Lecture 01. Biochemistry & Metabolism Flashcards Preview

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Anatomy & Subdivisions


The study of the structures of the body.

Subdivisions of Anatomy:

Gross (Macroscopic) Anatomy: Structures studied with the unaided eye.

  • Regional Anatomy: Approach used in medical school; studies all structures associated with the hand or neck.
  • Systemic Anatomy: Approach used in introductory courses; studies the body system by system.
  • Surface Anatomy: Study of surface form (morphology) or structures of the exterior body.

Microscopic Anatomy: Study of structures not visible to the unaided eye.

  • **Cytology: **Study of cells.
  • Histology: Study of tissues.​

Physiology & Subdivisions


The study of the function of the body.

  • *Cardiovascular Physiology: **Studies functions of the heart and blood vessels.
  • *Endocrinology: **Study of chemical regulators in the blood and how they control body functions. (Hormones).
  • *Exercise Physiology: **Studies changes in cell and organ functions as a result of muscular activity.
  • *Immunology: **Study of how the body defends itself against disease-causing agents.
  • *Neurophysiology: **Studies functional properties of nerve cells.
  • *Pathophysiology:** Studies functional changes associated with disease and aging.
  • *Renal Physiology:** Studies functions of the kidneys.
  • *Respiratory Physiology: **Studies functions of the air passageways and lungs.


Define Homeostasis


The ability of the body to maintain relatively stable internal conditions even though the outside world changes; indicates a dynamic state of equilibrium.

  • Negative Feedback
  • Positive Feedback

Homeostatic Control Systems


The compensating mechanisms that regulates the activities of cells, tissues and organs.

  • **Stimulus: **Sends signals to the receptor.
  • Receptor: Monitors the variable (receives and transmits **stimulus **via the afferent pathway).
  • Control Center: Integrates information and compares it to a set point (decides on appropriate response) and transmits command.
  • Effector: Receives and executes response to stimulus via efferent pathway.

Negative Feedback


In negative feedback systems the response of the effector negates or opposes the stimulus (shuts off the original stimulus).

Responses are controlled by:

  • Extrinsic control systems
  • Nervous system
  • Endocrine systems
  • Intrinsic control systems (autoregulation)


  • Internal body temperature has a set point at around 98 degrees. If external temperature causes internal temperature to drop below that set point the body sends signals along the afferent pathway to the control center (hypothalamus) that cause certain responses that are sent back through the efferent pathway in order to get back to that set point. E.g. Curling up or shivering.
  • The control of blood sugar (glucose) by insulin - When blood sugar rises, receptors in the body sense a change. In turn, the control center (pancreas) secretes insulin into the blood effectively lowering blood sugar levels. Once blood sugar levels reach homeostasis, the pancreas stops releasing insulin.

Positive Feedback


Enhances the original stimulus causing a greater deviation from the set point.
(Activates infrequent events that require immediate action. Most are not related to the maintenance of homeostasis).


  • Blood clots
  • Uterine contractions in childbirth (stretch releases oxytocin from posterior pituitary)

Cell Signalling

  • **Endocrine Signaling: **Refers to the collection of glands of an organism that secrete hormones directly into the circulatory system to be carried towards a distant target organ. The major endocrine glands include the pineal gland, pituitary gland, pancreas, ovaries, testes, thyroid gland,parathyroid gland, hypothalamus, gastrointestinal tract and adrenal glands.
  • Autocrine Signalling: A form of cell signaling in which a cell secretes a hormone or chemical messenger (called the autocrine agent) that binds to autocrine receptors on that same cell, leading to changes in the cell.
  • Paracrine Signalling: A form of cell-cell communication in which a cell produces a signal to induce changes in nearby cells, altering the behavior or differentiation of those cells. Signaling molecules known as paracrine factors diffuse over a relatively short distance (local action), as opposed to endocrine factors (hormones which travel considerably longer distances via the circulatory system), juxtacrine interactions, andautocrine signaling.
  • **Intracrine Signaling: **Refers to a hormone that acts inside a cell, regulating intracellular events. Steroid hormones act through intracellular (mostly nuclear) receptors and, thus, may be considered to be intracrines.

