BIOL 4843: EXAM 1
144 Cards in this Set
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Genotype
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word used to describe the "blueprint" or genetic potential of an organism.
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Ionic
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a type of strong chemical bond that involves the transfer of electrons between atoms.
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mRNA
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the only type of RNA that is considered "coding"
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Covalent
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the type of bond that is important for holding together the building blocks of all three molecules of the Central Dogma.
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Crick
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last name of the scientist who played an important role in determining the structure of DNA and came up with the Central Dogma.
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Phosphodiester
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the type of bond that joins the building blocks of nucleic acids.
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Methylation
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a common post-synthetic modification of DNA that can influence replication, gene expression, and DNA protection from enzymes.
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Resonance
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something that can occur when a single bond is next to a double bond in a molecule and affects the characteristics of peptide bonds.
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Silent
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the name for a mutation involving a change in DNA sequence that does not result in a protein with altered amino acid sequence.
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Phosphorylation
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a common post-synthetic modification of proteins that can influence their shape and function.
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Ribosome
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is made up of both RNA and protein and catalyzes protein bond formation
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Nonpolar
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word to describe a molecule with balanced charges
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Miescher
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Last name of scientist who first isolated DNA (called it nuclein)
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Functional
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the type of RNA that is never translated
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Nucleoside
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the name for a molecule made up of a 5-C sugar and a base.
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Hydrogen bonding
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the type of bond holding two DNA strands together.
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Beadle
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last name of one of the scientists that contributed to formulating the "one gene-one enzyme" hypothesis.
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Puckering
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a term used to describe the non-polar conformations of the sugar ring in a nucleotide
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Secondary Structure
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hydrogen bonding is the main bond/interaction used in this level of protein structure.
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Translocase
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a name that describes proteins that move along dsDNA or dsRNA, but don't separate strands
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Quaternary Structure
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not all proteins have this level of protein structure
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Flexibility
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a protein characteristic that is often important for both protein-ligand interactions and enzymatic activity
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Isomerase
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a type of protein that catalyzes structural rearrangements of proteins.
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Guanine
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a type of base that is a purine and contains a carbonyl group
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Active Site
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the name of the site that a substrate binds in an enzyme
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Denaturation
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a word describing the separation of two DNA strands
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Modulator
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binds to an enzyme and induces a conformational change that affects enzyme activity
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Holoenzyme
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the name given to an enzyme that is catalytically active (contains all subunits)
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Cofactor
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a molecule that is required for enzyme activity (could be inorganic or organic)
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Affinity
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a type of column chromatography that you would use if you wanted to isolate a protein that binds to a ligand
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Specific
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the category of DNA-binding proteins that would encompass proteins involved in regulating gene expression.
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Motor proteins
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a class of proteins involved in nucleic acid metabolism that are involved in moving, separating, and/or joining molecules.
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Peptide Bond
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main type of bond contributing to primary protein structure and has a partial double bond characteristic due to resonance.
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Domain
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an independent folding unit within a polypeptide chain
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Glycosidic bond
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a covalent bond between the base and sugar in a nucleotide
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Phosphorylation
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a common modification of amino acid residues that can affect regulation of protein function
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Chaperone
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a type of protein that binds and helps fold unfolded or improperly folded proteins
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NMR
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a technique for determining protein structure that can only be used on small proteins, but doesn't require making a protein crystal.
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Palindrome
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a word used to describe a specific DNA sequence that can result in the formation of hairpins and/or cruciforms.
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Subunit
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a term that will only be used in association with proteins with quaternary structure, and indicates an individual polypeptide chain.
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Nonspecific
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the category of DNA-binding proteins that would encompass proteins involved in DNA compaction.
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Chargaff
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the name of the rules about base composition in DNA
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Disulfide
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these types of linkages (bonds) are considered part of primary protein structure
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Primary Structure
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the level of protein structure that contains all the instructions for how a protein should fold.
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Binding Site
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name of the site that a ligand binds in a protein
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Hydroxyl Groups
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a chemical group that is different in deoxyribonucleotides and ribonucleotides and contributes to the flexibility of RNA structures in RNA and DNA.
