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BIO 181 Lecture Notes Exam 1 and 2

by: Daniella Simari

BIO 181 Lecture Notes Exam 1 and 2 BIO 181

Marketplace > Arizona State University > Biochemistry > BIO 181 > BIO 181 Lecture Notes Exam 1 and 2
Daniella Simari
GPA 3.8

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About this Document

These notes cover what was on the first exam and most of what will be on the second exam, as discussed in class.
General Biology 1
Chakravadhanula, Farrokh, Konikoff
Bio, Biology, Biology 181, bio 181, Cellular Respiration, krebs cycle, TCA Cycle, ETC
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This 16 page Bundle was uploaded by Daniella Simari on Thursday January 28, 2016. The Bundle belongs to BIO 181 at Arizona State University taught by Chakravadhanula, Farrokh, Konikoff in Winter2015. Since its upload, it has received 44 views. For similar materials see General Biology 1 in Biochemistry at Arizona State University.


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Date Created: 01/28/16
Wednesday, January 13, 2016 Weeks 1-3 - Thinking Skills • Bloom’s Taxonomy • Cognitive Load Theory - Observation - Hypothesis - Prediction • Concept Maps (method to organize info) hypotheses for Amazon Fly story: Why was the fly pop. so low that day? • - frogs/other predators - temperature change - less humidity • “theory” - broader in scope than a hypothesis - supported by a large body of evidence in comparison to a hypothesis • What is Life? - reproduction/replication (DNA) - one or more cells and their internal organization - use energy (conversion) - adaptability (response to environment) - evolution - regulation/homeostasis - waste/by-products - growth and development 1 Wednesday, January 13, 2016 Organization Level Example Analogous Size multicellular organism plant/human Earth organ liver/heart/brain Texas cell red blood cell battle ship molecular structure rough ER/ golgi apparatus soft ball chain molecule/macromolecule protein tennis ball simple molecule/monomer amino acid box of tic-tact atom hydrogen tic-tac - molecules that have partial/full charges can easily dissolve in water - hydrophobic molecules would clump up and not interact w water molecules - biochemical composition of cells: • atoms (elements) • molecules • macromolecules (chain molecules) - proteins (pep) - carbohydrates (ose, gly, glu, sacch) - nucleic acids (DNA, RNA) - lipids (lip) Monomer Polymer Bond amino acid protein peptide monosaccharide polysaccharide glycosidic fatty acids??? lipid, phospholipid nucleotide DNA, RNA phosphodiester - carbohydrates • carbohydrates are hydrophilic and polar because they have C-O bonds, which are usually hydrophilic • function of carbohydrates in the cell: provides energy 2 Wednesday, January 13, 2016 • being both hydrophilic and hydrophobic means it has hydrophilicity - proteins • R groups make every amino acids different from each other • proteins fold (there are different levels of protein structure - there are enzymes whose jobs it is to fold proteins in cells - hemoglobin has quaternary structure - proteins tend to be globs because of the folding • proteins are hydrophilic and hydrophobic because it has N-H bonds and C-O bonds, which are usually hydrophilic (as well as P-O bonds) • almost every protein as at least one of every amino acid cytoplasm in the cell is 70% water • - proteins in the cytoplasm exposes its hydrophilic amino acids and hides its hydrophobic amino acids inside (has to know how to fold a protein, whether its destined for the cytoplasm where hydrophilic is on the outside, or the membrane where hydrophobic is on the outside) - lipids • sterols, triglycerides, and phospholipids • saturated fatty acids (straight bonds and no double bonds between the carbons) and unsaturated fatty acids (double bonds between the carbons and bent) • saturated fatty acids are able to pack closely together, and are solid at room temperature - (unsaturated fatty acids in oils make it a liquid, not solid, at room temp) • fatty acid tail is hydrophobic —> this characteristic of phospholipids allows them to form a bilayer • fatty acid head is hydrophilic and polar overall, lipids are hydrophobic • • you can expect to find