Bio1030 Chemistry & Cells Outline Fall 2024 PDF

**Biology 1030, Human Anatomy and Physiology 1 Dr. Rebecca J. Flietstra, Fall 2024** **INTRODUCTION: Anatomical Terms, Chemistry and Cells** **ANATOMICAL TERMS:** ***Body Planes:*** ***Regional Terms:*** ***Orientation and Directional Terms:*** I. Anatomy: Structures of the Body A. Gross Anat...

**Biology 1030, Human Anatomy and Physiology 1 Dr. Rebecca J. Flietstra, Fall 2024** **INTRODUCTION: Anatomical Terms, Chemistry and Cells** **ANATOMICAL TERMS:** ***Body Planes:*** ***Regional Terms:*** ***Orientation and Directional Terms:*** I. Anatomy: Structures of the Body A. Gross Anatomy 1\. visible body parts 2\. spatial relationships between visible body structures B. Microscopic Anatomy 1\. Cytology 2\. Histology 3\. Microscopy a\. Light microscope 1\) light passes through specimen 2\) able to see general features of cell (DNA, organelles, etc.)  b\. Electron microscope 1\) Transmission electron microscope (TEM) a\) electrons pass through specimen b\) can see details of cell structure 2\) Scanning electron microscope (SEM) a\) electrons bounce off specimen b\) can see details of cell surface C. Developmental Anatomy 1\. Follows the changes in anatomy over time 2\. Early events determine spatial relationships II\. Physiology: Functions of the Body A. Cellular Physiology 1\. the common activities of all cells 2\. the specific activities of specialized cells B. System Physiology 1\. depends on the interactions between cells, tissues, organs 2\. although systems studied separately, they are not independent C. Homeostasis 1\. The maintenance of a relatively constant internal environment a\. not equilibrium b\. goal-oriented 2\. Generally involve reversible reactions III\. Principle of Complementarity of Structure and Function A. The structure of the cell/tissue/organ determines the function of the cell/tissue/organ B. Levels of Structural Function *figure 1.3* 1\. Chemical Level a\. atoms and molecules b\. everything that happens in a living organism is dependent on its chemicals c\. the characteristics of the chemical determine how it is used 2\. Cellular Level a\. cell is basic structural and functional unit of all living things b\. have specific structure---with some variability 3\. Tissue Level a\. Tissue b\. matrix extracellular substances 4\. Organ Level distinct structure composed of two or more tissue types with one or more common functions 5\. Organ System Level *figures 1.4, 1.5* group of organs classified as a unit because of a common function  IV\. Elements and Atoms A. Elements 1\. A substance that cannot be broken down or changed into another substance by ordinary chemical processes 2\. Elements used by living organisms *figure 2.4* a\. approx. 20 used by all living organisms b\. elements which make up more than 99% of the atoms in the body: 1\) C (carbon) 2\) H (hydrogen) 3\) N (nitrogen) 4\) O (oxygen) B. Atom 1\. the smallest piece of an element that retains the characteristics of the element 2\. Composition *figure 2.3* a\. Nucleus b\. Electron shells C. Proton 1\. a particle that has a single positive charge 2\. located in nucleus 3\. Atomic Number a\. an element is defined by the number of protons found in the nucleus b\. **atomic number** **=** element \# **=** \# of protons D. Neutron 1\. a particle that has a neutral charge 2\. located in nucleus  E. Electron 1\. a particle that has a single negative charge 2\. arranged in shells a\. \# of electrons possible in each shell 1\) 1^st^ shell 2\) 2^nd^ shell 3\) 3^rd^ shell b\. shells are filled in order 3\. arrangement of electrons determines behavior of atom 4\. Ions a\. a charged atom 1\) initially assume: \# electrons = \# protons 2\) gain or loss of electron b\. anion 1\) gains electron(s) 2\) \# positive charges \< \# negative charges c\. cation 1\) loss of electron 2\) \# positive charges \> \# negative charges F. Atoms You Must Know 1\. Hydrogen a\. symbol b\. atomic number c\. shells 2\. Carbon a\. symbol b\. atomic number c\. shells 3\. Nitrogen a\. symbol b\. atomic number c\. shells 4\. Oxygen a\. symbol b\. atomic number c\. shells 5\. Sodium a\. symbol b\. atomic number c\. shells 6\. Chlorine a\. symbol b\. atomic number c\. shells V. Molecules A. Two or more atoms joined together by bonds 1\. can be two of the same element, or