New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here

Week 2 Notes

by: Lauren Zuniga

Week 2 Notes BIO 65

Lauren Zuniga
Fresno State

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

notes for the second week of class Ch. 1 - Human Body Orientation Ch. 2 - Chemistry Ch. 3 - Cells
Class Notes
Human, body, orientation, Chemistry, cells, chemical, bonds, biochemistry, celltheory
25 ?




Popular in Physiology

Popular in Biology

This 27 page Class Notes was uploaded by Lauren Zuniga on Monday September 5, 2016. The Class Notes belongs to BIO 65 at California State University Fresno taught by Chooljian in Spring 2015. Since its upload, it has received 10 views. For similar materials see Physiology in Biology at California State University Fresno.


Reviews for Week 2 Notes


Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 09/05/16
1. Three types of RNA are involved in protein synthesis: transfer RNA (tRNA), messenger RNA (mRNA) and ribosomal RNA (mRNA). mRNA serves as the template (instructions) to make the protein. Recall that the mRNA was produced from the original DNA gene that contained the instructions to make the protein. rRNA makes up the physical structure of the ribosome itself. There are about 45 different types of tRNA molecules, each capable of binding to a specific amino acid. Each one contains an anticodon(the complement of a codon) on one end and the corresponding amino acid on the other end. For example, if an mRNA codon is UUU, the corresponding tRNA anticodon will be AAA. 2. The ribosome is more than just a passive attachment site for mRNA and tRNA. Besides its binding site for mRNA, there are three binding sites for tRNA; an A site for the incoming tRNA molecule, a P site for the tRNA holding the growing protein chain and an E site for the outgoing tRNA. The ribosome holds the tRNA and mRNA closely together to coordinate the coupling of codons and anticodons and positions the incoming amino acid for addition to the growing polypeptide chain. 3. Transcription is the process whereby mRNA is copied from a gene on the DNA. This process involves the breaking part of the DNA segment where transcription is to take place (unzipping). One by one, each triplet on the DNA template is copied into a corresponding mRNA codon. This process is directed by the enzyme RNA polymerase. Start codons tell the process where to begin, and stop codons tell the process where to end. This process occurs in the nucleus. Once the mRNA strand is complete, it is exported out of the cytoplasm to the ribosomes. 4. Translation is the process whereby the mRNA strand will be then be used to create a protein. The mRNA strand binds to the ribosomal subunits, and one by one, tRNA brings the correct anticodon (base pair triplet) that corresponds to each codon on the mRNA strand. Each tRNA molecule has an anticodon on one end and the corresponding amino acid on the other. This beads- on-a-string assembly process continues until a codon is reached, the protein is complete and detaches from the ribosome. C. Cytosolic Protein Degradation 1. In order to function in their physiological roles, proteins must be in the right place, at the right time and in the right amounts. 2. Proteins eventually degrade over time. Proteins found in organelles are digested by lysosomes, but lysosomes cannot access damaged proteins found in the cytosol. 3. These proteins are marked for attack by attachment of proteins call ubiquitins in an ATP-dependent reaction. 4. The tagged proteins are hydrolyzed (broken down) to small peptides by soluable enzymes or by giant waste disposal complexes called proteasomes. ** Know order of mitosis, meiosis: Meiosis: Pizza Makes A Triangle Ch. 9 Muscles and Muscle Tissues I. Overview of Muscle Tissues a. Characteristics of muscle tissue i. Excitability—has the ability to receive and respond to stimuli (any change in the environment, whether inside or outside the body. The stimulus is usually chemical—the release of neurotransmitter or local change in pH. The response is generation of an electrical impulse across the sarcolemma (muscle cell plasma membrane) that causes the cell to contract. ii. Contractility—has the ability to shorten forcibly when stimulated. This property sets muscle tissue apart from all other tissue types. iii. Extensibility—has the ability to be stretched. Muscle fibers shorten when contracting, but they can be stretched, even beyond their resting length, when relaxed. iv. Elasticity—has the ability to return to the resting length after being stretched. b. Muscle Functions i. Producing movement—skeletal muscles are responsible for all locomotion and manipulation of objects. Skeletal muscles allow us to respond quickly to changes in the environment, often to avoid danger. The beating of the heart and smooth muscle in the vasculature helps to maintain blood pressure. Smooth muscle in the digestive, urinary, and reproductive tracts moves various substances from one place to another. ii. Maintaining posture and body position—skeletal muscles can produce continuous adjustments to allow us to sit in a chair without falling out of it, or to stand without falling over. iii. Stabilizing joints—skeletal muscles stabilize and strengthens joints in the skeleton. iv. Generating heat—muscles generate heat as the contract, which is vitally important to maintaining body temperature. v. Additional functions—skeletal muscle protects internal organs; smooth muscle forms valves and constricts the eye pupils and forms the errector pili muscles that move hair. II. Skeletal Muscle a. Sliding Filament Model of Contraction i. The term contraction refers only to the activation of myosin’s cross-bridges, which are the forces generating sites. Shortening occurs when the tension generated by the cross bridges on the thin filaments exceeds the forces opposing shortening. Contraction ends when the cross bridges become inactive and the tension generated declines, inducing relaxation of the muscle fiber. ii. The sliding filament theory of contraction states that during contraction the thin filaments slide past the thick ones so that actin and mysosin filaments overlap to a greater degree. In a relaxed muscle fiber, the thick and thin