proteins (both hydrophobic and hydrophilic) in phospholipid membranes 3 Wednesday, January 13, 2016 - DNA/RNA • nucleotides always have a base, ribose sugar (5-carbon sugar/carb), and a phosphate • DNA is double-stranded • RNA is single-stranded • nucleic acids are found in the nucleus - not for prokaryotes (bacteria)!!! • nucleic acids are hydrophilic - Golgi apparatus: tells packaged proteins where to go in the cell (usually to the membrane) • bacterial cells do not have a Golgi apparatus - Common Features of cells • cell membrane: barrier or boundary that separates the internal milieu of the cell form the environment • genes that encode all proteins • cytoplasm containing organelles - structure of cell membrane and how it aids in functions • fatty acid tails are hydrophobic but heads are hydrophilic phospholipids form a bilayer which is like a “lake” in which a variety of proteins • “float” - fluid mosaic model: • selective permeability - some substances can pass through, but not others - passive transport: no energy input required • simple diffusion • facilitated diffusion - active transport - energy required 4 Wednesday, January 13, 2016 - there is potential energy stored in a concentration gradient across a permeable membrane (so the movement of molecules from one side to the other releases energy) - it is not effective over long distances (only effective small distances like cells) - the higher the concentration the quicker the molecules will diffuse across the membrane • temperature and size of the molecule and polarity of the molecule will matter when moving across the membrane - passive transport: diffusion from high concentration to lower concentration - active transport: movement from lower to higher concentration - small, hydrophobic molecules can cross over the membrane - small, hydrophilic molecules cannot cross over the membrane - water can cross over the membrane but do very slowly with the help of aquaporins - solutions are always described by solute concentrations (not water concentrations) • EXAMPLE: osmosis depends on water concentration • hypotonic and hypertonic - during osmosis, water will move in both directions because movement of any molecules is random, but more will move down the concentration gradient - integral membrane proteins help: ? - aquaporins • key residues allow water to pass but block ions and larger molecules - key residues (i.e. amino acids) • amino acids on the inside of the protein are hydrophilic, while the outside of the protein has to be hydrophobic (TRUE FOR MOST TRANSPORT PROTEINS) - transporting glucose against the concentration gradient: ATP not directly used (the energy is provided by the Na+ gradient) (the potential energy from the concentration gradient) • when the Na/K pump is blocked, glucose transport into the cell stops but not immediately 5 Wednesday, January 13, 2016 - if you’re going against a concentration gradient, you need active transport (requires energy) - DNA • some phosphates in deoxy-nucleotides get cleaved off when linked together (there are 3) • carbons in ribose are numbered (DNA has one OH on its 3’ end & Phosphate on 5’ end) • 2 strands run anti-parallel & has complementary bases strands are held together by hydrogen bonds • • CH2 is the 5’ end & OH is the 3’ end • guanine and cytosine are pairs / adenosine and thymine are pairs • A double stranded DNA fragment w 100 nucleotides on each strand contains a total of 30 guanine (G) bases. How many adenines (A) does it contain? - answer is 70! (it’s 100 PER STRAND) • genetic material is precisely replicated in cell division - by complementary base pairing • DNA gets wrapped in a very orderly manner, twice around histones (in eukaryotic cells they have histone-like proteins, but not histones) • Females have XX & males have XY (gene on X chromosome is shorter than Y chromosome) • DNA is very negatively charged • opposite strand could also be written backwards • if there isn’t enough DNA is a blood stain, they can be amplified (replicated) • DNA replication is semi-conservative (each strand of the double helix is used as a template for a new strand) - dna polymerase (-ase indicates that it’s an enzyme) makes DNA polymers • DNA polymerase needs to have a: - FREE 3’ OH end to add the next nucleotide to 6 Wednesday, January 13, 2016 - template strand (parent strand) so it knows which nucleotide to put in - 4 nucleotides • DNA is synthesized in the 5’ to 3’ end!!!!!! (meaning it’s created in the 5’ to 3’) NEVER synthesized in 3’ to 5’!!!!!!! • in chromosomes in eukaryotic cells there are multiple origins of replication (ori) • the way that we start replicating in any cell is w/ an RNA primer (RNA polymerase) • NEED TO KNOW: functions (and limitations) of DNA polymerase - Polymerase Chain Reaction (PCR) (takes place in a test tube) • heating step separates out the double strand of DNA, add the primers, let them extend, and repeat • in PCR the functional equivalent of helicase (unwinds the DNA) is heat • in PCR, the composition of the primer is DNA, NOT RNA (in our cells it’s RNA) - DNA examination: • Short Tandem Repeats (STRs) - highly variable between different people, usually in regions that are not coding for genes • 1 STR isn’t enough - alleles taken from 2 chromosomes bc we are diploid - why DNA replication is so accurate: DNA polymerase is self-correcting (proofreads from 3’—>5’) • • RNA polymerase doesn’t proofread, and therefore makes a lot more mistakes - if repairs aren’t made then mutations occur • mismatch repair occurs too (cuts out incorrect bases and replaces them w new ones) - DNA does not replicate all the time in cells - CELL CYCLE • in cell division you have to duplicate everything in the cells (esp. chromosomes) 7 Wednesday, January 13, 2016 - no traditional cell cycle in bacteria like there is in eukaryotic cells • G1: growth and normal metabolic roles • Synthesis: synthesis of DNA • G2: growth and preparation for mitosis • Mitosis: when cells divide (separating out the chromosomes in the dividing cells) - prophase - metaphase - anaphase - telophase - Rb protein: tumor suppressor (blocks cell division) - Tumors: • benign (no cancer bc it doesn't spread, although can eventually becomes malignant) • malignant - cancer (potentially spreads to other parts of body) • how cancer begins: - tumor suppressors are inactive - positive regulators are overactive or excessive - transcription • DNA —> RNA (transcription) • RNA —> protein (translation) • “Central Dogma” - DNA transcribed to RNA translated to proteins (one codon for one amino acid/ one gene for one protein) - DNA vs. RNA • RNA has an OH while DNA has an H • RNA uses U for DNA’s T 8 Wednesday, January 13, 2016 - RNA polymerase know where to start by the promoter (start signal) • after we initiate transcription, we elongate - made in 5’ to 3’ direction (antiparallel to the DNA template strand) - RNA polymerase doesn’t proof-read (we can just make another piece of RNA) - site at which the RNA polymerase knows it has to stop - “genes are transcribed” = “genes are turned on” or “genes are expressed” - newly synthesized RNA is not proofread and will therefore have more mutations than DNA - DNA doesn’t have to be replicated before it can be transcribed!!!! - genes have non-coding regions called “introns” which have to be spliced out so that “exons" can be put together to make mRNA • @ junctions between introns and exons, which are splice sites (made of bases) that tell the enzyme complexes (spliceosomes) to cut there - transcription happens in the nucleus!!! (in eukaryotes, but not in bacteria bc bacteria doesn’t have nucleus) Characteristic Transcription Replication primary enzyme? RNA polymerase DNA polymerase all of genome copied/ transcribed? product contains which nucleotides? enzymes do editing? direction of synthesis of new strand? template read in what direction? name of initiation site? what provides energy? - all RNAs are made during transcription (mRNA, tRNA, and rRNA) - translation 9 Wednesday, January 13, 2016 - tRNA bound to codons of mRNA - ribosomes contain rRNA & ribosomal proteins - tRNA anticodon binds to mRNA codon (“charging” the tRNA w an amino acid) - ribosomes are made of rRNA and proteins • “workbench” for protein synthesis • programmable machines prokaryotes are 70s / eukaryotes are 80s [size] • - tRNA enters A site when it is “charged” (w an amino acid,) and its anticodon matches the codon on the mRNA • P site provides peptide bonds for growth of the mRNA