different elements 2\. chemical (molecular) formula B. Chemical Bonds *figures 2.8, 2.9* 1\. atoms form bonds (connections) with each other based on the number of electrons found in outer electron shell a\. electron shell composed of series of orbits 1\) 1^st^ shell 2\) 2^nd^ shell 3\) 3^rd^ shell b\. shells are filled in order c\. the atom is most stable when outer electron shell is full  2. Inert Elements a\. outer shell is already full b\. can't form bonds 3\. Ionic Bond *figure 2.8* a\. attraction bond formed by a cation and an anion b\. an electron is transferred from one atom to another the resulting cation and anion are then attracted to each other, creating an ionic bond c\. used by atoms with outer shells that can easily be filled or emptied 4\. Covalent Bond *figure 2.9* a\. bond formed when two atoms share a pair of electrons b\. used by atoms that cannot easily "grab" electrons or give them away  c\. Polar Covalent Bond *figure 2.10* 1\) covalent bond in which atoms don't equally share the shared pair of electrons 2\) larger atoms take a little more than they give a\) larger atom will be slightly negative b\) smaller atom will be slightly positive d\. Non-polar Covalent Bond 1\) covalent bond formed when atoms equally share the shared pair of electrons 2\) molecule doesn't have local charges 5\. Hydrogen bond *figure 2.11* a\. weak bond formed by a polarized hydrogen with a charged part of another molecule 1\) polarized hydrogen has a polar covalent bond within a molecule 2\) once charged, the polarized hydrogen forms a hydrogen bond with another atom or molecule b\. the slightly positive H is attracted to: 1\) slightly negative atoms of other polar molecules 2\) anions c\. cumulatively can be strong  6\. Important molecule: Water (H~2~O) a\. Polar molecule b\. Water demonstrates **cohesion** 1\) The attraction between water molecules c\. Water demonstrates **adhesion** 1\) the attraction between a water molecule and a polar surface d\. Water has a **high heat capacity** 1\) takes a lot of heat to raise temperature 2\) helps us with temperature homeostasis a\) body temperature doesn't quickly change b\) heat is spread out uniformly e\. Water has a **high heat of vaporization** 1\) takes a lot of heat to change water from liquid phase to gas phase 2\) applications a\) do not quickly dehydrate by water evaporation b\) heat absorbed by water is removed from body when the water evaporates f\. Water is the **universal solvent** 1\) a solvent is a liquid that dissolves solutes 2\) water dissolves all ionic substances 3\) water dissolves many polar substances 4\) water does not dissolve non-polar substances VI\. Chemical Reactions A. Definition: Any process that breaks and/or forms chemical bonds. B. Synthesis Reaction 1\. two or more reactants combine to make larger product 2\. anabolic  C. Decomposition Reaction 1\. large reactant is broken down into two or more smaller products 2\. catabolic D. Reversible Chemical Reactions 1\. all reactions reversible 2\. usually one direction tends to be favored 3\. readily reversible reactions depend on concentrations a\. forward reaction when higher levels of reactants b\. reverse reaction when higher levels of products F. Chemical Reactions Convert Energy 1\. Kinetic Energy a\. "energy in action" b\. energy that can be used to move objects c\. energy that can be used to create a bond in another molecule d\. typically produced by decomposition/catabolic reactions 2\. Potential Energy G. Important Reaction: pH (acidity of solutions) *figures 2.16, 2.17* 1\. Water "Instability" a\. small percentage of water breaks apart into H^+^ and OH^-^ b\. neutral solution: equal amounts of H^+^ and OH^-^  2. pH *figure 2.17* a\. scale which measures relative acidity or alkalinity of a solution 1\) specifically focuses on the concentration of H^+^ rather than OH^-^ 2\) pH is a negative log b\. Neutral Water 1\) concentration of H^+^ = 10^-7^ 2\) pH7 3\. Acid a\. definition: proton donor 1\) breaks a covalent or ionic bond with hydrogen 2\) increases the levels the H^+^ in solution b\. contains more H^+^ than OH^-^ c\. pH \< 7 d\. strong acid e\. weak acid f\. examples: 1\) hydrochloric acid: HCl 2\) carbonic acid: H~2~CO~3~ 4\. Base a\. definition: proton acceptor 1\) forms a covalent bond with a hydrogen 2\) decreases