filaments only overlap at the ends of the A band. Upon nervous system stimulation, the myosin heads latch onto mysosin binding sites on actin in the thin filaments and the sliding begins. These cross bridge attachments are formed and broken several times during a contraction, acting like tiny ratchets to generate tension and propel the thin filaments towards the center of the sarcomere. As this even occurs simultaneously in sarcomeres throughout the cell, the muscle cell shortens. As the thin filaments slide to the center, the Z discs to which they are attached are pulled toward the thick filaments. The I bands shorten, the distance between Z discs is reduced, the H zones disappear and the A bands move closer together but don’t change in length. b. Physiology of skeletal muscle fibers i. The sliding filament model explains how a muscle fiber contracts. The muscle fiber must be stimulated by a nerve ending to cause a change in membrane potential. An action potential must be generated and propagated along the sarcolemma, and finally a short-lived rise in intracellular calcium ions is the final trigger for contraction to occur. ii. The axons of motor neurons form junctions with individual skeletal muscle fibers in what is known as the neuromuscular junctions. The tiny space between each neuron and muscle fiber is called the synaptic cleft. The axon terminal contains synaptic vesicles that contain the neurotransmitter acetylcholine (ACh). The muscle fiber contains millions of receptors for Ach. iii. When a nerve impulse reaches the end of an axon, the axon terminal releases Ach into the cleft, which diffuses across the cleft and attaches to the receptors on the other side. This triggers the generation of an action potential. An enzyme, acetylcholinesterase, quickly breaks down the ACh, preventing continued muscle fiber contraction in the absence of further nervous system stimulation. iv. Steps of the sarcolemma action potential 1. Local depolarization and generation of an end plate potential—binding of ACh to receptors opens ligan-gated channels to allow Na+ to pass in and K+ to pass out. Since more Na+ pass in than K+ pass out, the inside of the membrane becomes less negative (become depolarized). 2. Generation and propagation of the action potential—the initial depolarization is localized and called the end plate potential. This depolarization spreads across the sarcolemma, causing the opening of voltage gated Na+ channels, allowing Na+ to enter. Once a certain minimum voltage is reached (the threshold), an action potential is generated. (pg 280-281) 3. The sarcolemma is restored to its initial polarized state during repolarization, which is a result of changes in membrane permeability. Na+ channels close, and K+ channels open. Since K+ concentration is higher inside the cell than outside, K+ diffuses rapidly out of the muscle fiber, restoring negatively to the inside. 4. The refractory period is the time period during which the muscle fiber cannot be stimulated again until repolarization is complete. v. Excitation-contraction coupling is the sequence of event by which the spreading of an action potential along the sarcolemma causes the sliding of myofilaments. It consists of the following steps: 1. The action potential propagates along the sarcolemma and down the T tubules. 2. This causes the T tubules to release Ca+2 into the sarcoplasm, where it becomes available to myofilaments. 3. Some of this Ca+2 binds to troponin, which changes shape and removes the blocking action of tropomyosin. 4. The removal of the blocking action of tropomysosin allows the myosin heads to attach and pull the thin filaments toward the center of the sarcomere. 5. The short-lived Ca+2 signal ends about 30 msec after the action potential is over, due to the action of the ATP dependent pump that moves Ca+2 back into the sarcoplasmic reticulum to be stored for later use. 6. The inactive state occurs when intracellular Ca+2 levels drop too low for the amount of Ca+2 needed for contraction to bind to troponin, so the tropomyosin blockade is reestablished, the myosin-actin interaction is inhibited. Cross bridge activity ends and relaxation occurs. vi. Muscle Fiber Contraction—to sum up, contraction of a muscle fiber occurs in the following steps: 1. MUST HAVE CALICIUM and ATP in order for muscles to contract! *** 2. Cross bridge formation—the activated myosin heads are strongly attracted to the exposed binding sites on actin , and cross bridges form. 3. The power stroke—during the power stroke, the myosin head pivots, which pulls on the thin filament, sliding it toward the center of the sarcomere. 4. The ATPase in the myosin head hydrolyzes ATP to ADP and P, which provides the energy to return the myosin head to its prestrike high- energy position. c. Contraction of skeletal muscle i. The principles of contraction of a single muscle fiber and an entire skeletal muscle are about the same. Contracting muscles exert a tension against an opposing weight (the load). ii. A motor unit consists of a motor neuron and all the muscle fibers it supplies. When a motor neuron transmits an action potential, all the muscle fibers it innervates contract. iii. The response of a motor unit to a single action potential of its motor neuron is called a muscle twitch. This twitch has three phases: 1. The latent period is the first few milliseconds following stimulation when excitation- contraction coupling is occurring. 2. The period of contraction is when the cross bridges are active. If the tension generated is greater than the load, the muscle shortens. 3. The period relaxation is initiated by the reenter of Ca+2 back into the sarcoplasmic reticulum. iv. Graded muscle responses—contractions of healthy muscles are smooth and vary due to the demands placed on them. Muscle contractions can be graded either by changing the frequency of stimulation or by changing the strength of stimulation. 