Exam 1 study guide
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This 4 page Study Guide was uploaded by Brenna Eisenberg on Monday October 3, 2016. The Study Guide belongs to 327 at Syracuse University taught by erdman in Fall 2016. Since its upload, it has received 56 views. For similar materials see Cell Biology in Biology at Syracuse University.
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Date Created: 10/03/16
Exam 1 study guide Thursday, September 22, 20112:55 PM • The central dogma of molecular biology is DNA(replication)----(transcription)---> RNA---(translation)----> protein • Mitochondria and chloroplasts are thought to have endosymbiont origins, as they have their own DNA and a double membrane • Acids- release protons when dissolved in water [H+] • Bases- accept protons when dissolved in water. [OH-] • Condensation reactions: expels a molecule of water as the bond is formed • Hydrolysis reactions: consumes a molecule of water as it breaks the bond • Sugars: ○ 2 monosaccharides can be joined with a glycosidic bond to form a disaccharide ○ Form rings with lots of protons and hydroxyls. Very soluble in water ○ The backbone can be branched • Lipids/ fatty acids: Long chains of hydrophobic hydrocarbons. Saturated carbon tails ○ Hydrophobic substances tend to be hydrocarbons. They tend to aggregate and remain immiscible in water ○ Sterols are lipids that are important for membrane and steroid hormones ○ Carboxyl group is hydrophilic Ionic and polar substances tend to be hydophilic ○ Amphipathic- contains hydrophobic and hydrophilic regions ○ Lipids serve as a concentrated food reserve in cells ○ Form phospholipid bilayer • Amino acids and proteins ○ Carboxylic acid group and amino acid group connected to alpha carbon ○ Peptide bonds are formed between amino acids through condensation reactions ○ Proteins only exist as L form isomers ○ Svedburg determined the polymeric nature of proteins by ultracentrifugation. Sedimented as a band ○ General types of amino acids: Acidic, basic, uncharged polar, nonpolar. Acidic and basic can make ionic bonds and interact strongly with water Uncharged polar are often sites of modifications Hydrophobics important towards creating globular protein structures. □ Cysteine- can make disulfide bonds. Helps stabilize protein structures. Stable outside of the cell. Can be intra/interchain bonds Hydrophobic/ nonpolar-can be rings, lots of methyl groups. Uncharged polar- usually OH or NH2 group Acidic side chains carry a negative charge Basic side chains carry a positive charge • Nucleotides/DNA/RNA ○ ATP, GTP act as short term carriers of energy ○ Store biological information • Conditional mutants- proteins may be normal at one temp, but unfold at another temp • Kinases- phosphorylate. Take the terminal P from an ATP and tack it onto something else, possibly changing its function. Exam 1 study guide Page 1 • Kinases- phosphorylate. Take the terminal P from an ATP and tack it onto something else, possibly changing its function. • Covalent bonds are the strongest bonds, then ionic bonds. • Weak bonds are good, because they allow for the specific interactions within the cell • Catabolism- breaking down of foodstuffs into smaller molecules, generating energy • Anabolism- using energy harnessed from catabolism to drive the synthesis of molecules • Entropy- measure of disorder in a system. Systems tend to move toward disorder. • Energy is extracted from food molecules by gradual oxidation ○ Oxidation is the removal of electrons from an atom. Number of C-H bonds decreases. - ○ Reduction is the gain of an electron. Ex: Cl --> Cl . Number of C-H bonds increases. • ∆G: measures the amount of disorder created in the universe when a reaction occurs ○ Needs to be negative for a reaction to occur spontaneously • V : the active sites of all enzyme molecules are fully occupied by Overall rate the cycle can be run, how fast the enzyme can go max • K m the concentration of substrate at which the enzyme works at half of its maximuBest describes the ability of an enzyme to associate with its substrate molecule. Measures affinity ○ Small m : substrate binds very tightly ○ Large K : indicates weak binding. m • Activated carriers- small organic molecules that contain one or more energy rich covalent bonds. ○ Store energy as a readily transferable chemical group or high energy electrons. ○ • Reductions done by NADPH are prevalent in anabolic processes • Oxidations by NADH predominate in catabolic processes to break down food • Coupled reactions: An energetically favorable reaction is used to drive an energetically unfavorable one that produces an activated carrier or useful molecule. • Liberating heat generates order within the cell. • Equilibrium constant K: products/ reactants • Proteins: ○ N-Terminus- the end with the amino group. ○ C-terminus- the end with the free carboxyl group ○ Protein folding is assisted by chaperone proteins, making the process more efficient ○ Proteins fold into conformations that represent energy minima ○ Reliable, reproducible structure ○ Water greatly influences how proteins fold Nonpolar side chains like to bury within themselves to avoid the water ○ α helix: common folding patterns of proteins. ○ Helix resembles a spiral staircase. ○ A single polypeptide chain turns around itself to form a rigid cylinder ○ Can be found crossing the lipid bilayer ○ Coiled-coils- stripe of hydrophobic amino acids of one helix wraps around the stripe of another to minimize the exposure of hydrophobic AA side chains to the aqueous environment ○ β sheets: polypeptide chains lay side by side ○ Form rigid structures at the core of many proteins ○ Parallel β sheets run in the same orientation ○ Modifications like N- and O- linked glycosylation can influence structures ○ Often proteins moved to the outside of the cell ○ Sugars added post- translationally ○ Helps the proteins extend the polypeptide chain ○ Primary structure- a proteins amino acid sequence ○ Secondary structure- form within certain sequences