Membrane Transport

(3 Systems)


The cell membrane is a barrier that needs to be overcome in order to let in nutrients (glucose, amino acids, lipids) and let out products and waste (proteins, carbondioxyde). Ease at which substances can get in and out from cell membrane is called permeability (impermiable, freely permiable, selectively permeable).

Movement occurs through:

  • Diffusion & Osmosis (neither require ATP)
  • Carrier-mediated Transport (Active and Passive)
  • Vesicular Transport

Ease of movement based on:

  • Size (smaller molecules - oxygen, carbondioxide can go in and out passively)
  • Charge (harder for charged ions)
  • Shape (especially in interactions with channels)
  • Lipid Soluability (the more soluable, the easier to cross - steroid hormones, caffeine, heroine)



The net movement of a substance (e.g., an atom, ion or molecule) from a region of high concentration to a region of low concentration until there are equal numbers of particles in the two areas. This is also referred to as the movement of a substance down a concentration gradient.

Types of Diffusion:

  • Simple Diffusion (Passive Diffusion): Particles that move from an area of high-concentration to an area of low concentration. Does not require energy - happens through random motion.
  • Channel-Mediated Diffusion: Materials which pass through transmembrane proteins (channels) - small, water-soluble molecules and ions only.
  • Carrier-mediated Transport (Facilitated Diffusion): a type of passive transport that is dependent on single transport protein carriers. These protein carriers operate on a bind, flip, release mechanism. Facilitated diffusion is non-diffusional because the molecule moves along with the carrier.

Factors that affect rate:

  • Size of gradient
  • Charge
  • Lipid solubility
  • Temperature (increase heat means faster diffusion)
  • Size of molecules (smaller molecule means faster diffusion)
  • Distance (smaller distance means faster diffusion)



Osmosis is the diffusion of water across the cell membrane from an area of high water concentration to area of low water concentraion.

How osmosis works:

  • More solute molecules, lower the concentration of water molecules
  • Membrane must be freely permeable to water, selectively permeable to solutes

Factors affecting rate:

  • Concentration gradient
  • Opposing osmotic or hydrostatic pressure
  • Number of aquaporins (water channels)

Substances involved:

  • Water only (all cells)



The osmotic effect of a solute on a cell:

  • Two fluids may have equal osmolarity, but different tonicity
  • **Isotonic: **iso - same (same solutes/same water) = cell stay the same
  • Hypertonic: hyper - higher = higher tonicity (higher solutes/less water) cell would shrink, water flows out of the cell.
  • Hypotonic: hypo - less = lower tonicity (lower solutes/more water) water moves into the cell (red blood cells into distilled water creates cell fragments).

Carrier-mediated Transport


Movement of substances across the plasma membrane by protein carrier molecules (integral membrane protein).

  • Used when molecule cannot cross membrane or crosses very slowly
  • Protein carrier molecules are embedded in lipid, and have site which specifically binds the molecules
  • Binding of the molecule to the site promotes a conformational change in protein carrier, resulting in transport of molecule across membrane.

Types of Carrier-mediated transport of ions and organic substrates:

  • Facilitated Diffusion (passive)
  • Active Transport: Requires ATP. Moving something against its concentration gradient wihch requires energy.
  • Secondary Active Transport

Characteristics of Carrier-Mediated Transport:

  • Specificity: The transport proteins are specific for particular substrate.
  • Saturation limits: Saturate all of the transport proteins mean you have reached transport limit - cannot move anything in or out there are no more available transport proteins.
  • Regulation: up-regulate or down-regulate the number of transporters.



Two substances move in the same direction at the same time.

(happens in small intestine moving sodium and glucose)




One substance moves in while another moves out.


Facilitated Diffusion


Carrier proteins passively transport solutes across a membrane down a concentration gradient.

How Facilitated Diffusion Works:

  • Passive (does not require ATP)
  • Carrier Mediated
  • Carrier proteins transport molecules too large to fit through channel proteins (glucose, amino acids).

Factors affecting rate:

  • Size of gradient
  • Temperature
  • Availability of carrier proteins

Substances involved:

  • Glucose and amino acids (all cells but several different regulatory mechanisms exist)

Active Transport


Carrier proteins actively transpot solutes across a membrane, often against a concentration gradient. Require energy, such as ATP (Adenosine Triphosphate).