1. Changes in stimulus frequency—The nervous system achieves greater muscular force by increasing the firing rate of motor neurons. If two identical nerve impulses are delivered to a muscle in rapid succession, the second twitch will be stronger than the first, a condition known as temporal (wave) summation. This occurs because the second contraction occurs before the muscle has completely relaxed. If stimulus strength is constant and the muscle is stimulated at an increasingly faster rate, a condition known as unfused (incomplete) tetanus occurs. Fused (complete) tetanus occurs under maximal muscle tension. 2. Changes in stimulus strength—The force of muscular contraction is more precisely controlled by multiple motor unit summation (recruitment). Each muscle contains anywhere from a few to thousands of motor units. The smallest muscle fibers are innervated by motor neurons with a very low threshold stimulus (the minimum voltage required to stimulate the muscle fiber). These are the motor units activated first in response to a stimulus. As the stimulus increase, increasing numbers of larger motor units with higher thresholds of stimulus are activated. Maximum stimulus results in recruitment of all motor units in a muscle, producing the maximum force the muscle can exert. v. Muscle Metabolism 1. ATP provides the energy for cross bridge activity and for operation of the Ca+2 pump in the sarcoplasmic reticulum. 2. Very little ATP is store in muscle tissue, enough for a few seconds of activity, and must be remade as fast as it is broken down. 3. There are 3 pathways of ATP formation: a. Direct phosphorylation of ADP by creatine phosphate (14-16 seconds of activity) b. Anaerobic glycolysis, which converts glucose to lactic acid (30-40 seconds of activity). c. Aerobic respiration—produces 95% of the ATP used during rest and prolonged activity. III. Smooth Muscle a. Contraction i. Contraction of smooth muscle is similar to skeletal muscle in many ways. ii. However, when Ca+2 activate myosin they do so by interacting with a regulatory molecule called calmodulin. Calmodulin interacts with an enzyme called myosin kinase. iii. Smooth muscle takes 30 times longer to contract and relax than does skeletal muscle. iv. Smooth muscle takes 1% as much energy to operate as does skeletal muscle. (pg 309) b. Regulation of contraction i. Smooth muscle may be regulated by neural input, just like skeletal muscle. ii. Smooth muscle may be reulated by hormones and other chemical factors, such as lack of oxygen or excess CO2, histamine and low pH. Down conc gradient- goes from where there is more to less III. The Small Intestine and Associated Structures A. The Small Intestine 1. The small intestine is the body’s major digestive organ.  Within it,  digestion is completed and virtually all absorption occurs. 2.  The intestinal glands secrete 1 to 2 liters of intestinal juice daily.  The  major stimulus for production is distension or irritation of the intestinal  mucosa by hypertonic or acidic chyme.  Intestinal juice is slightly alkaline  (pH 7.4 – 7.8), and is isotonic with blood plasma. B. The Liver and Gallbladder 1. The liver and gallbladder are accessory organs associated with the small  intestine.  The liver has many metabolic and regulatory functions.  Its  digestive function is to produce bile, which is then stored in the gallbladder.  Bile is a fat emulsifier; that is, it breaks fats up into tiny droplets so that they are more accessible to digestive enzymes. 2.  Bile is a yellow­green alkaline solution containing bile salts, pigments,  cholesterol, triglycerides, phospholipids and electrolytes.  Bile salts are the  chemical responsible for fat emulsification. 3.  When no digestion is occurring, the hepatopancreatic sphincter (guarding  the entry of bile and pancreatic juice into the duodenum), is closed, causing  bile to back up into the cystic duct, where it is stored in the gallbladder until  needed.  The major stimulus for gallbladder contraction is cholecystokinin  (CCK), an intestinal hormone that is released to the blood when acidic, fatty  chyme enters the duodenum.  CCK also stimulates the secretion of  pancreatic juice and relaxes the hepatopancreatic sphincter so that bile and  pancreatic juice can enter the duodenum. C. The Pancreas 1. The pancreas is an accessory digestive organ that produces enzymes that  breakdown all categories of food, which the pancreas delivers to the  duodenum.  This exocrine product, called pancreatic juice, is produced by  the acini (clusters of cells), and drains from the pancreas via the main  pancreatic duct, which fuses with the bile duct as it enters the duodenum. 2. 1200 to 1500 ml of pancreatic juice is produced daily.  This juice is  alkaline (pH 8), which helps to neutralize the acidic chyme as it enters the  duodenum.  Pancreatic proteases (protein digesting enzymes) are released in  inactive forms and activated in the duodenum.  If the enzymes were  produced in active forms within the pancreas, they would digest the pancreas itself; therefore, they are produced in inactive forms and only activated upon reaching the duodenum. D. Digestive Processes of the Small Intestine 1. By the time food reaches the small intestine, proteins and carbohydrates  have been partially degraded, but virtually no fat digestion has occurred.  Most of the substances required for chemical digestion—bile, enzymes and  bicarbonate ions, are imported from the liver and pancreas.  2.  The other function of the small intestine, absorption, is accomplished by  its absorptive cells with huge numbers of microvilli.  These microvilli vastly increase the surface area of the small intestine to facilitate absorption. 3.  Optimal digestive activity depends on the slow, measured delivery of  chyme from the stomach, which is carefully controlled by the pyloric valve. IV. The Large Intestine A. Digestive Processes 1. The major function is to absorb most of the remaining water from  indigestible food residue, store the residue for a while, and then eliminate  them from the body as feces.  Illnesses, such as food poisoning, cause the  body to greatly speed up the movement of fecal material through the  intestines in order to try to rid the body of the infection.  This causes the  feces to be watery (diarrhea).  2. Except for a small amount of digestion of the residue by enteric bacteria,  no further breakdown of food occurs in the large intestine.  Humans don’t  really benefit from this bacterial breakdown, but the unfortunate byproduct  of the bacterial action is intestinal gas.  