Bio 160 Exam 1 Lecture Notes PDF

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Bio 160 Lecture 1 (08/27) Learning Catalytics Session ID: 26641529 ★ The focus of this course is c  ells. ○ Cells ■ The building block of life. ■ Organized unit of life. ■ The smallest unit of life. ○ Characteristics of cells (living things) ■ Ability to grow and reproduce. ■ Energy transformation: take up energy sources & metabolize them. ■ Maintain homeostasis. ■ Respond to environmental stimuli. ■ DNA as genetic (heritable) information. ○ Two main cell types ■ Prokaryotic cells ● Do NOT have a membrane-bound nucleus ● Do NOT have membrane-bound organelles ● DNA is floating around the cytoplasm, the “n  ucleoid” ● RIbosomes ● 10x smaller than eukaryotes ■ Eukaryotic (“true nucleus”) cells ● DNA is contained within a membrane-bound nucleus ● Membrane-bound organelles ● 10x larger than prokaryotes ○ The Cell Theory - Organisms are cellular ■ In 1665, Robert Hooke devised a crude microscope (30x) and examined cork (bark tissue from an oak tree). ■ Hooke coined the term “cells,” small pore-like compartments ■ Shortly after, Anthony van Leeuwenhoek developed much more powerful microscope (300x). ● He worked with fabrics and created the scope in order to examine fabrics and not cells. Had nothing to do with science. ○ The complete Cell Theory ■ In 1858, Rudolph Virchow added to the claim: ● All organisms are made of cells, and all cells come from pre-existing cells. ● Two competing hypotheses.. ○ Spontaneous Generation ■ The belief that living things can arise from non-living material ■ Was a widely held belief that took many years to disprove. ○ All cells come from pre-existing cells.

★ Research Experiment for Cell Theory ○ Questions: Do cells arise spontaneously or from other cells? ○ Hypotheses ■ Spontaneous Generation Hypothesis ■ All Cells from Cells Hypothesis ○ Experiment ■ 1. Pasteur w/ straight-necked flask (contaminated - organisms were growing everywhere - not sterile) ■ 2. Pasteur w/ swan-necked flask (not contaminated - organisms were in trap - sterile) ○ Results: what were the results of each of these experiments and what did they allow Pasteur to conclude? ○ Conclusion: Cells arise from pre-existing cells, NOT spontaneously from non-living material ★ The Cell Theory cont. ○ Francesco Redi ○ In 1668, Redi carried out his famous experiment. ■ Flask w/ flies, meat, and maggots. ● One flask completely unsealed. ● One flasked completely sealed w/ cork (air flow is not present). ● One flask covered w/ gauze (air flow is present). **Dates are not important for exams** Bio 160 Lecture 2 (08/29) ★ Atomic Structure ○ Atoms are composed of: ■ Protons: positively charged particles ■ Neutrons: neutral particles ■ Electrons: negatively charged particles ○ Protons and Neutrons are located in the nucleus. ○ Electrons are located in orbitals surrounding the nucleus.

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Atomic number: every atom has a characteristic number of protons in the nucleus. ○ Atoms with the same  atomic number ■ Have the same c hemical properties. ■ Belong to the same  element. Electron Arrangement around the Nucleus ○ Electrons move around atomic nuclei in specific regions called orbitals. ■ Each orbital can hold UP TO two electrons. ■ Orbitals are grouped into levels called electron shells. ○ Electron shells are numbered 1, 2, 3, and so on. ■ Numbers indicate their relative distance from the nucleus. ■ Smaller numbers = closer to nucleus ○ Each electron shell contains a specific number of orbitals. ○ The electrons of an atom fill the innermost shells first, then fill the outer shells. Chemical Bonding ○ Unfilled electron orbitals allow formation of chemical bonds. ■ Atoms are most stable when each orbital is filled ■ Molecules are substances held together by covalent bonds ■ Covalent bonds are when each atom’s unpaired valence electrons are shared by both nuclei to fill their orbitals. ● Electrons are NOT always equally shared. ● An atom in a molecule with a high electronegativity ○ Holds electrons more tightly - has a partial negative charge. ○ The other atom will have a partial positive  charge. ● Differences in electronegativity dictate how electrons are distributed in covalent bonds. ○ Nonpolar covalent bond ■ Electrons are evenly shared between two atoms. ■ The bond is symmetrical ○ Polar covalent bond ■ Electrons are asymmetrically shared. ■ Ionic bonds are when electrons are transferred from one atom to another. The resulting attraction between oppositely charged ions. Ions and Ionic Bonds cont. ○ Ion: an atom or molecule that carries a charge. ○ Cation: an atom that LOSES an electron and becomes POSITIVELY charged. ○ Anion: an atom that GAINS an electron and becomes NEGATIVELY charged. The Electron-Sharing Continuum ○ The degree in which electrons are shared in chemical bonds forms a continuum. ■ From equal sharing in nonpolar covalent bonds. ■ To unequal sharing in polar covalent bonds. ■ To the complete transfer of electrons in ionic bonds.