the concentration of H^+^ in solution b\. contains more OH^-^ than H^+^ c\. pH \> 7 d\. strong base e\. weak base f\. examples: 1\) sodium hydroxide: NaOH 2\) bicarbonate: HCO~3~^-^ 5\. pH Buffers a\. Compounds that stabilize the pH through adding or removing free H^+^ from the solution b\. buffer contains weak acid and weak base 1\) prevents large changes in hydrogen concentration 2\) pH stays relatively constant c\. examples: 1\) H~2~CO~3~ H^+^ + HCO~3~^-^ 2\) HPO~4~^-2^ + H^+^ H~2~PO~4~^-^ VII\. Aqueous Solutions A. Most solutions in the body are water based 1\. Solution = solvent + solute(s) 2\. Water is the universal solvent *(review)* B. Common solutes 1\. glucose 2\. gasses 3\. amino acids 4\. soluble proteins 5\. ATP 6\. salts VIII\. Cytoplasm A. Cytoplasm = Cytosol + Cytoskeleton B. Cytosol ("cell water") 1\. semi-solid, mostly aqueous 2\. dissolved substances *(as mentioned above)* C. Cytoskeleton *figure 3.18* 1\. Protein structures a\. Microtubules 1\) composed of tubulin (protein) 2\) form an easily assembled and dissembled hollow tube 3\) functions a\) framework b\) moving vesicles within cell c\) cellular locomotion b\. Intermediate filaments 1\) smaller than microtubules 2\) mechanical strength c\. Actin filaments 1\) composed of actin (protein) 2\) functions a\) shape of cell b\) in muscle, contraction 2\. Cytoskeleton can form membrane extensions a\. Cilia 1\) short membrane extensions 2\) usually occur in large numbers 3\) moved by collections of microtubules 4\) move substances past stationary cells b\. Flagella 1\. long membrane extension 2\. usually only one on a cell 3\. move a cell c\. Microvilli  1) very small projections of the cell membrane 2\) increase surface area of the cell  IX\. Movement of Molecules within and between Solutions A. Diffusion across plasma membrane 1\. Diffusion: net, random movement of molecules from higher to lower concentration  2\. diffusion rate limits cell size a\. minor increases in distance will greatly increase diffusion time b\. if it takes too long for nutrients/O~2~ to get to the center of the cell, it will die c\. cells must also have access to the blood supply 3 surface area to volume ratio (s.a./v) limits cell size a\. as cells grow, their volume increases more rapidly than their surface area b\. surface area allows diffusion into and out of cell ("supply") c\. volume indicates the bulk of the cell that uses the diffused chemicals ("demand")  4\. types of diffusion into/out of cells *figures 3.5, 3.6* a\. Simple Diffusion 1\) molecules diffuse across lipid bilayer 2\) small and/or non-polar molecules b\. Facilitated Diffusion 1\) large/polar molecules use protein channels in the plasma membrane 2\) when protein channels are open, they enable movement of solute down its concentration gradient C. Osmosis and Osmotic Pressure *figure 3.7* 1\. Osmosis a\. diffusion of water down its concentration gradient b\. particularly as it occurs across a selectively permeable membrane 2\. Osmotic Pressure a\. As water moves by osmosis across a selectively permeable membrane, it generates pressure b\. Hyperosmotic solution 1\) a solution that has a higher concentration of particles than a comparison solution such that water moves down its concentration gradient into the hyperosmotic solution 2\) physiological example c\. Hyposmotic solution 1\) a solution that has a lower concentration of particles than a comparison solution such that water moves down its concentration gradient out of the hyposmotic solution. 2\) physiological example d\. Isosmotic solution a solution that has the same concentration of particles as a comparison solution such that there is no net water movement into or out of the solution C. Tonicity *figure 3.8* 1\. the effect water flow (osmosis) and pressure (osmotic pressure) has on the cell's shape 2\. Hypertonic solution a\. a solution [outside the cell] that has a higher concentration of particles than the cytoplasm, such that water moves out of the cell and causes the cell to crenate b\. physiological example 3\. Hypotonic solution a\. a solution [outside the cell] that has a lower concentration of particles than the cytoplasm, such that water moves into the cell and causes the cell to swell b\. physiological example 4\. Isotonic solution a\. a solution [outside the cell] that has