Some foods, like beans and cabbage,  are known for producing large amounts of this gas. Part 3: Physiology of Chemical Digestion & Absorption I. Chemical Digestion A. Enzymatic Hydrolysis 1. Chemical digestion is a catabolic process in which food is broken down  into chemical building blocks which are small enough to be absorbed by the  GI tract lining. 2. The enzymatic breakdown of food is hydrolysis because it involves the  addition of a water molecule to each molecular bond broken. B. Chemical Digestion of Food Groups 1. Carbohydrates a) The simple sugars glucose and fructose, which are  monosaccharides, are ready to be absorbed immediately upon  ingestion. b) The more complex disaccharides like sucrose and the  polysaccharides glycogen and starch must be broken down. c) Breakdown of starch begins in the mouth with salivary amylase.   Digestion continues in the small intestine with the enzymes pancreatic amylase, dextrinase, glucoamylase, maltase, sucrase and lactase. d) Chemical digestion officially ends in the small intestine; however,  some digestion of complex carbs continues in the large intestine via  the action of bacteria, although we don’t benefit nutritionally from  this action. 2. Proteins a) Protein digestion begins in the stomach when pepsinogen secreted  by the chief cells is activated to pepsin.  Proteins are broken into  polypeptides and free amino acids.  Pepsin is inactivated in the high  pH environment of the duodenum. b) Protein digestion continues in  the small intestine under the actions of other enzymes—trypsin and  chymotrypsin from the pancreas, as well as carboxypeptidase,  aminopeptidase and dipeptidase. 3. Lipids a) The small intestine is the sole site of lipid digestion, since the  pancreas is the only source of lipases (fat digesting enzymes). b) Fats must be “pre­treated” with bile salts to begin their digestion.   Fat globules are coated with detergent­like bile salts, which have both  polar and non­polar parts.  The non­polar parts cling to fat droplets,  while the polar parts allow them to interact with water.  This results in an emulsion, which greatly increases the ability of the lipases to  interact with the fat droplets. c) The lipases catalyze the breakdown of fats by cleaving off two of  the fatty acid chains, yielding free fatty acids and monoglycerides  (glycerol with one fatty acid attached). 4. Nucleic acids a) Both DNA and RNA are present in the nuclei of ingested foods. b) They are hydrolyzed to their nucleotide monomers by pancreatic  nucleases present in pancreatic juice.  The nucleotides are then broken apart by intestinal brush border enzymes (nucleosidases and  phosphatases), which release the free bases, pentose sugars and  phosphate ions. Ch. 1 Human Body Orientation I. An Overview A. Anatomy/Physiology defined 1. Anatomy = study of structures. 2. Physiology = study of functions. B. Complementary nature of structure/function 1. It is difficult to study physiology w/o an understanding of anatomy. 2. Function always reflects structure. 3. This is called the principle of complimentary of structure and function. a) Bones can support/protect bc they contain hard mineral deposits. b) Blood flows in one direction bc of valves that prevent backflow. II. Levels of Structure Organization. A. Life is organized 1. All organisms exhibit organization, from the simplest single cell to the largest, most complex life forms. 2. Organization allows for organisms to function efficiently. B. Levels of Structural Organization 1. The chemical level is the simplest- Atoms combine to form molecules; also form organelles (ie. Mitochondria, which form the basic components of cells) 2. The cellular level is the next most complex. Cells are the basic building blocks of all life forms. All life forms have at least one cell. Humans have trillions of cells. 3. Tissue level is next- Tissues are groups of similar cells that have a common function; 4 basic tissue types: epithelium, muscle, connective, and nervous tissue 4. Tissues combine to form organs. Organs are composed of at least 2 different types, although many have all 4 types. Organs allow for the body to perform complex functions. The stomach has all 4 tissue types to allow it to store food, secrete digestive juices, and mix the stomach contents. 5. Organ systems are combinations of organs working together to perform a common purpose. There are 11 organ systems in the human body: integumentary, skeletal, muscular, immune, respiratory, digestive, nervous, endocrine, cardiovascular, urinary, and reproductive. (ie. the respiratory system is made up of structures in the nose/throat, as well as the lungs/muscles in the chest. 6. The final organization level is the organism itself. An organism, like a human, represents the sum total of all the organizational levels working together to produce a viable person. III. Maintaining Life A. Necessary Life Functions 1. Maintenance of boundaries a) Single-celled organism maintain their boundary via their plasma membrane which selectively admits/restricts what substances can flow in/out of the cell. b) Multicellular organisms also have plasma membranes surrounding their cells. Additionally, the integumentary system covers the entire body and helps to protect the cells within and maintain homeostasis. 2. Generation of movement a) The skeletal and muscular systems allow animals to purposely move from one place to another. b) Smooth muscles within the body allow for fluids like blood and solids, like food, to be moved from one place to another. 3. Responsiveness (1) Organisms have the ability to sense changes in the environment and respond rapidly to them. Some of these responses are reflexive (like removing the hand from a hot stove) while others require higher-level thinking. (2) Some responses are automated via centers in the brainstem, such as sensing/responding to high levels of the CO2 in the blood. 4. Digestion (1) Digestion is the process of breaking down ingested food into small molecules that can be absorbed into the blood and transported to cells. (2) Digestion begins in the mouth, continues in the stomach, and is finished in the intestines. **Most of the digestion occurs in the small intestine! 