Factors affecting rate:

  • Availability of carrier, substrates
  • **ATP **(Adenosine Triphosphate)

Substances involved:

  • NA+, K+, Ca2+, MG2+ (all cells)
  • Other solutes by specialized cells

Sodium-Potassium Exchange Pump

  • Responsible for cells’ containing relatively high concentrations of potassium ions but low concentrations of sodium ions (Active Transport).
  • Moves these two ions in opposite directions across the plasma membrane.
  • Found in almost all neurons and all skeletal and cardiac muscle cells.
  • Moves 2 potassium ions into the cell for every 3 sodium ions pumped out of the cell.
  • Uses 20-30% resting matabolic rate.



Secondary Active Transport


Carrier proteins passively transport two solutes, one (normally Na+) moving down its concentraion gradient. The cell must later expend ATP to eject the Na+.

  • Na+ (sodium) concentration gradient drives glucose transport
  • ATP energy pumps Na+ (sodium) back out and potassium back in

Factors affecting rate:

  • Availability of carrier substrates
  • ATP

Substances involved:

  • Glocose and amino acids (specialized cells)

Although ATP is not used directly in secondary active transport, it is necessary for the primary active transport of Na+ (sodium) out of cells. Because it is the Na+ concentration gradient across the plasma membrane that provides the energy for most secondary active transport systems, a decrease in ATP production will decrease primary active Na+ transport, leading to a decrease in the sodium ion concentration gradient and thus to a decrease in secondary active transport.


Vesicular Transport


Also called bulk transport: happens when you do not need to move a molecule, but a fragment, bacteria or cellular debris.

Endocytosis (endo = into) moves things into the cell:

Creation of membranous vesicles containing fluid or solid material

Factors affecting rate:

  • Stimulus and mechanics incompletely understood
  • Requires ATP

Substances involved:

  • Fluids, nutrients (all cells)
  • Debris, pathogens (specialized cells)

Receptor Mediated Endocytosis

  • Pinocytosis: “Cell Drinking”
  • **Phagocytosis: **“Cell Eating”

Exocytosis (exo = out of) moves things out of the cell:

Fusion of vesicles containing fluids or solids (or both) with the cell membrane

Factors affecting rate:

  • Stimulus and mechanics incompletely understood
  • Requires ATP

Substances involved:

  • Fluids, debris (all cells)

(Vesicular Transport)

Receptor-Mediated Endocytosis


A process by which cells internalize molecules (endocytosis) by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules being internalized.




A specialized form of endocytosis. A way of moving water into the cell. A mode of endocytosis in which small particles are brought into the cell, forming an invagination, and then suspended within small vesicles.

• Pinocytosis (cell drinking)




A specialized form of endocytosis. A way of breaking a substance down within the cell either to use parts of it or eject it using exocytosis. The process by which a cell—often a phagocyte or a protist—engulfs a solid particle to form an internal vesicle known as a phagosome.

• Phagocytosis (cell eating)




The durable, energy-consuming process by which a cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space.

Is the reverse of endocytosis


Organic Molecules

  • Always contain carbon and hydrogen
  • Many contain long chains of covalently linked carbon
  • **Many are soluble in water **
  • Four Major Classes

(Organic Molecule)
(3 Classes)


Provide the body with glucose, which is converted to energy used to support body functions.

  • Contains carbon, hydrogen and oxygen
  • Provide a ready, easily used source of cellular fuel


  1. Monosaccharides: Simple sugars, the simplest carbohydrate form. In general, the basic molecular formula is (CH2O)n. Monosaccharide’ function: a source of energy for organisms. Examples: Glucose, galactose, and fructose.
  2. Disaccharides: Consist of two monosaccharides joined together by a covalent bond. This bond is generally between the number 1 carbon of one monosaccharide and the number 4 carbon of the other molecule. Disaccharides’ function: a nutritional source of monosaccharides. Examples: sucrose or table sugar, maltose, and lactose.
  3. Polysaccharides: Composed of thousands of monosaccharides. The addition of new monosaccharides could continue indefinitely making a huge molecule forming a long (and branched via the 6- carbon) chain of glucose molecules. This long chain is known as a polysaccharide. Polysaccharides’ function: an easily accessible storage form of glucose. Examples: starch and glycogen.