a concentration of particles equal to the cytoplasm such that there is no net movement of water into/out of the cell and the cell's shape is maintained  D. Active Transport across cell membrane 1\. moving molecules against concentration gradient 2\. requires energy input in the form of ATP a\. primary active transport directly uses ATP b\. secondary active transport uses concentration gradient of another atom/molecule 3\. proteins in cell membrane move molecules across membrane X Organic Chemistry A. Carbon-based molecules 1\. carbon primarily forms nonpolar covalent bonds a\. each carbon forms 4 covalent bonds b\. the more carbon atoms in a molecule, the more nonpolar the molecule will be 2\. types of organic molecules a\. carbohydrates b\. proteins c\. lipids d\. nucleic acids B. Lipids 1\. high percentage of C atoms, so strongly nonpolar 2\. Cholesterol *figure 2.23* a\. multi-ringed lipid b\. uses 1\) NOT USED FOR ENERGY 2\) part of cell membranes; gives membranes flexibility 3\) modified to form steroids  3\. Fatty acids *figure 2.22* a\. long carbon chains ending with a -COOH b\. saturated fatty acids 1\) only single bonds between all carbons 2\) solid at room temperature c\. unsaturated fatty acids 1\) one or more double bonds in the carbon chain 2\) liquid at room temperature 4\. Triglycerides *figure 2.21* a\. glycerol + three fatty acids b\. uses 1\) long-term energy storage 2\) insulation (esp. against cold) 3\) shock-absorption  5\. Phospholipids *figure 2.23* a\. glycerol + two fatty acids + phosphate group b\. amphipathic 1\) non-polar region 2\) polar region c\. major component of cell membranes C. Carbohydrates (starches and sugars) 1\. Structure 2\. Monosaccharides *figure 2.18* a\. "one sugar" b\. soluble c\. examples 3\. Disaccharides *figure 2.19*  a\. "two sugars" b\. soluble c\. already too large to be absorbed from digestive tract d\. examples 4\. Polysaccharides *figure 2.20* a\. structure 1\) mostly insoluble 2\) highly-branched b\. examples 1\) glycogen in animals 2\) starch and cellulose in plants 5\. Uses a\. glucose is used to create energy within cells b\. glycogen 1\) used to store glucose in animals 2\) regularly broken down and built up 3\) can be digested by humans c\. starch 1\) used to store glucose in plants 2\) can be digested by humans d\. fiber (cellulose) helps move the feces through the bowels 1\) structural polysaccharide in plants 2\) can't be digested by humans D. Proteins 1\. Amino Acids *figure 2.24* a\. central carbon b\. carboxyl group -COOH c\. amino group -NH~2~ d\. side group -R  2\. Primary Structure (1º structure) *figure 2.26* a\. sequence of amino acids in a peptide or protein b\. the covalent bond between amino acids is called a peptide bond *figure 2.25* 1\) covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid 2\) as covalent bond is formed, H~2~O is released c\. 1º structure determined by genetic instructions 3\. 2º, 3º, and 4º structures of proteins a\. as soon as a protein is manufactured, it starts to fold into a particular shape b\. Secondary structure (2º structure)  1) local, repetitive shapes within the protein 2\) determined by hydrogen bonding between R groups c\. Tertiary structure (3º structure) 1\) shape of the entire protein 2\) determined by d\. Quaternary structure (4° structure) 2\) not all proteins have quaternary structure 4\. Denaturation a\. loss of 2° and/or 3° and/or 4° structure b\. protein becomes non-functional c\. potential causes 1\) heat 2\) pH 3\) toxic chemicals 4\) radiation 5\. Proteins categorized by shape: the shape of a protein determines its function a\. Fibrous proteins 1\) lengthy proteins 2\) insoluble in water 3\) highly stable, with a low turnover rate 4\) structural proteins b\. Globular proteins (globins) 1\) compact structures 2\) soluble in water 3\) chemically active, with a high turnover rate 4\) functional proteins 6\. Uses of Proteins a\. Structural 1\) Cytoskeleton---cell shape 2\) Intracellular joining\-\--holds neighboring cells together 3\) Anchor cells to extracellular matrix b\. Enzymes (biological catalysts) *figure 2.27* 1\) catalysts decrease the activation energy needed to start the reaction 2\) as a result, catalysts increase the rate of a reaction without being changed 3\) structure and activity 4\) naming c\. channels and