5. Metabolism (1) Metabolism is the sum of all the biochemical reactions taking place in the body. Some reactions are catabolic (breaking down) while others are anabolic (building up) (2) Nutrients and oxygen are used to produce ATP, the power of cellular activities. 6. Excretion (1) The process of removing waste products from the body. (2) The digestive system removes indigestible food residue. The urinary system removes nitrogen-containing wastes, and CO2 is removed by the circulatory/respiratory systems. 7. Reproduction can occur at the cellular/organismal level (1) Cellular reproduction produces new cells via mitosis (reproduction of body cells; produces diploid cells; same cells replaced; body fixes cuts with mitosis) and meiosis (produces egg or sperm depending on gender; produces haploid cells; half of the cells are the original cells). (2) Organismal reproduction occurs when egg and sperm fuse to produce a new organism. b) Growth of cells/organism itself is a characteristic of living beings. 8. Survival Needs a) In order to survive, living organism must have access to a number of factors. b) Nutrients, oxygen, and H2O must be present for humans to exist. c) Also, a normal body temp must be maintained, and atmospheric pressure must be normal. (The higher you go, the lower your atmospheric pressure.) IV. Homeostasis A. Homeostasis defined 1. Homeostasis is the maintenance of a steady-state environment within the body. 2. There are a number of factors that the body strives to maintain in homeostasis-body temp, blood gas levels of O2 and Co2, water balance, glucose balance, pH, temperature, blood pressure, and so forth. 3. Receptors sense changes in these various parameters, control centers in the brain determine the correct set point for each parameter and respond with effectors, generally components of the nervous and/or endocrine systems, in order to keep all factors within normal limit points. B. Feedback Mechanisms 1. Homeostasis can be maintained via either negative or positive feedback mechanisms. 2. Most homeostatic control mechanisms involve negative feedback, these mechanisms cause the variable to change in a direction opposite to that of the initial change. For example, if the brain senses that blood glucose levels are too high, it instructs the pancreas to release insulin in the blood in small amounts. Once glucose returns to normal levels, output of insulin is stopped. 3. In positive feedback mechanisms, the response increases the original stimulus, so that activity increased. These mechanisms usually control infrequent events that don’t require constant adjustments. An example is the release of oxytocin from the hypothalamus. Ch. 2 Chemistry Part 1: Basic Chemistry I. Matter and Energy a. Matter i. Matter occupies space and has mass. ii. Matter exists in three phases- solid, liquid, and gas b. Energy i. Energy is the capacity to do work. ii. Potential energy is stored energy, like water behind a dam. iii. Kinetic energy is energy in motion, like water flowing over a dam and turning turbine to make electricity. iv. Energy exists in several forms- chemical, electrical, mechanical, and radiant, II. Atoms and Elements a. Atomic structure i. Atom= basic unit of matter and cannot be broken down further by ordinary means. ii. Atoms are composed of smaller subatomic particles- protons, neutrons, and electrons. Protons and neutrons are found in the atomic nucleus, while the electrons orbit the nucleus. The electrons are found in shells (also called valence or energy levels). iii. Protons are positively charged, neutrons have no charge and electrons are negatively charged. iv. An element is a pure form of matter containing only one kind of atom. b. Identifying Elements i. The atomic mass of an element = the # of protons and neutrons. ii. The atomic number of an element = the # of protons. iii. The atomic weight of an element = average of all the masses of isotopes of an element as they exist in nature. iv. Isotopes contain the same number of protons, but have different numbers of neutrons. (i.e. Carbon 13 has 6 protons and 7 neutrons.) Some isotopes are stable, while others, radioisotopes, emit radiation as the decay into a stable state. III. Molecules and Mixtures a. Molecules and compounds i. molecule =two or more atoms held together by chemical bonds, like H2. ii. Compound = two or more different kinds of atoms bonded together, like H2O. b. Mixtures i. Mixture = two or more components physically intermixed. 1. Solution = homogeneous mixture of a solute dissolved in a solvent. 2. Colloids (emulsions) are heterogeneous mixtures that often appear cloudy or milky. Gelatin is an example of a colloid. 3. Suspension = heterogeneous mixture with large, often visible solutes that tend to settle out. Blood is an example of a suspension. IV. Chemical Bonds a. The role of electrons in chemical bonding i. Atoms are held together by chemical bonds, which are relationships b/w the electrons of reacting atoms. ii. There are up to 7 levels of electrons surrounding nuclei of atoms. Only the electrons in the outer energy level react. Shell number 1 holds 2 electrons; shell 2 holds 8 and shell 3 holds 18. The other shells hold increasingly larger numbers of electrons. iii. Only the electrons in the outer shell are reactive. If an atom’s outer shell is full, the atom is unreactive, or inert. The noble gases, like helium and neon, are inert. Atoms whose outer shell is less than full are reactive, as the combine with other atoms in order to achieve full outer shells. b. Types of chemical bonds i. Ionic bonds form when ions form and are transferred from one atom to another. An ion is an atom or group of atoms that have a positive or negative charge. Anions are negative, cations are positive. The formation of salt from sodium and chloride is an example of an ionic bond. ii. Covalent bonds form when 2 or more atoms share electrons in their outer shells. Atoms may share 1,2, or 3 pairs of electrons, resulting in single, double, or triple covalent bonds. The pairing of 2 H atoms together is a single covalent bond. iii. Covalent bonds may be polar or nonpolar. Polar bonds exhibit slight positive and