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Gregor Mendel
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3 basic laws of inheritance
a. allele pairs segregate during gamete formation
b. different genes assort independently
c. Law of Dominance
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(Johan) Friedrich Miescher
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Discovered DNA (nuclein)
-used white blood cells from old puss bandages
-discovered an acid containing phosphorus
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Genotype
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Genetic constitution of an organism, distinct from its physical characteristics
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Phenotype
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observable characteristics of an organism
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Walter Sutton
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studied grasshopper and showed that during mitosis, one complete set of chromosomes partitioned into each daughter cell.
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Thomas Hunt Morgan
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studied Drosophila to examine Chromosome Theory of Inheritance
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Chromosome Theory of Inheritance
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theory that genes are located on chromosomes
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Law of Independent Assortment
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in the formation of gametes there is independent assortment of alleles for different genes (Mendel's 2nd law)
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Law of Segregation
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in the formation of gametes there is an equal segregation of alleles. In other words, a haploid gamete contains one copy of each gene. (Mendel's 1st law)
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Oswald Avery
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-Reproduced Griffith's experiment and showed that DNA was the chemical of heredity
-Extracted virulent DNA, purified it, and injected it into non-virulent bacteria.
- Non-virulent bacteria turned virulent
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Frederick Griffith
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-Studied streptococcus pneumoniae which exists as two types, virulent and non virulent
-Virulent shaped smooth
-Non-Virulent shaped rough
-Found heat killed virulent bacteria transformed live non-virulent bacteria into live virulent bacteria.
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Sir Archibald Garrod
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-Studied alkaptonuria, protein that causes black urine.
-recessive trait that was a mutation of an inactive gene that caused an enzyme to not be produced.
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Beadle and Tatum
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-Mutated Neurospora, then germinated individual spores on a medium to obtain pure colonies.
-pure colonies tested for ability to germinate
-Inability to grow indicates a mutation, which are called auxotrophs.
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Franklin, Wilkins
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used x ray diffraction to find DNA structure
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Watson, Crick
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discovered DNA was double helix
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Central Dogma
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organizing principle of molecular biology proposed by Crick
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mRNA (Messenger)
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-complementary to only one DNA strand. Carries the genetics message from the chromosome to the ribosome.
-"only coding RNA"
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tRNA (Transfer)
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-combines covalently with a specific amino acid for use in protein synthesis
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rRNA (Ribosomal)
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-class of RNA that serves as components of the ribosomes.
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Transcription
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DNA→RNA
1. RNA polymerase opens the DNA duplex and uses one strand as a template for RNA synthesis
2. Polymerase matches base pairs and advances along the template strand.
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Translation
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RNA→Protein
1. Occurs at P and A site and binds to tRNA
2. Two tRNA's form base pairs with adjacent triplets on mRNA
3. tRNA @ P site→carries growing polypeptide chain
4. tRNA @ A site→carries amino acids
5. Ribosome catalyzes P site chain to A site amino acid
6. Ribosome shifts re…
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Silent Mutation
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does not change the sequence of a protein or how a protein is regulated.
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Harmful
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change the sequence of a protein
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Sickle-Cell Anemia
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-mutation of beta chain of hemoglobin
-hemoglobin contains 4 subunits (2 alpha and 2 beta chains)
-Sickle-cell is a recessive genetic disease that inherits 2 copies of beta-linked sickle cell chains.
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Nucleotide
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contains nitrogen base, pentose sugar, and phosphate
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Nucleoside
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contain nitrogen base and pentose sugar. No phosphate.
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Phosphodiester
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chemical grouping that contains two alcohols esterified to one molecule of phosphoric acid, which serves as a bridge.
- 3' OH and 5' carbon
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Polypeptide
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long chain of amino acids
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Methylation
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-modification of a nucleotide that is critical for accurate DNA replication
-In bacteria→protects DNA from degradative enzymes
-In Eukaryotes→activates and silences gene expression.
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Peptide Bond
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substituted amide linkages between the alpha-amino group of one amino acid and the alpha-carboxyl group of another.
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Calmodulin
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Ca²⁺ binding protein
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Dicer
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Enzyme that cleaves double stranded DNA
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Hemoglobin
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Oxygen carrier in RBCs
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Phosphorylation of Proteins
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-modified post-synthetically
-OH of serine is frequently phosphorylated.
-modifications alter the behaviors of proteins containing the altered residue.
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Covalent Bond
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when 2 atoms share a pair of electrons between positively charged nuclei
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Ionic Bond
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complete transfer of one or more electrons from one atom to another
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Resonance
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multiple structures that alternate between single and double bonds.