in the polypeptide chain, include α helix and β sheets ○ Tertiary structure- the full 3D conformation formed by an entire polypeptide chain ○ Quaternary structure- the complete structure of a protein molecule if it is formed from more than one polypeptide chain. Organization of protein complexes ○ Peptide bonds have no rotation and are planar ○ Dimer- a protein composed of two structurally similar components ○ Globular proteins- PPchains fold up into a compact shape like a ball ○ Fibrous proteins- elongated 3D structure ○ Ligand- any substance that is bound by a protein ○ Feedback inhibition-an enzyme acting early in a reaction is inhibited by a late product of that pathway. When large quantities of product accumulate, the product binds to an earlier enzyme and slows down its action Exam 1 study guide Page 2 When large quantities of product accumulate, the product binds to an earlier enzyme and slows down its action Type of negative regulation-prevents the enzyme from working ○ Positive regulation-enzyme is stimulated by a regulatory molecule ○ Allosteric enzymes have 2+ binding sites that influence one another Can adopt 2 or more slightly different conformations ○ Phosphorylation can cause conformational changes Kinases catalyze phosphorylation Phosphatases dephosphorylate Can create docking sites where other proteins can bind ○ Ribozymes- catalytic RNA molecules that act as enzymes ○ Prions- proteinaceous infectious particles ○ Carry information ○ Involved in transmissible diseases ○ No nucleic acid component ○ Species barriers ○ The half-life of a protein is half the average of the time the protein spends in the cell. Half of the material has degraded ○ Determined by pulse chase experiment ○ Proteasomes- multi-protein complexes that degrade damaged proteins or proteins marked with ubiquitin. ○ Lysosomes- dedicated to degrading proteins found in membranes or soluble proteins imported into the cell ○ Sequestration- sequestering proteins bind and prevent assembly. Hold protein after their production in the cytoplasm. ○ Localization- Ex- some transcription factors held in the cytosol until there are signals that modify, allow entry into nucleus where they can function • Phosphorylation can be inhibitory • Active site on enzymes bind to substrate • Interphase chromosomesare stretched long and thin but are still organized ○ Heterochromatin- the most highly condensed form of interphase chromatin. Concentrated around the centromere and telomeres. Tends to be repressive toward gene expression. Many repeating regions. Found at/near telomeres and centromeres ○ Position effect seen in fruit flies- white gene near heterochromatin due to chromosomal inversion makes part of the eye white ○ Euchromatin- the rest of the interphase chromatin • Replication origin- nucleotide sequence where replication begins • Nucleolus- where the different chroms carrying genes that encode ribosomal RNAs cluster together. RRNAs are synthesized here and combine with proteins to form ribosomes • Histones are responsible for the first level of chromatin packing- the nucleosome ○ Beads on a string ○ High proportion of positively charged amino acids that help the histones bind tightly to the negatively charged backbone of DNA ○ Tend to be associated with regions of active gene expression • Chromatin remodeling complexes- use energy from ATP hydrolysis to change the position of the DNA wrapped around nucleosomes. Can make DNA more or less accessible to other proteins in the cell. • Transcription: copying the nucleotide sequence of a gene into RNA • Promoter- gene region that contains a specific sequence of nucleotides that lies immediately upstream of the starting point for RNA synthesis Exam 1 study guide Page 3 synthesis ○ RNA polymerase binds to the promoter region • Eukaryotes have 3 kinds of RNA polymerases. RNA polymerase II transcribes the majority of eukaryotic genes ○ Only dephosphorylated RNA polymerase II can initiate RNA synthesis • General transcription factors- accessory proteins that assemble on the promoter and position the RNA polymerase & pull apart the DNA helix in eukaryotic cells. Binds to TATA box of promoter region • mRNA is transported out of the nucleus through nuclear pores. ○ RNA capping- RNA will be capped by a G nucleotide bearing a methyl group. At 5' end ○ Polyadenylation- poly-A tail is added to 3' end ○ Introns- long noncoding sequences of DNA. Intervening sequences ○ Removed from pre-mRNAs by RNA splicing in the form of a lariat structure ○ Exons- scattered pieces of coding sequence. Expressed sequences ○ Small nuclear RNAs (snRNA)- carry out RNA splicing. Packaged with additional proteins to form snRPS, that recognize the splice site ○ snRPS form the core of the spliceosome- the large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus. Bind specific sequences that designate the removal of the intron ○ Alternative splicing- allows for different proteins to be produced from the same gene • DNA replication begins at origins of replication • Telomeres and centromeres frequently have very simple repetitive sequences ○ Not all of chromosomal sequence is coding • Replication occurs bi-directionally. ○ Leading strand and lagging strand ○ Polymerases polymerize nucleic acids from 5' to 3' • Simple sequences tend to be found in large numbers of copies • More complex sequences can be single copy or repetitive • Single copy or a few copies- genes • Mildly repetitive- transposable elements "jumping genes" • Highly repetitive- blocks of simple sequences • Can have repressors or activators. Tend to work at promoter (start site of transcription) ○ Binding sites for regulatory proteins may be far away from the promoter in eukaryotes Intervening DNA can loop • TFIID binds to the TATA box, nucleates the rest of the proteins ○ Bends the DNA • RNA polymerase must be activated by phosphorylation ○ Done by kinase TFIIH • Operon- one RNA can encode several proteins. In prokaryotes Exam 1 study guide Page 4
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