negative charges at either end of the molecules. This influences the shape and reactivity of the molecule. CO2 is a nonpolar linear molecule, and is unreactive. Water is a polar, V-shaped molecule. Water molecules tend to stick together and are also reactive with a wide variety of other compounds, which is why water is often called the universal solvent. iv. Hydrogen bonds are weak bonds between hydrogen atoms and other atoms. An example is the weak bond that exists between the H and O atoms of water molecules. It’s these H bonds that create the surface tension of water. DNA contain weak hydrogen bonds between the pairs that are easily broken during DNA replication. c. Chemical equations i. Chemical reactions can be written in symbolic form as chemical equations. ii. A chemical equation is typically shown with the reactants on the left side of an arrow, and the products on the right side of the arrow. The reactions must be balanced that is, there must be the same number of each type of element of each side of the arrow, indicating that matter is neither created nor destroyed, just changed into different forms. d. Patterns of reactions i. Reactions may by either anabolic (synthesizing) or catabolic (decomposing) or exchange (a combination of both) ii. Oxidation/reduction (redox) reactions are important in living systems in that they are decomposition reactions that convert food into energy (ATP production). Redox reactions involve the exchange of electrons between the donor, which is oxidized, and the receiver, which is reduced. Cellular respiration, which is the opposite of the photosynthesis reaction, is an example of a redox reaction. e. Energy flow in chemical reactions i. Reactions that release energy are called exergonic. Most catabolic and oxidative reactions are exergonic. ii. Reactions that require the input of energy in order to occur are called endergonic. Anabolic reactions are typically endergonic. f. Reversibility of chemical reactions i. Theoretically all chemical reactions are reversible; that is reactants and products can be formed and uniformed. When the rate of formation and breakdown is equal, the reaction is said to be in chemical equilibrium. ii. Most biochemical reactions show little tendency to go in the reverse direction, so they are irreversible for all practical purposes. g. Factors that influence the rate of chemical reactions. i. Increased temperature increases the rate of reaction. ii. Increased concentration of reactants increases the rate of reaction. iii. Smaller particle size of reactants increases rate of reaction. iv. The presence of catalysts (enzymes) in biological systems increases the reaction speed. Part 2: Biochemistry I. Inorganic compounds a. Water i. Water is the most abundant and important inorganic compound in living systems. ii. Its high heat capacity, high heat of vaporization and polar solvent properties are essential for helping living systems to maintain homeostasis. b. Salts i. A salt is an ionic compound that contains ions other than H+ and OH- ii. When salts are dissolved in water, they dissociate into their component ions, like NaCl dissolves into Na+ and Cl- c. Acids and bases i. An acid is a substance that releases H+ when dissolved in water. Acids are also known as proton (H+) donors. ii. A base is a substance that releases OH- when dissolved in water. Bases are also known as proton acceptors. iii. Acids and bases are measured on a scale known as the pH scale, which ranges from 0 (most acidic) to 14(most basic). A pH of 7 is taken to be neutral. With a few notable exceptions, most bodily fluids are neutral to slightly basic. iv. When acids and bases are mixed together, they neutralized, forming a salt and water. v. The body contains buffering systems, like the carbonic acid/bicarbonate system that help the body to absorb excess H+ or OH- to help to maintain a homeostatic pH balance. II. Organic Compounds a. Carbohydrates i. Carbs are sugars and starches that provide energy, and are made entirely of C, H & O. ii. There are 3 major types of carbs: 1. Monosaccharides are made of one monomer, like glucose and fructose. 2. Disaccharides are made of two monomers, like sucrose (ie. Table sugar) 3. Polysaccharides are made of long chains of monomers bonded together, like glycogen and cellulose. a. Glycogen-source of energy; good for immediate usage b. Lipids i. Lipids are fat molecules, which are non-polar and hydrophobic. 1. Triglycerides are fats and oils made of one glycerol molecule and 3 fatty acid chains. May be either saturated (having no double bonds; saturated with hydrogen molecules) and tending to be solid at room temperature, unsaturated (having one double bond and tending to be liquid at room temperature) or polyunsaturated (having multiple double bonds and tending to be liquid at room temperature). 2. Phospholipids are made of glycerol, 2 fatty acid chains and a phosphate group. These molecules are polar; the fatty acid tail is hydrophobic and the phosphate head is hydrophilic. These molecules make up the plasma membrane that surrounds cells. ii. Steroids are made of 4 carbon rings and functional groups. Cholesterol and the sex hormones are examples of steroids. c. Proteins i. A protein is a chain of amino acids at least 50 A.A. long. ii. Proteins are the most abundant type of molecule in the body. d. Enzymes i. Enzymes are specialized proteins with catalytic activity. ii. The molecules they affect are called substrates iii. They accelerate reactions without being destroyed or forming byproducts. iv. An enzyme’s functionality depends upon its shape. If this shape is changed by extremes in temperature or pH, the enzyme may lose functionality (become denatured) e. Nucleic Acids i. The two types of nucleic acids are DNA and RNA. ii. They are composed of nucleotide monomers, which are made of 3 parts, a 5-carbon sugar, a phosphate group and one of 5 bases. iii. DNA is composed of deoxyribose sugar, a phosphate group and 4 bases—Adenine, Guanine, Cytosine, and Thymine. iv. RNA is composed of ribose sugar, a phosphate group and 4 bases—Adenine, Guanine, Cytosine, and Uracil. There are three types of RNA—tRNA, rRNA, and mRNA. v. DNA’s shape is double standard molecule