What the fuck is this?


Steps to produce ATP.

  1. Glycolisis: Glucose undgoes glycolisis which makes 2 ATP and 2 Pyruvate.
  2. Krebs Cycle: The Pyruvate enters the Krebs Cycle which will then be converted to Pseudo-Coenzyme A. Another 2 ATP is then made, which requires 4 waters and produce 4 carbon dioxide.
  3. Oxidative Phosphorilation: The NADH and FADH enters oxidatidive phosphorilation which makes another 34 ATP.

1 glucose molecule + 6 oxygen + 38 ATP + 38 inorganic phospahate = 6co2 6h2o and 38 ATP

(C6H12O6 + 6O2 +38APT +38Pi = 6CO2 + 6H2O + 38ATP)

(number of atp varies 32-40 depending on text and conditions atp is being made. 38 is most accepted number).


(Organic Molecule)
(5 classes)


Contain carbon, hydrogen and oxygen

Lipids are a group of naturally occurring moleculesthat include fats, waxes, steroids, fat soluble vitamins (such as vitamins A, D, E, and K), monoglycerides,diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include storing energy, signaling, and acting as structural components of cell membranes.

Five classes:

  1. Fatty acids: Used to synthesize triglycerides and phospholipids or catabolized to generate adenosine triphosphate (ATP).
    * *Saturated:** When all the carbons in a fatty acid are linked by single covalent bonds because both of the remaining available bonds in each carbon atom are occupied—or saturated—with covalently bound H. Tend to be solid at low temperatures.
    * *Unsaturated: **Contain one or more double bonds between carbon atoms, (they have fewer C—H bonds than a saturated fatty acid). have a very low melting point, and thus they are liquids (oil) even at low temperatures.
  2. Eicosanoids: Have diverse effects on modifying responses to hormones, blood clotting, inflammation, immunity, stomach acid secretion.
    * *Prostaglandins: **The prostaglandins act as signals to control several different processes depending on the part of the body in which they are made. Prostaglandins are made at sites of tissue damage or infection, where they cause inflammation, pain and fever as part of the healing process.
    * *Leukotrienes: **Biologically active molecules, formed by leukocytes, mastocytoma cells, macrophages, and other tissues and cells in response to immunological and nonimmunological stimuli.
  3. Glycerides: (neutral fats) Protection, insulation, energy storage.
  4. Steroids: Distinctly different structure from those of the other subclasses of lipid molecules. Four interconnected rings of carbon atoms form the skeleton of every steroid. A few hydroxyl groups, which are polar, may be attached to this ring structure, but they are not numerous enough to make a steroid water soluble.
  • *Cholesterol: **Required to maintain both membrane structural integrity and fluidity.
  • *Estrogen and Testosterone: **Stimulate the growth of sex organs, breasts and pubic hair, regulate the functioning of the menstrual cycle, maintains condition of the vaginal lining and its elasticity, and in producing vaginal lubrication (women).
  • *Corticosteroids and Calcitriol: The hormonally active form of vitamin D. It i**ncreases the level of calcium in the blood by increasing the uptake of calcium from the gut into the blood, and possibly increasing the release of calcium into the blood from bone.
  • *Bile Salts: **Have a crucial role in hepatobiliary and intestinal homeostasis and digestion.
  1. **Phospholipids and Glycolipids: **Similar in overall structure to triglycerides, with one important difference - The third hydroxyl group of glycerol, rather than being attached to a fatty acid, is linked to phosphate. A small polar or ionized nitrogen containing molecule is usually attached to this phosphate. These groups constitute a polar (hydrophilic) region at one end of the phospholipid, whereas the two fatty acid chains provide a nonpolar (hydrophobic) region at the opposite end. Therefore, phospholipids are amphipathic. In aqueous solution, they become organized into clusters, with their polar ends attracted to the water molecules. This property of phospholipids permits them to form the lipid bilayers of cellular membranes.

