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161 Cards in this Set
- Front
- Back
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The three main branches of biochemistry are:
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structural biochemistry, metabolism, and molecular genetics
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The most abundant elements are...
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C, H, O, N, P, and Ca, K, S, Cl, and Na
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The four major classes of small molecules are:
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amino acids, monosaccharides, lipids, and nucleotides
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Compounds that have the same kinds and numbers of atoms but have different molecular arrangements are...
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stereoisomers
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Amino acids found in nature are generally in the...
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L-stereoisomer
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Building blocks of proteins
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amino acids
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Amino acids have important roles in...
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energy metabolism and cellular signaling
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Molecules found in sugars and starches that make up parts of nucleotides, and are present in some components of all cell membranes
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carbohydrates
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Characterized by limited solubility in water, and are essential components of membranes and important energy stores
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lipids
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Contain a carbohydrate component joined to one of four bases that make up the energy currency of the cell and form genetic information of the cell
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nucleotides
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Assembling polymer and producing monomers requires...
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energy for living, growing, and reproduction
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Energy cannot be...
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created or destroyed
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The heat content of a system is...
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enthalpy
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The measure of disorder of a system is...
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entropy
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In a spontaneous reaction, free energy...
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decreases
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The energy that can be converted to work
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free energy
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Free energy=
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enthalpy - temperature x entropy
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Free energy is positive for...
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nonspontaneous reactions
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Free energy is negative for...
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spontaneous reactions
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Cells are used for...
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compartmentalization, membrane selectivity, protective environment, concentrating components
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How do we know the age of the earth?
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Zircon crystals and uranium content
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The human body is about ____ water
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60%
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Bond strength of water
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Ionic>hydrogen>van der Waals
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Hydrogen bonds are strong enough to be useful in...
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DNA double stranding
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Aggregation to minimize the decrease in entropy is...
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hydrophobic effect
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Contain both polar and nonpolar groups
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amphiphilic molecules
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Kw of water is small, so there is low...
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amount of ionization
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Concentration of hydrogen in water is...
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1.0x10-7M
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At equilibrium, pH of water=
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-log (1.0x10-7) = 7
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Proton donor
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acid
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Proton acceptor
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base
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pK is equivalent to...
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the pH at which an acid and its conjugate base are in equal concentration
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A strong acid or base is one that...
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completely dissociates in water
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The stronger the acid...
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the greater the tendency to lose that protein
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Henderson-Hasselbalch equation
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pH=pKa + log [A-]/[HA]
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The pK values of weak acids are determined by...
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titration
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The pKa of carboxyl groups is about...
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4
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The pKa of amines is about...
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10
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Solutions that prevent changes in pH when bases or acids are added
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buffers
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Buffers consist of...
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weak acid and conjugate base
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Buffers work best at a pH of...
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+1 from pKa
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An example of a natural buffer system is...
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blood plasma-CO2-carbonic acid-bicarbonate buffer system; if the pH falls, increase in carbonic acid
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DNA polymerase uses...
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dNTPs to fill in single stranded DNA to make double stranded DNA
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Replication is carried out by...
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DNA polymerase
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Transcription is carried out by...
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RNA polymerase
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Translation is carried out by...
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ribosomes and tRNA
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Beer's law
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A=ECl
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UV absorbance can measure DNA concentration by...
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measuring the absorbance at 260nm and calculation the concentration using Beer's Law
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DNA sequencing uses...
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DNA polymerase, dNTPs, and ddNTPs
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ddNTPs cause...
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polymerization to stop
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DNA sequencing occurs by...
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1. denaturing the strands
2. adding a short DNA primer 3. adding DNA polymerase, dNTP, and ddNTP 4. separating the strands 5. migrating the strands through electric field 6. detecting fluorescent color as DNA passes |
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The human genome consists of...
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3 million base pairs of DNA on 23 chromosome pairs; over 100,000 proteins
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E. coli have about...
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4.5 million base pairs on one chromosome; 4000 different proteins
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PCR is used to...
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make many copies of a sequence of DNA
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Polymerases used in PCR include...
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Taq polymerase and Pfu polymerase
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Proteins can be...
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catalysts, structural, used for storage and transport, mechanical, hormones, specialized functions
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Amino acids contain...
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amino group, carboxy group, and side chain
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At pH 7, amino acids are called...
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zwitterions
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At pH 7, the amino group of an amino acid is...
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protonated
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At pH 7, the carboxyl group of an amino acid is...
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ionized
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Aliphatic means...
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R groups consist of carbons and hydrogens
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Aliphatic amino acids
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1. glycine
2. alanine 3. valine 4. leucine 5. isoleucine 6. proline |
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Aromatic amino acids
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1. phenylalanine
2. tyrosine 3. tryptophan |
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Sulfur containing amino acids
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1. methionine
2. cysteine |
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Alcohol amino acids
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1. serine
2. threonine |
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Basic amino acids
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1. histidine
2. lysine 3. arginine |
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Acidic amino acids
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1. aspartate
2. glutamate 3. asparagine 3. glutamine |
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If pH>pKa...