RIBOSOMES BIND THE 5’ END OF MRNA • - ribosomes aren't specific about which tRNA binds in the A site, P site, and E site • the genetic code of the mRNA dictates which tRNA will bind to the sites in the ribosome - start codon: methionine (for most proteins) (AUG) - stop codons: (UAG, UAA, UGA) - 64 possible codons • some amino acids have one possible codon • some specific amino acids can have more than one codon (called “wobble”) - you READ RNA from 5’ to 3’, then you TRANSCRIBE (meaning you start making it in the 3’ to 5’) BUT YOU LOOK at the parent strand at its 5’ end first to make your 3’ end on the daughter strand THEN READ THE DAUGHTER STRAND AGAIN from its 5’ end - what proteins do: in cell membrane and they transport; catalyzing reactions; structural roles - sequence of amino acids dictates the shape of protein - DNA replication occurs in synthesis phase - transcription & translation occur during every phase of the cell cycle!!! 10 Wednesday, January 13, 2016 - we are constantly accumulating mutations - substitution mutation (point mutation): most common type of mutation; when a nucleotide pair is switched - what we really care about w/ mutations is whether or not it affects the protein - classify diff. types of substitutions by their affect on protein sequence 1. silent mutation: no change in amino acid 2. nonsense mutation: amino acid that was changed by the DNA mutation is changed to a STOP CODON 1. makes protein a lot shorter (proteins usually have a few hundred amino acids 2. protein will not function at all 3. a nonsense mutation in the middle of the gene is more likely to be harmful than a nonsense mutation in the last codon at the end of a gene 1. however, most likely the mutation will not be near the end 2. most likely effect of a nonsense mutation on the cellular phenotype? 1. cell might or might not have a different phenotype from its wild type (normal phenotype) 3. missense mutations: amino acid is changed to a diff. amino acid 1. protein might still function, might not still function, or will function slightly less than the original will (depends on the amino acid) - PROKARYOTES • contain: - nucleic = information storage; information transmission - cytoplasm = energy conversion & metabolism - ribosomes = modification & packaging of cellular products (e.g proteins) - cell wall = structure - cell membrane = determine what moves into and out of cells 11 Wednesday, January 13, 2016 - EUKARYOTES • compartmentalized by membranes into organelles: - mitochondria: respiration - chloroplasts: photosynthesis - nucleus: DNA storage - Golgi complex: packaging site & transport - Endoplasmic reticulum (ER): protein synthesis & transport - centrioles: generate the protein fibrils that guide chromosomes to their proper destination during cell division - cells need energy to: creating ion gradients across membranes • • muscle contraction • cell movement • protein synthesis • DNA synthesis from nucleotides - free energy needed to create complex molecules from simple molecules - free energy released to create simple molecules from complex molecules - thermodynamics • 1st law: energy is neither created nor destroyed • 2nd law: takes energy to impose order on a system (entropy!!!) - protein is more ordered than free amino acids floating in the cytoplasm - cells get energy from: light (plant cells) • • chemicals (eukaryotic cells) - metabolic pathways • anabolic reactions: building complex molecules (require energy input) 12 Wednesday, January 13, 2016 • catabolic reactions: breaking down complex molecules (releases energy) - energy is stored/carried as: • ATP - adenosine triphosphate (adenine is a nucleotide in DNA) (ribose is a sugar) (phosphate bonds // a.k.a. high energy bonds) - the cleavage of one phosphate bonds releases free energy, and ATP becomes ADP - ADP —> ATP is a change in free energy (low energy to high energy needs energy input) - ATP —> ADP (ATP hydrolysis) releases energy - hydrolysis of ATP drives the reaction forward • energy use and release are coupled - Cells make ATP from: respiration, fermentation, photosynthesis (all metabolic pathways) • each reaction of metabolic pathways is catalyzed by enzymes - enzymes are biological catalysts - enzymes lower the activation