(Oranic Molecule)


(7 Major Functions)


Proteins account for about 50% of the organic material in the body (17% of the body weight), and they play critical roles in almost every physiological and homeostatic process. Proteins are composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur. They are macromolecules, often containing thousands of atoms; they are formed when a large number of small subunits (monomers) bond together via dehydration reactions to create a polymer.

Seven major protein functions:

  • Support
  • Movement
  • Transport
  • Buffering
  • Metabolic regulation
  • Coordination and control
  • Defense

Protein Types

  • **Fibrous: **insoluble, and play a structural or supportive role in the body, and are also involved in movement (as in muscle and ciliary proteins).
  • **Globular: **highly diverse group of proteins that are soluble and form compact spheroidal molecules in water. All have tertiary structure and some have quaternary structure in addition to secondary structure.


  • Chaperone: assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures.
  • **Enzymes: **allow the cell to carry out chemical reactions very quickly. These reactions allow the cell to build things or take things apart as needed.

Protein Combinations

  • Glycoproteins: in the immune system almost all of the key molecules involved in the immune response are glycoproteins.
    Large protein + small carbohydrate
  • Proteoglycans: in all connective tissues, extracellular matrix (ECM) and on the surfaces of many cell types. Proteoglycans are remarkable for their diversity
    Large polysaccharides + polypeptides

Nucleic Acids

  • Long chains of nucleotides form RNA and DNA



A nucleotide is an organic molecule made up of a nucleotide base, a five-carbon sugar (ribose or deoxyribose) and at least onephosphate group. Nucleotides make up the basic units of DNA and RNA molecules.



  • **RNA: **Ribonucleic acid is a family of large biological molecules that perform multiple vital roles in the coding, decoding, regulation, and expression of genes.
  • **DNA: **DNA in the cell nucleus contains the information needed to construct all of the proteins in the body.

Forms of RNA

  • Messenger RNA (mRNA): Carries information about a protein sequence to the ribosomes, the protein synthesis factories in the cell.
  • **Transfer RNA (tRNA): **A small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptidechain at the ribosomal site of protein synthesis during translation.
  • **Ribosomal RNA (rRNA): **Found in many bacteria and plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.


  • **Adenosine Diphosphate (ADP): **An important organic compound in metabolism and is essential to the flow of energy in living cells.
  • **Adenosine Triphosphate (ATP): ** Used in cells as a coenzyme. It is often called the “molecular unit of currency” of intracellular energy transfer. ATP transports chemical energy within cells for metabolism.



The addition of a phosphate group to a protein or other organic molecule. Phosphorylation turns many protein enzymes on and off, thereby altering their function and activity.


The Energy Molecule

  • Chemical energy stored in phosphate bonds.

Compounds Important to Physiology


Classes of organic and inoragnic substances


  • Water
    Building blocks: Hydrogen and Oxygen atoms
    Sources: Absorbed as liquid water or generated by metabolism
    Functions: Solvent; Transport medium for dissolved materials and heat; Cooling through evaporation; Medium for chemical reactions; Reactant in hydrolysis
  • Acids, bases, salts
    Builing blocks:
    H+, OH-, Various anions and cations
    Sources: Obtained from the diet or generated by metabolism
    Functions: Structural components; Buffers; Sources of ions
  • Dissolved gasses
    Builing blocks:
    O, C, N, and other atoms
    Sources: Atmosphere
    Functions: O2 required for cellular metabolism; CO2 generated by cells as a waste product; NO chemical messangers involved in cardiovascular, nervous, and lymphatic systems


  • Carbohydrates
    Builing blocks:
    C, H, O, in some cases N
    Sources: Obtained from the diet or manufactured in the body
    Functions: Energy sources; some structural role when attached to lipids or proteins; Energy storage
  • Lipids
    Builing blocks:
    C, H, O, N, In some cases N and P
    Sources: Obtained from the diet or manufactured in the body
    Functions: Energy source; Energy storage; Insulation; Structural componenets; Chemical messangers; Protection
  • Proteins
    Builing blocks:
    C, H, O, N, Commonly S
    Sources: 20 common amino acids; Roughly half can be manufactured in the body, others must be obtained in the diet
    Functions: Catalysts for metabolic reactions; Structural components; Movement; Transport; Buffers; Defense; Control and coordination of activities