★ Basilisk Youtube Video ** https://youtu.be/45yabrnryXk ★ Unequal electron sharing creates polar molecules ○ Water has atoms w/ different electronegativities ■ Oxygen attracts the shared electrons more strongly than hydrogen ■ So, the shared electrons spend more time near oxygen ■ The result is a polar covalent bond ★ The function of water (in living things) is determined by the structure of the molecule. ○ First p  roperty of water dependent on H bonds: ■ Water is a GREAT s olvent. ○ Hydrophilic atoms and molecules ■ Are ions and polar molecules that stay in solution ■ They stay in solution because of their interactions with water’s partial charges. ○ Hydrophobic molecules ■ Uncharged and nonpolar compounds ■ DO NOT dissolve in water ○ Hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in water. ○ Second m  ajor characteristic of water due to hydrogen bonds: Cohesion and Adhesion. ■ Cohesion ● Binding between like molecules ○ Binding to itself ● Results in high surface tension. ■ Adhesion ● Binding between unlike molecules ○ Binding to plastic or epithelial layers. ○ Third major characteristic of water due to hydrogen bonds: High specific heat and high heat of vaporization. ■ Because of hydrogen bonding, water has a greater ability to resist temperature change than other liquids. ● Heat is the energy associated with movement of atoms and molecules in matter. ● Temperature measures the intensity of heat. ■ Heat MUST be absorbed to break hydrogen bonds; heat is released when hydrogen bonds form. ○ The last c haracteristic of water due to hydrogen bonds: water expands as it freezes. ■ Denser as a liquid than a solid ● Water expands as it changes from a liquid to a solid ○ Therefore, the solid is less dense ○ This is why ice floats! Bio 160 Lecture 3 (09/03)

Quiz Thursday (09/05) over material covered up until this point. Chemistry of Life Powerpoint cont. ★ The Molecules of Life ○ Organic compounds are those with carbon backbone. ★ Carbon ○ The most versatile atom. ■ 4 valence electrons ■ Can form up to 4 covalent bonds. ○ The “skeleton” for molecules ○ Carbon-containing molecules can form a limitless array of molecular shapes. ○ Carbon is the 4th most common element in the universe and the second most common element in your body. ○ 6 elements make up the bulk of you. ■ Oxygen, Carbon, Hydrogen, Nitrogen, Phosphorus and Sulfur. ★ Functional Groups - Determinants of Chemical Behavior ○ The carbon atoms in an organic molecule furnish the skeleton that gives the molecule its overall shape. ■ Amino groups* ● Acts as a base ● Attract or drop a proton, respectively ■ Carboxyl groups ● Acts as an acid ● Tends to lose a proton ■ Carbonyl groups ● Sites that link molecules into more-complex compounds ■ Hydroxyl groups* ● Act as weak acids ■ Phosphate groups* ● Have two negative charges ■ Sulfhydryl groups ● Link together via disulfide bonds Shift to Nucleic Acids Powerpoint ★ Nucleic acid: a polymer of nucleotide monomers ○ 3 components: ■ Phosphate group ● Bonded to the sugar molecule ■ Five-carbon sugar ● Bonded to the nitrogenous base ■ Nitrogenous base ○ These two sugars differ by a single oxygen atom. ■ Ribonucleotides: the sugar is ribose. ● RNA ● Ribose has an -OH group bonded to the 2’ carbon