transporters a\) channels allow substances to enter and/or leave cell down concentration gradient b\) transporters actively move substances into and/or out of the cell  d\. receptors for communication a\) ligand: a chemical that binds to a cell membrane receptor b\) when the receptor protein changes shape it changes the activity of the cell E. Nucleotides / Nucleic Acids 1\. Nucleotides *figure 2.28* a\. base + sugar + phosphate 1\) five possible bases a\) adenine (A) b\) thymine (T) c\) cytosine (C) d\) guanine (G) e\) uracil (U) 2\) two possible sugars a\) ribose b\) deoxyribose b\. ATP (adenosine triphosphate) *figures 2.30* 1\) most common form of internal cell energy 2\) generated during cell respiration 2\. Nucleic acids are composed of multiple nucleotides  a. covalent bond formed between the phosphate of one nucleotide and the sugar of another nucleotide b\. Deoxyribonucleic acid (DNA) *figure 2.29* 1\) structure a\) sugar: deoxyribose b\) possible bases: 1\) adenine (A) 2\) thymine (T) 3\) cytosine (C) 4\) guanine (G) c\) forms a double helix 2\) used for storing genetic information c\. Ribonucleic acid (RNA) 1\) structure a\) sugar: ribose b\) possible bases: 1\) adenine (A) 2\) cytosine (C) 3\) guanine (G) 4\) uracil (U) c\) single-stranded 2\) temporary blueprint for making proteins  XI\. Lipid Bilayer of Cell Membranes A. Fluid Mosaic Model *figure 3.4* B. Lipid Bilayer 1\. Phospholipid (75% of lipid membrane) *figure 3.3* a\. structure *(review)* b\. amphipathic *(review)* c\. both sides of membrane are exposed to water, so will form a bilayer 2\. Glycolipid (5% of lipid membrane) a\. phospholipid with attached sugars b\. only found on outer surface c\. contributes to self-recognition 3\. Cholesterol (20% of lipid membrane) a\. stabilizes membrane b\. increases flexibility C. Plasma membrane: outer membrane of the cell D. Cell Junctions *figure 4.5* 1\. general features a\. glycoproteins as adhesives b\. membranes interdigitate 2\. tight junctions a\. interlocking proteins "glue" adjacent cells together b\. molecules cannot pass between cells 3\. desmosomes (anchoring junctions) a\. "rivets" that hold neighboring cells together b\. internal proteins reinforce junction c\. prevents cells from ripping apart under force 4\. gap junctions a\. channels between cells  b. enable greater communication and coordination E. Membrane Vesicles 1\. Small membrane sacs within the cell used to transport molecules 2\. Endocytosis *figure 3.10* a\. taking up substances into the vesicle b\. pinch off part of the membrane c\. types 1\) phagocytosis 2\) pinocytosis 3\) receptor-mediated endocytosis 3\. Exocytosis *figure 3.11* a\. releasing substances (generally proteins) from the vesicle b\. addition to the membrane F. Endomembrane System 1\. System of organelles that are structurally continuous or linked by vesicle transport 2\. Series of endocytosis/exocytosis  XII\. Cytoplasmic Organelles of the Endomembrane System *figure 3.13* A. Organelle: membrane-bound structure within the cell that has specialized functions B. Endomembrane System 1\. System of organelles that are structurally continuous or linked by vesicle transport 2\. Jointly function to a\. Produce, store and export biological molecules b\. Degrade potentially harmful substances C. Rough Endoplasmic Reticulum (RER) *figure 3.14* 1\. structure a\. continuous, highly folded membrane b\. ribosomes make it look "rough" 2\. Ribosomes 3\. function a\. ribosomes produce proteins b\. proteins packaged into vesicles c\. vesicles carry proteins to golgi apparatus D. Smooth Endoplasmic Reticulum (SER) *figure 3.14* 1\. structure a\. continuous, highly folded membrane b\. no ribosomes 2\. function a\. manufacture lipids, cholesterol b\. produce steroid hormones  c. intestinal cells: absorb, synthesize, transport fats d\. contain enzymes involved in drug detoxification e\. liver cells: breaks down glycogen into glucose E. Golgi Apparatus *figure 3.15* 1\. Structure: series of thin, stacked sacs 2\. Function a\. process proteins b\. package/sort proteins c\. send proteins F. Lysosomes 1\. vesicles that bud off the golgi apparatus 2\. contain degrading enzymes G. Peroxisomes *figure 3.17* 1\. vesicles that bud off the rough endoplasmic reticulum 2\. contain oxidases a\. protect cell from free radicals b\. especially