Midterm 1 Notes Review PDF

lOMoARcPSD|34711042 Midterm 1 Notes Review Cell, Mol & Dev Bio I (Drexel University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Mimi Kreger ([email protected]) ...

lOMoARcPSD|34711042 Midterm 1 Notes Review Cell, Mol & Dev Bio I (Drexel University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 Bio 209 Exam 1 Study Guide Basic Elements of Biological Macromolecules:  What is a macromolecule? o Weak Interactions  Electrostatic  Hydrogen bonding  Van der Waals interactions  Hydrophobic Effect Chemical Bonds:  Covalent (strong) o Enzymes change covalent bonds  Noncovalent (weak) o Protein folding o Membranes o Transport o Substrate Binding Types of Noncovalent Bonds:  Hydrogen bonding  Ionic interactions  Hydrophobic Interactions  Van der Waals Interactions Amino Acids: The Building Blocks of Proteins Aspartic Acid Asp D Negative Glutamic Acid Glu E Negative Arganine Arg R Positive Lysine Lys K Positive Histidine His H Positive Asparagine Asn N Uncharged Polar Glutamine Gln Q Uncharged Polar Serine Ser S Uncharged Polar Threonine Thr T Uncharged Polar Tyrosine Tyr Y Uncharged Polar Alanine Ala A Nonpolar Glycine Gly G Nonpolar Valine Val V Nonpolar Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 Leucine Leu L Nonpolar Isoleucine Ile I Nonpolar Proline Pro P Nonpolar Phenylalanine Phe F Nonpolar Methionine Met M Nonpolar Tryptophan Trp W Nonpolar Cysteine Cys C Nonpolar Diversity Seen in Amino Acid R Groups:  Size  Shape  Charge  Hydrogen bonding capacity  Chemical reactivity Only L-amino acids are constituents of proteins:  Only L-amino acids appear in nature Higher Order Structures of Proteins:  Linus Pauling and Robert Corey: o Used X-Ray crystallography to determine bond angles and distances  Predicted two ordered structures: o -helix (intrachain hydrogen bonding) o -pleated sheet (interchain hydrogen bonding Ɑ-helix:  Tightly coiled  Rod-like arrangement of amino acids  Backbone consists of repeating units of N-C -C  Amino acid R groups radiate outward  Helix is stabilized by extensive hydrogen bonding between NH and CO groups in the structure o N+4 rule  3.6 amino acids per turn: o Amino acids three or four apart in the linear sequence are spatially close to one another  Amino acids tow apart sit on opposite sides of the helix  Most -helices in proteins are right-handed o Right-handed helices are energetically favored:  Less steric hindrance between R groups and the backbone  -helices have a direction based upon rotation as they grow  Two or more -helices can intertwine to form a “coiled coil” o Coiled coils are found in keratin, myosin, and fibrin  Helix content varies vastly from protein to protein: Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 o Hemoglobin has a high -helix content o Chymotrypsin lacks -helices all together -Pleated Sheets  Extended polypeptide chains  Form sheets via hydrogen bonding between NH and CO groups of different chains  Adjacent chains can run parallel, antiparallel, or mixed (strands running both parallel and antiparallel Distribution of Polar vs. Nonpolar Amino Acids in Folded Polypeptide in an Aqueous Environment:  Nonpolar side chains create a hydrophobic core region in the folded conformation of a polypeptide  Polar side chains line the outside of the molecule and can form hydrogen bonds with water Four Levels of Protein Structure:  Folding is choosing near neighbors to minimize total free energy  Primary Structure: o Amino Acids  Secondary Structure: o -helices o -pleated sheets  Tertiary Structure: o Polypeptide chain  Quaternary Structure: o Assembled subunits Folded proteins form functional structures called domains Protein Assemblies:  Exact structure depends on the orientation of binding sites on each subunit  Assemblies are also known as polymers o Some polymeric structure exhibit polarity but not in the electrical sense  Rigid Structures: o Collegen  Very tightly packed in a triple helix  Elastic Structures: o Elastin  Elastin molecules cross link to one another and are able to stretch and relax due to those cross links  Covalent Bonds: o Disulfide bonds help stabilize protein structure  Can occur interchain or intrachain  Formation of Sheets or Tubes: o Some proteins can form sheets or tubes through multiple points of contact with other subunits  Viral Capsids  Interactions between two proteins or another kind of molecule and a protein involve specific non-covalent interactions that determine the specificity of binding Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042  Amino acids involved in binding are often far apart from one another in the unfolded protein but are