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Deoxyribonucleotides: the sugar is deoxyribose (deoxy means lacking) ● DNA ● Deoxyribose has an H instead, at the same location ■ In both of these sugars an -OH group is bonded to the 3’ carbon. How are nucleic acids made from nucleotides? ○ Monomers and Polymers ■ Monomers link together (polymerize) to form polymers. ○ Polymerization ■ Requires energy ■ Is nonspontaneous ○ Monomers polymerize through condensation (dehydration) reactions ■ That release (remove) a water molecule ○ Hydrolysis (hydration) is the reverse reaction ■ That breaks polymers apart by adding a water molecule. ○ Nucleic acids form when nucleotides polymerize. ■ Phosphodiester linkage (bond) occurs between: ● The phosphate group on the 5’ carbon of one nucleotide. ● And the -OH group on the 3’ carbon of another. ■ Forms through condensation reaction ■ 2 types of nucleotides are involved: Ribonucleotides (RNA) & Deoxyribonucleotides (DNA) The Sugar-Phosphate Backbone is Directional ○ The sugar-phosphate backbone of a nucleic acid is directional (has polarity). ■ One end has an unlinked 5’ carbons. ■ The other end has an unlinked 3’ carbon. ○ The nucleotide sequence is written in the 5’ → 3’ direction. ■ Reflects the order that nucleotides are added to a growing molecule. ■ The nucleic acid’s primary structure is the nucleotide sequence. ○ In a single strand of RNA or DNA ■ One end has an unlinked 5’ phosphate ■ The other end has an unlinked 3’ hydroxyl In-Class Nucleic Acids Structure Worksheet Watson and Crick’s Model of DNA’s Secondary Structure ○ DNA strands run in an antiparallel configuration ○ DNA strands form a double helix ■ Hydrophilic sugar-phosphate backbone faces the exterior ■ Nitrogenous base pairs face the interior ○ Purines always pair with Pyrimidines ■ Strands form complementary base pairs A-T & G-C ● A-T have two hydrogen bonds ● C-G have three hydrogen bonds ○ DNA has two different-sized grooves: major and minor Stability of DNA molecule

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The molecule is stabilized by ■ Hydrogen bonds ■ Hydrophobic interactions in it’s interior ○ By hydrogen bonding between ■ The complementary base pairs ■ A-T & G-C ★ Function of DNA ○ DNA can store and transmit biological information ○ DNA carries the information required for the organism’s growth and reproduction. ○ The language of nucleic acids directs PROTEIN SYNTHESIS. ★ DNA’s Stability ○ Makes it reliable store for genetic information ○ Less reactive than RNA ○ More resistant to chemical degradation ★ RNA Structure and Function ○ The primary structure of RNA differs from DNA ■ RNA contains Uracil instead of Thymine ■ RNA contains Ribose instead of Deoxyribose ● The presence of the -OH group on ribose makes RNA ○ Much more reactive ○ Less stable than DNA

Bio 160 Lecture 4 (09/05) Nucleic Acids PPT cont. ★ DNA stores info to make-○ 3 kinds of RNA: mRNA, tRNA, rRNA ■ mRNA (messenger RNA): stores info to make protein. ■ tRNA (transfer RNA): catalytic RNA involved in translation. ■ rRNA (ribosomal RNA) : catalytic RNA involved in translation. ● Part of ribosome ★ RNA’s Secondary Structure ○ RNA is a single stranded molecule; unlike DNA ○ RNA’s secondary structure results from complementary base pairing. ○ The bases of RNA typically form hydrogen bonds with complementary bases on the same strand. ○ The RNA strand folds over, forming a hairpin structure. ■ The bases are on one side of the fold ■ The bases align with an antiparallel RNA segment on the other side of the fold. ★ RNA’s versatility