in the shape of a helix. vi. DNA is a single stranded molecule. vii. DNA is the inherited genetic material; genes are segments of DNA. viii. RNA relays instructions from genes to guide each cell to make proteins needed for cellular function. DNA vs. RNA Double stranded single stranded Deoxyribose ribose A, T, G & C A, U, G, & C Genetic material directs protein synthesis f. ATP i. ATP is the body’s main source of energy. ii. ATP is composed of adenine, ribose sugar, and 3 phosphate groups. When the other phosphate group is broken off, the breaking of the bond releases energy. Ch. 3 Cells I. The Cellular Basis of Life a. Overview i. Cells are the structural units of all living things—from one to trillions per organism ii. Robert Hooke observed and named cells in the late 1600s. He called them cells due to their shape resembling the tiny rooms that monks occupied. b. Cell Theory i. A cell is the basic structural and functional unit of living organisms. ii. The activity of an organism depends on the individual and collective activities of cells. iii. The principle of complementarity states that the biochemical activities of cells are dictated by the relative numbers of their specific subcellular structures iv. Continuity of life has a cellular basis. II. Structure of the Plasma Membrane a. The Fluid Mosaic model i. The fluid mosaic model describes the plasma membrane as a bilayer of phospholipid molecules with protein molecules dispersed in it. Each phospholipid molecule has a polar hydrophilic head and a nonpolar hydrophobic tail. The hydrophilic heads lie on the outer surfaces of the membrane, while the hydrophilic tails are the center of the membrane. ii. Membranes also contain glycolipids, which are phospholipids with attached sugar groups, as well as a variety of proteins, which be either integral (completely within the membrane) or peripheral (not completely embedded in the membrane). iii. The glycocalyx is the sticky sugar coating at the cell surface b. Membrane Specializations i. Microvilli are tiny projections from the cell surface that greatly increase surface area and are typically found on the surface of absorptive cells, such as those in the intestines. ii. Some cells, such as blood cells, move freely in the body, while others, like epithelial cells, are tightly held together. A variety of junctions, such as tight junctions, desmosomes and gap junctions bind cells together. 1. Tight junctions are formed by a series of integral protein molecules in the plasma membranes of adjacent cells that fuse together, forming an impermeable junction that encircles the cell. These junctions help to prevent molecules from passing through the extracellular space between cells. Tight junctions are found in cells lining the digestive tract to keep digestive enzymes and microorganisms from leaking out into the bloodstream. 2. Desmosomes are anchoring junctions, that can be thought of like rivets, that are scattered along the sides of cells to hold them together. These junctions help to hold together tissues that are under mechanical stress, like skin and heart muscle. 3. Gap junctions are communicating junctions between cells. Cells are connected by hollow cylinders called connexons, composed of transmembrane proteins. Ions, simple sugars and other small molecules can pass through these channels from one cell to the next. These junctions are found in electrically excitable tissues such as heart and smooth muscle, to help synchronize their electrical activity and contraction. III. Plasma Membrane Function a. Membrane Transport i. Cells are surrounded by an extracellular fluid called interstitial fluid. This fluid contains nutrients, hormones and waste products, among other things. Cells need to expel wastes and take in nutrients in order to remain healthy. ii. The plasma membrane possesses a characteristic called selective permeability, in which is allows good substances in and keeps bad substances out. iii. Substances can move across the membrane either passively or actively. Passive processes require no energy, while active processes require the input on energy (ATP). iv. The passive process of diffusion is the movement of molecules down a concentration gradient, from where there are more of them to where there are less of them, until equilibrium is reached. Speed of diffusion is influenced by molecular size (smaller is faster) and temperature (higher is faster). Simple diffusion is the movement of nonpolar and fat-soluble substances through the membrane unaided. v. Facilitated carriers are transmembrane integral proteins that move specific molecules, such as sugars and amino acids across the membrane. This process most likely works by allowing the carrier to envelop and then release the transported substance shielding in a long the way from the nonpolar regions of the membrane. vi. Channels are transmembrane proteins that move ions and H2O across the membrane. Channels may be open all the time (leaky) or gated (opened and closed by chemical or electrical signals). Channels tend to be specific for the molecules that pass through them and molecules always move down their concentration gradient. vii. Osmosis is a type of diffusion that involves a solvent, typically water, moving down a concentration gradient until equilibrium is reached. H2O moves freely across the membrane through channels called aquaporin. Osmosis occurs whenever the H2O concentration differs on the two sides of a membrane. As water diffuses into a cell, the point is finally reached where the hydrostatic pressure ( the back pressure exerted by water against the membrane) within the cell is equal to its osmotic pressure (the tendency of H2O to move into the cell by osmosis). At this point there is no further net movement of H2O. Osmosis is extremely important in determining distribution of H2O in the various fluid- filled compartments of the body (in cells and blood, for example). viii. The total concentration of all solute particles in a solution is called osmolarity. ix. The ability of a solution to change the shape (tone) of a cell by altering their H2O volume is called tonicity. Solutions with the same concentration of solutes as those found in cells are said to be