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Polar Covalent
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has a dipole moment with a difference in electronegativities
example: water
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Nonpolar Covalent
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no dipole moment with balanced electronegativities
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Van der Waals
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-weak interaction due to changing polarization
-van der Waals radius is the optimal distance of attraction.
-examples include binding pockets of antibodies and antigens and are what allow Geckos to climb vertical surfaces.
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Hydrophobic Interaction
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-association of nonpolar groups with each other in aqueous systems, driven by tendency of the surrounding water molecules to seek most stable (disordered) state.
-stabilize protein structures of DNA
-examples include hemoglobin and stabilizing stacking of adjacent base pairs in DNA.
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Hydrogen Bonds
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1. Hydrogen is bonded to strong electronegative atom
2. Electronegative atom attracts electronegative cloud around the hydrogen atom, which causes the hydrogen to be partially positive.
3. Hydrogen bonds cause DNA to have alpha-helix shape.
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Primary Structure
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-sequence of amino acids that makes up the polypeptide chain.
-typically 1° structures involve 100-1,000 amino acids.
-contain the instructions for folding.
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Nonpolar Aliphatic Amino Acids
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-have hydrocarbon chains as R groups.
-hydrophobic interactions
-Glycine allows for conformational flexibility
-Proline is very rigid.
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Polar Uncharged Amino Acids
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-contain hydroxyl groups, thiol groups, and amide groups.
-can H-bond to water or other R groups
-2 cysteins can form disulfide bonds
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Polar Charged Amino Acids
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-either a negatively charged R group or positively charged R group.
-all can form H bonds
-can form ionic interactions
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Nonpolar Aromatic Amino Acids
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-have aromatic rings
-are hydrophobic.
-Tyrosine and Tryptophan can H bond. Phenylalanine can NOT.
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Peptide Bonds
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-can present in cis or trans isomers, with the trans isomer the favorite.
-is a linkage between amino acids.
-has resonance→partial double bond character adds rigidity.
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Disulfide Bonds
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-1° structure
-Bond between thiol groups of cysteines in close proximity
-Can contribute to the stability of the protein .
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Secondary Protein Structure
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-regularly repeating, hydrogen bonding structures within a polypeptide chain.
-main types are alpha helix and beta sheet
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Alpha Helix Structure
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-R groups stick out
-Right handed spiral
-H- bonds point in the same direction (electric dipole) with partial positive on N terminus and partial negative on the C terminus.
-Diameter is 12 A
-Proteins interact with major groove.
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Residues Found in Alpha Helix
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Tyrosine, Proline, and Glycine are less common in alpha helix.
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Beta Sheet Structure
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-consists of 2 or more beta subunits
-Anti parallel→strands are opposite
-Parallel→strands are in the same direction
-H bonding occurs in both
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Adjacent Beta Strands Structure
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-separation between R groups allows for conformations with large R groups that form beta barrels.
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Tertiary Protein Structure
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-3D orientation of all 2° structures within a single polypeptide chain.
-Myoglobin is an example.
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Domains
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Independently folding units within a polypeptide chain.
-Each domain has a separate function.
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Myoglobin
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3° protein with 1 domain
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DNA Polymerase I Klenow Fragment
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3° protein with 4 domains.
3rd domain used for synthesis
4th domain used for proof reading.
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Supersecondary Structure
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-building blocks of domains
-stable and common arrangements of 2° structure elements.
-Examples: antiparallel beta sheet, beta barrel, alpha/beta barrel, and helix-turn-helix
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Quaternary Structure
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-Need 2 or more polypeptide chains that join to form the final 3D functional protein subunit.
-Not found in all proteins
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Homodimer
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quaternary protein with the same subunits.
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Heterodimer
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quaternary protein with different subunits.
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How Was Protein Folding Discovered?
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1. Extracted pure ribonuclease
2. Denatured in test tube from 3°→1°
3. Removed chemical that denatured and allowed protein to refold
4. Denatured ribonuclease returned to 3° protein.
This was lucky, does not happen in all proteins.
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Chaperones
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Help other proteins fold.
Example: HsP70 Family
1. Binds to the hydrophobic regions of the unfolded protein.
2. Continues the cycle for multiple rounds until a native protein is attained.
3. If native conformation is not attained, it is sent to the Gro EL/ES system.
USES ATP!