○ RNA can function as a catalytic molecule ■ Ribozymes are enzyme-like RNAs. ○ The ribosome (organelle that carries out protein synthesis) is a ribozyme made of catalytic RNA and protein. Switch to Proteins PPT ★ Protein: a polymer constructed from amino acid monomers. ○ Involved in almost all of a cell’s activities ○ As enzymes: ■ They regulate chemical reactions ■ Protein catalysts ★ Proteins are macromolecules made from amino acids linked by peptide bonds. ○ Protein diversity ■ Based on different arrangements of a common set of 20 amino acid monomers. ★ Structure of Amino Acids ○ All proteins are made from just 20 amino acid building blocks. ○ Amino acids have a central carbon atom that bonds to: ■ H, NH2 , COOH, and have a variable side chain (R-group) (a)

○ In water (pH 7), the amino and carboxyl groups ionize to NH3+  and COO-, respectively (b). ■ This helps amino acids stay in solution and makes them more reactive. ★ Nature of Side Chains ○ Amino acid side chains to distinguish the different amino acids and can be grouped into 4 general types: ■ Acidic

■ Basic ■ Uncharged polar ■ Nonpolar ★ Functional Groups Affect Reactivity ○ Nonpolar R-groups: hydrophobic ■ Lack a full or partial charge ■ Don’t form hydrogen bonds ■ Coalesce (clump) in water ■ Lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. ○ Polar/Charged R-groups: hydrophilic ■ Have a full or partial charge ■ Form hydrogen bonds ■ Readily dissolve in water ★ Peptide Bond ○ Condensation reactions ■ Bond the carboxyl group of one amino acid ■ To the amino group of another ○ Polypeptide: chain of amino acids linked by peptide bonds ■ Oligopeptides: polypeptides containing fewer than 50 amino acids ■ Proteins: polypeptides containing more than 50 amino acids ★ Polypeptide Characteristics ○ Peptide bonds form a backbone with 3 key characteristics: ■ R-group orientation ■ Directionality ● Free amino group, on left, is N-terminus ● Free carboxyl group, on right, is C-terminus ■ Flexibility ★ What do proteins do? ○ Catalysis ○ Defence ○ Movement ○ Singaling ○ Structure ○ Transport --Given R group on exam, and then draw the rest of the common part of the amino acid.*

Bio 160 Lecture 5 (09/10) ★ Four basic levels of structure:

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Primary Secondary Tertiary Quaternary ■ Primary: a unique sequence of amino acids ● Limitless, 20 types of amino acids available, and lengths range from two amino acid residues to tens of thousands. ● Primary structure is fundamental to the higher levels of protein structure. ● The amino acid R-groups affect a polypeptide’s properties and function ○ A single amino acid change can completely alter protein function. ○ Sickle cell anemia example ■ Secondary: formed by h  ydrogen bonds. ● Hydrogen bonds occur between: ○ Carbonyl group of one amino acid ○ And the Amino group of another ● Hydrogen bonding is between sections of the same backbone ○ Is possible only when a polypeptide bends in a way that put C=O and N-H groups close together forming: ■ alpha - helices ■ beta - pleated sheets ■ Tertiary results from: ● Interactions between R-groups ● OR between R-groups and the peptide backbone ○ These contacts cause backbone to bend and fold ○ Bending & folding creates a 3-D shape ■ R-group interactions include: ● Hydrogen bonds ● Hydrophobic interactions ○ Increases stability of surrounding water molecules by increasing hydrogen bonding. ● Van der Waals interactions (balloon example, rubbing balloon on head to create static & attraction) ○ Weak electrical interactions between hydrophobic side chains ● Covalent disulfide bonds ○ Between sulfur-containing-R-groups ● Ionic bonds

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Between groups that have full and opposing charges. ■ Quaternary: bonding of two or more distinct polypeptide subunits. ★ Protein Folding and Function ○ Folding is often spontaneous ■ B/c of hydrogen bonds and van der waals interactions ■ Makes the molecule more stable ○ Denatured (unfolded) protein: unable to function normally ○ Correct folding is not spontaneous and proteins called molecular chaperones help proteins fold correctly in cells. ■ Some present in ER, and help fold protein as it comes off the ribosome ■ Others are heat-shock proteins (high temp.--fever) ○ Function of a protein is dependent on its shape ○ Misfolding can be “infectious” ○ Prions: improperly folded forms of normal proteins ■ Present in healthy people ■ Amino acid sequence does not differ from a normal protein ■ Shape is radically different ■ Can induce normal protein molecules to change their shape to the altered form....