against disease and infection. Some leukocytes carry on phagocytosis. Others produce enzymes that detoxify dangerous substances, and still others produced antibodies that destroy or inactivate certain kinds of foreign substances called “antigens.”
The Endocrine System
The endocrine system, the tissues that produce and release hormones in animals are termed “endocrine tissues.” The hormones are secreted more or less directly into the blood, which then transports them to other parts of the body.
The pancreas secretes insulin and glucagon, which regulate the blood sugar level. Insulin acts to reduce the blood glucose concentration. Glucagon causes an increase in the blood glucose concentration. The two adrenal glands located above the kidneys consist of an inner medulla and an outer cortex, which remain functionally distinct.
Epinephrine and Norepinephrine
The adrenal medulla secretes two hormones—adrenalin and noradrenalin. Both help to prepare the body for emergencies by stimulating reactions that increase the supply of glucose and oxygen to the skeletal and heart muscles. This is sometimes called the “fight-or-flight responds.”
Glucocorticoids and Mineralcorticoids
The adrenal cortex produces many different steroid hormones which may be grouped into three functional categories—one, those regulating carbohydrate and protein metabolism, the glucocorticoids; two, those regulating salt and water balance, i.e., the mineralocorticoids; and three, those that function as sex hormones.
The thyroid gland is located just below the larynx. Two of the hormones it secretes are thyroxin and triiodothyronine. These two thyroid hormones stimulate the oxidative metabolism of most tissues in the body; thus, they increase the metabolic rate.
Calcitonin and Parathyroids Hormone
The thyroid also secretes calcitonin which prevents the excessive rise of calcium ions in the body. The parathyroids are four small P-like organs located on the surface of the thyroid. The parathyroid hormone, sometimes called “parathormone,” regulates the calcium phosphate balance between the blood and other tissues.
It acts primarily on the kidneys, the intestines, and the bones. The posterior pituitary is connected to the hypothalamus by a stalk. It stores and releases two hormones—oxytocin and vasopressin, which are produced in the hypothalamus and flow along nerves in the stalk to the posterior pituitary.
The hormones are released upon nervous stimulation from the hypothalamus. Oxytocin stimulates the contraction of uterine muscles. Vasopressin causes constriction of the arterioles with a consequent rise in blood pressure. Vasopressin also stimulates the kidney tubules to reabsorb more water. The anterior pituitary produces many hormones with far reaching effects. Prolactin stimulates milk production by the mammory glands and also participates in reproduction, osmoregulation, growth, and metabolism of carbohydrates and fats.
Growth hormone promotes normal growth. The anterior pituitary also secretes a number of hormones that help control other endocrine organs. Thyrotrophic hormone stimulates the thyroid gland. Adrenocorticotropic hormone stimulates the adrenal cortex and the two gonadotropic hormones – FSH and LH – act on the gonads. The interaction between these glands and the anterior pituitary is an example of negative feedback. The activity of the anterior pituitary is in-tern regulated by the hypothalamus, which produces special peptide releasing hormones or releasing factors. These hormones are carried by portal system to the anterior pituitary where they stimulate its secretory activity. Therefore, the hypothalamus is the point at which information from the nervous system influences the endocrine system and is also one of the major sites of feedback from the endocrine system.
The Nervous System
The nervous system, the typical neuron consist of the cell body, which contains the nucleus, and one or more long nerve fibers call “axons” and “dendrites” that extend from the cell body. Sensory neurons lead from receptor cells. Motor neurons lead to effector cells and interneurons lie between the sensory and motor neurons.
Junctions between neurons are called “synapses.” A reflex arc is a simple neural pathway linking a receptor and an effector. Most somatic reflex arcs begin with a sensory neuron that conducts the impulse to interneurons in the spinal cord. These in turn synapse with motor neurons in the cord. And the impulses are conducted to the effectors usually skeletal muscles, which respond to the stimulus. Reflex arcs always inter connect with other neural pathways.
A nerve consists of a number of neuron fibers bound together. The autonomic nervous system consists of nervous pathways that conduct impulses from the central nervous system to various internal organs. These pathways usually involve to motor neurons. The autonomic nervous system regulates the body’s involuntary activities. There are two divisions of the autonomic nervous system—the sympathetic and parasympathetic systems. The sympathetic system associated more with fight-or-flight responses and the parasympathetic system associated more with vegetative responses.
Most internal organs are innervated by both with the two systems usually functioning in opposition to each other. A nerve impulse is a wave of electrochemical change moving along and their fiber. The potential stimulus must be above a particular threshold to initiate an impulse. If the axon fires, it will fire maximally or not at all. This is called the “all-or-none response.” The inside of a resting nerve fiber is negative with respect to the outside. When a fiber stimulated, sodium ions rush into the cell making the inside positively charge relative to the outside. And instant later, potassium ions, which are in higher concentration inside the cell, rush out of the cell restoring the original charge. This cycle of changes is called the “action potential.” A sodium potassium pump, ATPase pump, restores the original ion distribution.
When an impulse traveling along the axon reaches the synaptic boutton, it causes the synaptic vesicles to discharge their stored transmitter chemical into the cleft. The transmitter molecules diffuse across the cleft and alter the membrane potential of the next neuron. Synaptic transmission is slower than impulse conduction along the neuron.