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Chaperonins
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Gro EL/ES system creates a "caged" microenvironment that allows protein to fold properly.
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Isomerases
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-Enzymes that catalyze structural rearrangement
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Protein Disulfide Isomerase
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helps correct disulfide bonds to form
-breaks incorrect bonds and forms correct bonds.
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Peptide Prolyl Cis-Trans Isomerase
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-converts between proline isomers
-convert to less common cis form for tight turns in secondary structures.
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Predicting Protein Folding
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-Though all the info for folding is in the 1° structure, we can't predict protein folding yet, though computers can help.
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Column Chromatography
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helps isolate specific proteins to be studied
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Ion-Exchange Resin Column Chromatography
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separates proteins based on charge
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Gel-Exclusion Resin Column Chromatography
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separates proteins based on size via holes
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Affinity Resin Column Chromatography
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separates proteins via a ligand
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Ways of Determining 3D Shape of Proteins
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Complex techniques
1. X Ray crystallography
2. NMR
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Protein Binding to a Ligand
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-reversible
-structural and/or regulatory function
-DNA compaction
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Motor Proteins
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proteins that use energy to generate forces for movement along DNA strands
-separate DNA strands
-polymerases
-topoisomerases
Combine ligand binding and catalysis
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Ligand
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molecule that binds to the binding site
-can have more than 1 binding site with different ligands
-Ligand=DNA or RNA
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Induced Fit Theory of Proteins
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-protein changes shape via conformational change for ligand binding
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DNA Binding Proteins
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-Does not alter the covalent structure of DNA
-involved in protecting, regulating, and organizing DNA
-2 types: nonspecific and specific
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Nonspecific DNA Binding Proteins
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-bind to the DNA independently of the DNA sequence
-Example: SSB (Single Stranded DNA Binding Protein)
a. tetramer that binds and protects single stranded DNA
b. SSB is nonspecific and likes to bind to DNA
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Specific DNA Binding Proteins
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-recognizes specific sequences
- affinity for sequences 10⁴-10⁶ times more than random sequences
-proteins recognize surface features in the major groove.
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E. Coli and the Lac Repressor
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-Specific DNA binding protein
-Initially, binds to DNA via non specific binding site
-Moves along DNA until it finds a specific binding site.
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Enzymes
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-proteins that build nucleic acids
-have specific jobs
-Active site→location where substrate binds.
-Catalysis often requires conformation changes in the protein/enzyme
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Cofactor
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Inorganic ion or coenzyme required for enzyme activity
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Coenzyme
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Organic cofactor required for the action of certain enzymes
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Holoenzyme
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Catalytically active enzyme
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Apoenzyme
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Protein portion of an enzyme, exclusive of cofactors that might be required for catalytic activity.
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DNA Polymerase
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Enzyme that catalyzes phosphodiester bond formation
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Helicases
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-Examples of motor proteins that separate paired strands of nucleic acids (unwinding)
-spinds and unwinds DNA
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Translocases
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-Examples of motor proteins that move along double stranded DNA without separating strands.
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Allosteric Enzymes
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A regulatory enzyme with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site.
-Modulator binds to regulatory site to induce a conformational change so that the substrate can bind to the catalytic site.
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Autoinhibition
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the reduction or elimination of a molecule's activity by one of its own segments or domains.
-enzyme is available, but generally not active.
-To activate, need a conformation change
a. self assembles into oligomers
b. binding of another protein or ligand
Example: Autoinhibited RIG…
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Reversible Covalent Modification
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the addition, dissociation, or rearrangement of an atom or functional group covalently bonded in a molecule.
-Example: phosphorylation
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Proteolytic Cleavage
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enzyme-catalyzed breakage of peptide bonds in proteins (IRREVERSIBLE)
-Inactive protein protein (precursor) is cut free by a protease to form the active protein.
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ATP (Nucleoside Triphosphate)
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building blocks of RNA and DNA
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Purines
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9 membered rings that include adenine and guanine
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Pyrimidines
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6 membered rings that include cytosine, thymine, and uracil.
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Sugar Puckering
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In nucleotides, sugars are in a closed, 5 member ring form that is not planar. It has 4 possible conformations.
a. C-2' Endo→favorited in DNA
b. C-2' Exo
c. C-3' Endo→favorited in RNA
d. C-3' Exo
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BIOL 4843: EXAM 2