prominent in liver and kidney cells XIII. Other Organelles A. Mitochondria *(sing., mitochondrion)* *figure 3.16* 1\. Structure a\. small, rod-shaped b\. inner cristae 2\. Function: produces ATP B. Nucleus *figure 3.19* 1\. Structure 2\. Function a\. contains all hereditary material b\. encodes for all the proteins of the body XIV. Nucleus *figure 3.29* A. Prominent structure generally near center of cell 1\. most cells have one nucleus 2\. some cells are multinucleate B. Function 1\. contains hereditary material 2\. encodes for all the proteins in the body C. Specialized Structures 1\. Nucleolus a\. darker region of the nucleus b\. site where ribosomes are made 2\. Nuclear Envelope a\. a double membrane---two phospholipid bilayers b\. outer phospholipid bilayer is continuous with RER 3\. Nuclear Pores a\. found in the nuclear envelope b\. larger than protein channels  D. Chromosomes 1\. Humans have 23 pairs of chromosomes 2\. composed of DNA *figure 3.23* a\. DNA monomers (nucleotides or nucleic acids) 1\) nitrogenous base a\) adenine (A) b\) cytosine (C) c\) guanine (G) d\) thymine (T) 2\) sugar: deoxyribose 3\) phosphate b\. DNA strand 1\) covalent bond between the phosphate of one nucleotide with the sugar of the next nucleotide 2\) nitrogenous bases project to the side c\. DNA double-helix 1\) two DNA strands form a coiling "ladder" 2\) hydrogen bonds connect the nitrogenous bases of the two strands d\. Chromatin *figure 3.22* 1\) storage form of DNA ("condensed") 2\) DNA is coiled around proteins 3\) when genes are not used, the chromosome is "condensed" and is tightly packed 4\) "active" parts of chromatin/DNA (being used to make mRNA) are more lightly stained than "inactive parts" (that aren't currently used to make mRNA)  XV\. DNA Synthesis (Replication) and Cell Cycle A. DNA Replication *figure 3.24* 1\. Process a\. Initiation 1\) helicase breaks hydrogen bonds 2\) helicase unwinds the two strands of DNA b\. Elongation 1\) Each side of the double helix used to make another strand 2\) Semiconservative replication a\) one side of new helix is original strand b\) other side of new helix is new strand 3\) DNA polymerase a\) matches new nucleotides with the original strands b\) links neighboring nucleotides c\. Termination 2\. Result: two double helices just like the original double helix A = C = T = C = T = A = G = C = A : : : : : : : : : T = G = A = G = A = T = C = G = T 3\. mutation a\. an error in the DNA introduced during DNA replication b\. potential causes 1\) DNA replication 2\) radiation 3\) chemicals 4\) UV light c\. types of mutations (according to cell type) 1\) somatic mutation: mutation in a body cell that can affect function of a tissue or organ 2\) germ line mutation: mutation in a sperm or egg cell that can affect the offspring B. Cell Cycle *figure 3.30* 1\. G~1~ phase a\. variable length 1\) in rapidly dividing cells, minutes to hours 2\) in slowly dividing cells, days to years 3\) some cells never leave this stage b\. metabolically active cell, producing proteins c\. cell growth 2\. S phase: DNA synthesis 3\. G~2~ phase a\. preparation for cell division b\. protein synthesis 4\. Mitosis a\. most common form of cell division b\. results in two cells identical to the original parent cell 5\. Meiosis a\. cell division that happens in gametes b\. results in four cells that have one set of chromosomes (23) XVI\. Using DNA to Make Proteins A. Information Flow 1\. DNA contains blueprint 2\. a copy of mRNA is produced using the DNA blueprint 3\. mRNA used to make protein B. structure of Ribonucleic Acid (RNA) *figure 2.28* 1\. monomer: nucleotide a\. nitrogenous base 1\) adenine (A) 2\) cytosine (C) 3\) guanine (G) 4\) uracil (U) b\. sugar: ribose c\. phosphate 2\. polymer a\. covalent bonds between phosphate and sugar c\. nitrogenous bases project to one side 3\. always single-stranded 4\. messenger RNA (mRNA) carries the instructions for making proteins C. Transcription 1\. production of messenger RNA (mRNA) using the DNA template 2\. DNA serves as template for RNA a\. template strand b\. base pairing (DNA::RNA) a\. C::G b\. G::C c\. T::A d\. A::U (uracil) 3\. Initiated when a transcription factor binds to the promotor region a\. transcription factors are chemicals that indicate the need for a particular protein b\. genes are activated according to the body's needs 4\. Termination signal is part of the DNA that indicates the end of the gene; transcription ends D. Translation 1\. mRNA gives the instructions to make a protein 2\. translation occurs as ribosomes in the RER "read" the mRNA 3\. The Genetic Code a\. triplet codon: three nucleic acids encode for one amino acid b\. 