isotonic. Cells placed in isotonic solutions will not change shape. Solutions with a higher concentration of solutes than found in cells are said to be hypertonic. Cells placed in hypertonic solutions will shrink. Solutions within lower concentration of solutes that are found in cells are said to be hypotonic. Cells placed in hypertonic solutions will expand and may burst. x. Primary active transport used ATP to drive molecules, typically ions, against their concentration gradient. An example is the sodium-potassium pump that forces Na+. xi. Secondary active transport uses the energy create by the primary active transport to move molecules across membrane. For example, as Na+ leaks back into the cell, sugars can be co-transported along with the Na+. xii. Molecules can cross the membrane in closed sacs called vesicles. Movement out of the cell is called exocytosis, while movement into the cell is called endocytosis. Phagocytosis is a type of endocytosis where solid material is engulfed by a cell; pinocytosis engulfs liquid. b. Resting Membrane Potentials i. A membrane potential is a different in voltage across the membrane. A voltage is electrical energy resulting from the separation of oppositely charged particles. In cells, the oppositely charged particles are ions, and the barrier that keeps them apart is the cell membrane. Cell is in a resting state maintains a membrane potential of -50 to -100 mV. The inside of the membrane is negative compared to the outside (it is polarized). ii. The membrane potential is generated primarily by the concentration gradient of K+. The resting plasma membrane is somewhat permeable to K+, so the leakage of K+ out of the cell causes the membrane interior to become negative. SEE Figure 3.15 iii. Cells exhibit a steady state in which diffusion causes ionic imbalances that polarize the membrane, and active transport processes (the Na+/K+ pump) maintain that membrane potential as well as the cell’s osmotic balance. c. Cell-Environment Interaction i. Cell adhesion molecules are sticky glycoproteins called cadherins and integrins found on the surface of most cells. They play roles in embryonic development and would repair. Some functions included serving to allow cells to anchor themselves to molecules in the extracellular space and to each other, to form the “arms” that allow migrating cells to move past each other to contract white blood cells to infected areas to serve as mechanical sensors that respond to local tension at the cell surface and to transmit intracellular signals that direct cell migration, proliferation, and specialization. ii. Membrane receptors are integral glycoproteins that play roles in contract signaling (cell recognition) and chemical signaling. Signaling chemicals that bind to membrane receptors are called ligands (like neurotransmitters/hormones). IV. The Cytoplasm a. Definitions i. Cytoplasm is the cellular material between the plasma membrane and the nucleus, and is the site where most cellular activities are accomplished. ii. The cytosol is the viscous fluid in which the cytoplasm elements are suspended. iii. Organelles are the metabolic machinery of the cell. Each organelle carries out specific functions, such as synthesizing proteins (ribosomes) or making ATP (mitochondria). iv. Inclusions are chemicals that may or may not be present in a cell, depending on the cell type. Examples are glycogen in liver and muscle. b. Organelles i. Some organelles such as the cytoskeleton, centrioles, and ribosomes, lack a membrane. 1. Ribosomes are small organelles of protein and ribosomal RNA composed of 2 subunits that fit together; sites of protein synthesis. 2. Some float freely in cytoplasm, while others are attached to membranes, forming the rough E.R. ii. The cytoskeleton is a series of rods running through the cytosol that gives the cell structure and support and allow for cellular movement. The cytoskeleton consists of tubular elements called microtubules as well as filament called microfilaments and intermediate filaments. Microfilaments are moved in cell motility and change in cell shape. Intermediate filaments help to resist pulling forces exert on cells. Microtubules help to determine the overall shape of the cell. iii. The centrosome is a site near the nucleus where the microtubules are anchored, and act as a microtubule- organizing center. The paired centriole plays a role in organizing the mitotic spindle that functions in cell division, and also forms the basic of cilia and flagella. c. Most organelles are bounded by a membrane similar to that of the plasma membrane. i. Mitochondria are the power plants of the cell, supplying ATP. Busier cells, such as liver and kidney, have hundreds of mitochondria per cell, while relatively inactive cells, like unchallenged lymphocytes, have just a few. Mitochondria are enclosed by two membranes that form shelf-like structures called cristae. As the metabolists of food are broken down, the energy released is used to attach phosphate groups to ADP to form ATP (cellular respiration). ii. The E.R. is a series of tubes and membranes enclosing fluid-filled cavities and comes in two types. Rough E.R. is studded with ribosomes with synthesize proteins. The ER itself is involved with the synthesis of membrane proteins and phospholipids. Smooth ER lacks ribosomes and is involved with lipid metabolism, cholesterol synthesis, steroid hormone synthesis, detox of drugs, and glycogen breakdown. iii. The Golgi apparatus is a series of stacked and flattened sacs and serves to modify, package, and transport proteins and lipids made in the rough ER.


Buy Material

Are you sure you want to buy this material for

25 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Kyle Maynard Purdue

"When you're taking detailed notes and trying to help everyone else out in the class, it really helps you learn and understand the I made $280 on my first study guide!"

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Parker Thompson 500 Startups

"It's a great way for students to improve their educational experience and it seemed like a product that everybody wants, so all the people participating are winning."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.