close to one another in the folded conformation How do Antibodies Generate Diversity of Binding to Thousands of Different Antigens Without Losing Basic Structure or Function?:  Noncovalent bonds mediate specificity of binding between molecules  The function of proteins is regulated by covalent modification Kinetic Properties of Enzymes:  Enzymes increase the rate of biological reaction without altering reaction equilibria o All chemical reaction can be described in terms of equilibrium  The degree in which a reaction will proceed forward to yield a product or backwards to the starting point  Decrease activation energy of a reaction  Accelerate reactions through stabilization of transition states  The enzyme active site Reaction Equilibrium:  Reaction equilibrium is linked to the standard free energy change (ΔG) o Energy states of reactants and products remain unchanged in both the enzyme-catalyzed and uncatalyzed reactions  Reaction rates are linked to the activation energy (E ) A o Enzymes increase the reaction rate by lowering the E A  As K’ increases, ΔG decreases eq Enzyme Active Site:  Enzyme is complementary to transition state  The catalytic site is relatively small compared to the rest of the enzyme  The catalytic site is three dimensional  Substrates are bound to enzymes by multiple weak noncovalent interactions: o Electrostatic bonds o Hydrogen bonds o Van der Waals interactions o Hydrophobic interactions Catalytic Site Forms Clefts or Crevices:  Substrate molecules bound within cleft  Water is normally excluded unless involved in catalysis  Overall nonpolar character of the cleft can enhance binding of substrate  Cleft may also contain polar residues which may take on catalytic properties within this nonpolar microenvironment Enzyme-Substrate Complex:  First step in catalysis  Enzymes derive much of their catalytic power by bringing in a substrate molecule at a favorable orientation o This is how enzymes reduce free energy  Enzymes have a saturation point where the velocity of the reaction cannot increase any more Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 Posttranslational Regulation of Enzyme Activity:  Allosteric Regulation: o Positive modulator increases activity of the enzyme o Feedback inhibition o A way of regulating levels of synthesized endproduct Regulation of Enzyme Activity:  Covalent Modification: o Attachment of another molecule to a substrate can modify enzyme activity  Proteolytic Modification: o Protease cleaves one or more bonds in a target protein to modify its activity Chapter 4: Proof that Genetic Information is Stored in DNA:  Evidence: o Most DNA is located in chromosomes  RNA and Proteins are distributed throughout the cell o Precise correlation between amount of DNA and number of chromosomes o Diploid organisms have somatic cells with 2x the DNA as germ cells o Molecular composition of DNA is unchanged throughout cells of organisms, which composition of RNA and proteins are variable in different cell types o DNA is more stable than proteins or RNA Bacterial Transformation:  Type R: o Lack polysaccharide capsule  Avirulent strain  Type S: o Large, round colonies are encapsulated  Protected from attack by white blood cells  Virulent Structure of DNA:  Packaged into chromosomes  “Form begets Function”  Nuclein: o Nitrogen and Phosphorus containing acidic material generated by treating pus cells with pepsin  Nucleotides: o Monomer Subunits o Pyrimidines:  Cytosine  Thymine o Purines:  Adenine  Guanine  Nomenclature: Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 o Nucleoside:  No phosphate group o Nucleotide:  Phosphate group o dNMP vs dNDP vs dNTP  (Deoxyribonucleotide mono/di/triphosphate) o dNTP vs NTP  Deoxyribonucleotide triphosphate vs ribonucleotide triphosphate Phosphodiester Linkage:  Formation of polynucleotide chain is formed by phosphodiester bonds  Occurs between the 5’ and 3’ ends of deoxyribose RNA Structure:  Differences between DNA and RNA: o RNA has 2’ OH group o In RNA Uracil replaced Thymine o Structure:  RNA is single stranded  RNA folds back on itself  Functions in expression of genetic information Chargaff:  [Thymine] = [Adenine]  [Cytosine] = [Guanine]  [T] + [C] = [A] + [G] DNA Replication Occurs in a Semiconservative Manner DNA Organization:  Organismal DNA divided into units called chromosomes Eukaryotic Chromosome Structure:  Humans have 23 different chromosomes Multineme vs Unineme  Multineme: o Multiple double helices running through chromosome  Unineme: o Single strand of DNA running through chromosome Unineme, so how does DNA condense?  