64 possible combinations of three nucleic acids to code for 20 amino acids c\. redundant code 1\) several similar codons will typically encode for the same amino acid  2) allows some mutations to be "silent" d\. special codons a\. start codon b\. stop codons D. Protein modification 1\. Proteins moved from RER to golgi apparatus 2\. Alterations of proteins in golgi apparatus a\. amino acids removed b\. addition of carbohydrates 3\. packaging of proteins from golgi apparatus a\. proteins sorted for different locations inside or outside cell b\. formation of lysosomes c\. some proteins released outside cell via exocytosis F. Protein degradation 1\. ubiquitin attached to unnecessary proteins 2\. proteasomes break down proteins labeled with ubiquitin XVII Genotypes and Phenotypes A. Gene 1\. section of DNA that encodes a protein 2\. determines a trait 3\. humans have 20,000-25,000 genes 4\. 99.9% of our genes are the same in everyone B. Phenotype 1\. the traits of an individual produced by genes 2\. depends on the type of protein made, how much, and when C. How genotype can affect phenotype 1\. Most cells produce only some proteins a\. This happens as cells differentiate, i.e., become specialized b\. keratinocytes produce keratin c\. goblet cells produce mucin 2\. Protein production can change over a person's life a\. melanin in hair follicle melanocytes b\. actin & myosin in males c\. lactase 3\. Even if people make the same protein, they can make different baseline levels a\. this generally happens because there are different controls of gene expression b\. melanin in skin melanocytes c\. liver enzymes 4\. Protein production can change according to body need a\. transcription factors activate gene expression by binding to promotor region b\. pancreatic amylase made when carbohydrates are in the small intestines c\. melanin production in melanocytes increases with exposure to UV light d\. actin and myosin production in skeletal muscle fibers increases following exercise 5\. Sometimes people have a gene that can't produce a protein a\. brown eyes vs. blue eyes b\. protein receptor for naringin D. Gene mutations and phenotype 1\. Allele a\. alternate forms of genes that determine different traits b\. produced by past germinal mutations that are then inherited through generations 2\. mutations are a change in the DNA sequence a\. germinal mutation 1\) happens in an ova (egg) or sperm 2\) can be inherited b\. somatic mutation 1\) happens in any cell that is not a gamete 2\) can't be inherited, but sometimes can lead to cancer 3\. causes of mutations a\. mistakes during DNA replication b\. radiation c\. ultraviolet light d\. chemicals 4\. types of mutations a\. Missense mutation 1\) mutation that changes the amino acid sequence in a protein 2\) alleles encode for similar, but different, proteins 3\) responsible for most of the differences between people 4\) some cause disease, others, just variety b\. Nonsense mutation 1\) mutation that introduces an early STOP codon into the mRNA sequence 2\) one allele produces a protein, the other allele doesn't produce a protein 3\) generally an "invisible" mutation, unless someone has two copies of the allele 4\) some cause disease, others, just variety c\. Silent mutation 1\) mutation that changes the DNA and mRNA, but makes no change to the protein 2\) redundancy of the genetic code  Trait Allele code Phenotype -------------------- ------------- ----------------------------- Blood type (ABO) I^A^ A-type blood   I^B^ B-type blood   i O-type blood Blood type (Rh) R Rh-positive blood   r Rh-negative blood Color blindness X^C^ normal color vision   X^c^ red-green colorblindness Cystic fibrosis C healthy   c cystic fibrosis Eye color B brown eyes   b blue eyes Hair texture K^S^ straight hair (round shaft)   K^C^ curly hair (flat shaft) Hemophilia X^H^ normal blood clotting   X^h^ hemophilia Sickle cell anemia H^A^ hemoglobin A (normal)   H^S^ hemoglobin S (sickle cell) XVIII\. Inheritance