energy (don’t change the free energy (delta G), they just make it go faster) • 3 ways to generate ATP: - substrate-level phosphorylation - photophosphorylation - oxidative phosphorylation • glycolysis, citric acid cycle, electron transport chain/proton gradient • (in ETC) occurs with ATP synthase - the cell gets energy to convert ADP to energy from the potential energy of the proton gradient • 3 protons passing into the mitochondria generates 1 ATP - ATP comes from energy released during electron transport to make the proton gradient 13 Wednesday, January 13, 2016 - energy is released as electrons are passed between carriers - start w/ NADH, passes an electron to each carrier until the final electron is passed to oxygen to form water (H2O) • each carrier down the chain has lower, and lower energy but higher and higher affinity to accept that electron (high redox potential) - so, electrons move spontaneously from one carrier to the next • so changed the pH as we pump protons down their concentration gradient (outside of mitochondria is much more acidic by the end of the gradient) oxidize NADH —> oxidation is loss of electrons (OIL) // reduction is gain of • electrons (RIG) • DON’T MIX UP ELECTRONS IN THE FORM OF H ATOMS; AND PROTONS: H+ • NADH carries electrons from food - oxidation of NADH releases lots of free energy - the C-H bonds in NADH have potential energy, so breaking those bonds releases energy • potential energy released with the proton gradient • protons flow through the the ATP synthase from high concentration to low concentration (we make the concentration gradient, and then we have to dissipate that gradient), and ATP is made in the top compartment • ATP is made in the mitochondria • IDEAL: 1 NADH oxidized, about 8 H+ pumped • 1 NADH yields 2 ATP • proton gradients: - creates an electrical charge across the membrane - heat production • hibernating animals and babies do this • “brown” fat cells 14 Wednesday, January 13, 2016 • protein (thermogenin) - uncouples ETC from ATP synthesis • DNP (dinitrophenol) can cross the membrane in both a protonated and deprotonated form - if a cell has it, then no proton gradient will be possible and no ATP generation by ATP synthase will form + • glycolysis gives us energy to convert from NAD to NADH (get energy from glucose, carbs, fats and proteins) - free energy is released from complete oxidation of a glucose to carbon dioxide • energy is released from glucose by oxidation and if burned in flame (creating CO2, H2O, and HEAT) - same equation for metabolism, but less energy lost to heat • net amount of 2 ATP from glycolysis - ATP synthesis - substrate level phosphorylation: • GLYCOLYSIS • passing a phosphate from one compound to ADP to make ATP • electrons are in the form of H atoms (glucose is our electron donor in glycolysis) - glucose is oxidized - NAD+ gains electrons (reduced) • ADP and NAD+ gain potential energy OXIDIZED IS LOSS OF ENERGY AND ELECTRON • ATP, NADH, and pyruvate capture the free energy that is “lost” when glucose is • converted to 2 pyruvate • cells regenerate NAD+ for the next round of glycolysis during the ETC - KREBS CYCLE = TCA cycle = citric acid cycle • net/glucose: - 8 NADH - 2 FADH2 15 Wednesday, January 13, 2016 - 2 ATP - 6 CO2 • substrate-level phosphorylation for krebs cycle to make ATP • pyruvate is oxidized to acetyl CoA as reaction before krebs cycle moves forward - NAD+ is being reduced because pyruvate is getting oxidized - free energy released from complete oxidation of a glucose molecule to carbon dioxide - make up to ~30 ATP per every glucose molecule • oxidative phosphorylation makes the most ATP per glucose molecule - MASS: • in glucose, O has the most energy and H has the least energy • in glycolysis, most of the mass in glucose (1) ends up in pyruvate (2) • in the Krebs cycle, most of the mass in glucose (1) ends up in CO2 (3) - if there’s no oxygen available in the cell • 1: cells die • 2: fermentation (pyruvate —> lactic acid) - 2 ATP/glucose is produced from glycolysis following by fermentation - glucose is not completely oxidized (lots of energy left over) - microbes can do other kinds of fermentation (pyruvate —> ethanol) 16


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