DNA is not naked in chromosomes o Chromosomes contain a lot of protein and even a small amount of RNA  Chromatin: complex of DNA with these components  Has two classes:  Basic:  Positive and neutral pH - Histones  Acidic: Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 Negative at neutral pH - Nonhistone chromosomal  proteins Nucleosomes are the basic subunit of eukaryotic chromosome structure:  DNA wrapped around a histone Histones:  Five classes of Histone proteins: o H1 o H2a o H2b o H3 o H4  Unique amino acid composition: o 20-30% Lysine and Arginine  Found in all eukaryotes chromosomes in amounts similar to DNA concentration  Specific Molar Ratios Observed: o 1 H1 : 2 H2a : 2 H2b : 2 H3 : 2 H4  2 molecules each of H2a, H2b, H3, and H4 form an octamer called the nucleosome core Types of Chromatin:  Heterochromatin: o Highly condensed, normally associated with low gene expression activity (gene silencing)  Euchromatin: o Less condensed, associated with active gene expression Chromatin Modification:  Chromatin can undergo changes and modifications o Some are reversible  Gene expression can be controlled or regulated o Has large implications for organismal development, activation and deactivation of cell function Nonhistone Proteins:  Large number of different proteins  Composition of fraction varies from cell type to cell type in the same organism  Function is regulating expression of different sets of genes Solenoid Model:  30nm fiber made up of nucleosome discs stacked on edge in the shape of a helix  Linker DNA buried in center of the helix, never passes through axis Zigzag Model:  30nm fiber made up of a zigzag pattern of nucleosomes formed through binding of histone H1  Linker DNA passes through the axis Final Level of Condensation: Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042  A scaffold of nonhistone proteins condenses the 30n chromatin fiber into loops supercoiled domains Several Levels of DNA Condensation: 1. DNA Double Helix 2. DNA + Histones 3. Solenoid or Zigzag 4. 30nm fiber organized into loops via chromatin scaffold Telomere:  At the end of chromosomes  Three Functions: o Prevents degradation o Prevents fusion of ends with other DNA molecules o Facilitates faithful replication of linear end of DNA  Single stranded overhang of the 3’ strand  G rich Chapter 5: Semiconservative Mode of Replication:  Each parental strand of DNA serves as a template for new daughter strands  New strand synthesis is in the 5’ to 3’ direction DNA Polymerases Catalyze the Synthesis of DNA Pyrophosphate hydrolysis gives energy to create the phosphodiester bonds in DNA DNA Replication:  Beginning: o Initiation  Middle: o Elongation  End: o Termination  Initiation at Origin o Prokaryotes:  Single point of origin o Eukaryotes:  Multiple points of origin o Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 Mutation, DNA Repair, and Recombination  Proofreading helps to ensure accurate replication of DNA between generations  Mutation: o Heritable change in genetic material o Refers to the process in which the change occurs o Mutant:  Organism that exhibits a novel phenotype resulting from a mutation Mutations:  Spontaneous Mutations: o Occur without a known cause / Rare  Inherent errors in replication  Unknown agents in the environment o Rate in Prokaryotes is lower and in Eukaryotes  Induced Mutations: o Mutations that result from a known cause  Exposure to physical or chemical mutagens  Ionizing radiation, Ultraviolet light and a variety of chemicals o Frequency of mutations depends on the agent  Rate can increase dramatically if the mutagen is potent  Up to 1% of genes in an organism can be mutated What Role Does Mutation Play in Evolution:  Mutation is the raw material of evolution  Mutation leads to genetic variation o Changes in genotype that can lead to changes in phenotype o Ability to respond to environmental changes  Can mutation level be too high??? o Compromise faithful transfer of genetic information from generation to generation  Lethal o Delicate balance is required  Mutations can occur in any cell at any time  Effects of mutation on phenotype depend on the cell type, where the organism i in its life cycle, dominance, and the type of mutation  Mutation can offer advantages: o Sickle Cell Anemia in Africa (helps with Malaria)  In animals, mutations can occurs in: 1. Germ-line cells: 1. Cells that give rise to gametes b. Somatic cells: 1. All other cells in an organism  Only mutations that occur in germ-line cells can be passed on to progeny Downloaded by Mimi Kreger ([email protected])  lOMoARcPSD|34711042 Do Most Mutations Result from Adaptive or Nonadaptive Processes?  Downloaded by Mimi Kreger ([email protected])