Patterns A. Used to predict the probability someone will inherit a trait from their parents B. Dominant/Recessive 1\. the dominant allele will determine the trait if it is present 2\. the recessive allele will determine the trait only if the dominant is not present 3\. usually this pattern is associated with an inherited nonsense mutation 4\. examples a\. eye color (simplified) b\. cystic fibrosis C. Codominance or Incomplete Dominance 1\. Two different alleles can show their effect even if only one copy of the allele is present a\. each allele is distinctly expressed (shows its characteristics) b\. phenotype is affected by both alleles c generally associated with an inherited missense mutation 2\. Example: ABO blood types 3\. Example: Sickle cell anemia a\. Description of disease 1\) common among populations of equatorial Africa and their descendants 2\) mutation in gene for hemoglobin: hemoglobin S (H^S^) normal hemoglobin: hemoglobin A (H^A^) 3\) under low oxygen conditions b\. Sickle cell anemia genotype: H^S^H^S^ c\. Sickle cell trait: H^A^H^S^ 1\) exhibited by heterozygous individuals 2\) hemoglobin S prevented from fully crystallizing due to presence of hemoglobin A 3\) appears to provide protection against malaria 4\. Example: Hair texture a\. straight hair: K^S^K^S^ b\. curly hair: K^C^K^C^ c\. wavy hair: K^S^K^C^ D. Multiple alleles 1\. More than two alternative alleles a\. most genes have more than two possible alleles b\. each parent can still have only two alleles 2\. Example: blood types (ABO) E. Polygenic Inheritance 1\. some characteristics depend upon simultaneous inheritance and expression of more than one gene 2\. Most traits have polygenic inheritance---with multiple possible alleles for each gene 3\. examples a\. height b\. hair color c\. skin color XVIII\. Karyotype A. Complete set of chromosomes 1\. 23 pairs (46) for most humans 2\. homologous chromosome pairs numbered from largest to smallest 3\. each chromosome has a certain staining pattern B. Categories of chromosomes 1\. Autosomes---the first 22 pairs of chromosomes 2\. Sex chromosomes---last pair of chromosomes, X and Y chromosomes C. Changes in chromosome number 1\. Usually addition or loss of chromosome causes embryo to die (spontaneous abortion) 2\. Down syndrome a\. Trisomy 21 b\. phenotype c\. increasingly seen in older women 3\. Turner syndrome a\. XO female b\. phenotype 4\. Klinefelter syndrome a\. XXY male b\. phenotype  D. Sex-linked genes 1\. depend on the differences between the X and Y chromosomes a\. X chromosome 1\) larger than the Y chromosome 2\) females have two X chromosomes b\. Y chromosome 1\) much smaller than X chromosome 2\) males have XY pair a\) Y chromosome contains unique genes that determine "maleness" b\) most genes on X chromosome not found in Y chromosome i\. in male, only one copy causes dominant expression ii\. in female, can have dominant/recessive, codominant, incomplete dominance... 2\. Example 1: colorblindness a\. Dominant/recessive pattern in females b\. X^C^X^C^ X^C^X^c^ X^C^Y X^c^Y 3\. Example 2: hemophilia a\. Dominant/recessive pattern in females b\. X^H^X^H^ X^H^X^h^ X^H^Y X^h^Y XIX\. Inheritance Calculations A. Requires knowledge of the parents' alleles 1\. Each parent has two copies (alleles) for each gene 2\. Each parent passes down only one allele for each gene to their offspring B. Use of Punnett square 1\. example 1: Parents: Male: BB Female: bb -- --- --- ---                   -- --- --- --- 2\. example 2: Parents: Male: Bb Female: Bb -- --- --- ---                   -- --- --- --- 3\. example 3: Parents: Male: I^A^I^B^ Female: ii -- --- --- ---                   -- --- --- --- 4\. example 4: Parents: Male: X^H^Y Female: X^H^X^h^ -- --- --- ---                   -- --- --- ---  XX\. Cancer Genes A. Genes that control cell cycle 1\. Each type of cell has its own proliferation rate 2\. Proliferation rates can change according to body needs 3\. Cell cycle genes regulate cell proliferation a\. tumor suppressor genes: slow down rate of cell proliferation b\. oncogenes: speed up rate of cell proliferation B. Some people inherit alleles for cell cycle genes that are "fragile" 1\. These cell cycle genes easily mutate 2\. When they mutate, the cells start rapidly proliferating, forming a tumor 3\. Example: BRCA1 on chromosome 17