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greater amount of the group is protonated
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If pH<pKa...
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greater ionization, so unprotonated
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Peptide bonds are formed by...
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condensation reactions
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Proteins can be...
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fibrous or globular
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Globular proteins have...
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mostly functional roles in the cell
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Fibrous proteins provide...
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mechanical and structural support
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Globular proteins are...
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soluble
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Fibrous proteins are...
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insoluble
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Linear sequence of amino acids
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primary structure
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Regular patterns formed by primary structure folding
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secondary structure
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Completely folded polypetide with one or more domains
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tertiary structure
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Association of multiple polypeptides
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quaternary structure
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3.6 amino acids
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pitch of alpha helix
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Globular proteins contain regions of...
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beta sheets
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Loops cause...
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directional change in polypeptide backbone
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Loops with about 5 amino acid residues are...
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turns
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Combinations of alpha helices, beta strands, and loops
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motifs
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Found in calcium-binding proteins
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helix-loop-helix
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Leucine zipper in transcription proteins
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coiled coil
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Composed of several independently folded compact units
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domains
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Techniques to analyze protein structures:
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X-ray crystallography and NMR
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X-ray crystallography
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pass X-rays through crystal and record positions and intensisites of scattered rays
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How does NMR work?
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1. a small volume of protein solution is placed in high magnetic field
2. structure calculated from frequencies of radio waves emitted |
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Proteins that assist with protein folding by binding to proteins before they are completely folded
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chaperones
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Major heat shock protein
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HSP70
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Chaperones usually bind to the...
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hydrophobic portions of a protein
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How is a recombinant protein formed?
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by inserting DNA that codes for human protein into E. coli
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Cut DNA at very specific sequences
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restriction enzymes
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Circular DNA that can be absorbed through bacteria
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plasmid
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Plasmids can be used to...
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introduce foreign DNA into bacteria
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How are plasmids formed?
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1. restriction enzymes cut DNA
2. added into plasmid 3. ligase covalently joins DNA |
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The heme group of myoglobin and hemoglobin is called...
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prosthetic group
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Heme consists of...
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protoporphyrin and iron atom
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The iron atom in the center of heme can form...
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6 bonds: 4 with nitrogens from protoporphyrin and 2 on either side of the plane
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The iron atom in heme can be in 2 states:
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ferrous (+2) or ferric (+3)
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Which state of the iron atom can bind oxygen?
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+2 (ferrous)
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Myoglobin is mostly composed of...
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alpha helices
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4 alpha helices in myoglobin are...
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terminated by proline residue
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In myoglobin, the heme group is located...
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in a crevice
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Iron atom in myoglobin is bound to...
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histidine in F8
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Binding of oxygen to heme in myoglobin must occur in...
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bent, end-on orientation
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Heme exposed to oxygen by itself...
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rapidly oxidizes to +3, which cannot bind oxygen
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Hemoglobin picks up oxygen in the...
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lungs and releases it to tissues that need it
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Hemoglobin has...
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4 peptide chains and 4 heme groups
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When one heme group is bound to oxygen, it increases the ability of other heme groups to bind oxygen
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cooperative binding
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Structural communication between 4 peptide chains of hemoglobin
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allostery
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Binding of oxygen in one subunit of hemoglobin triggers a conformational change that converts...
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T-state hemoglobin (low oxygen affinity) to R-state (high binding affinity)
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Carbon monoxide binds tightly to...
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hemoglobin at usual oxygen binding site
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Low pH in hemoglobin promotes...
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oxygen release from heme group
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BPG is a byproduct of...
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glucose metabolism
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BPG is found in...
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red blood cells
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BPG binds to...
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histidine on hemoglobin, lowering the affinity for oxygen, making the unloading of oxygen more efficient
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Fetal hemoglobin has different...
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gamma subunits
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Fetal hemoglobin binds BPG less well due to...
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fewer positive charges in BPG binding cavity
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Fetal hemoglobin has higher affinity for...
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oxygen
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A change from Glu to Val exposes...
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hydrophobic patch on hemoglobin, causing aggregation that changes shape of red blood cells
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Zeta chains are replaced by...
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alpha
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Epsilon chains are replaced with
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gamma, then beta
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Hemoglobin is different than myoglobin in that it...
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1. transports protons, CO2, and oxygen
2. is allosteric 3. cooperative binding 4. oxygen affinity is pH dependent 5. regulated by BPG |
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A decrease in pH does what to oxygen binding of hemoglobin?
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decreases
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Increase in CO2 causes...
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decrease in oxygen affinity
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Promotion of release of oxygen by increasing CO2
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Bohr effect
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Carbon dioxide is transported as ____ in red blood cells
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bicarbonate
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Carbamate forms...
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salt bridges that stabilize the T form to lower affinity
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Preparation of protein solution is done by...
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1. using centrifuge to separate into pellet and supernatant
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Fractionation
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1. ammonium sulfate interferes with noncovalent bonds between protein and other molecules
2. centrifuge to remove precipitated prtoein 3. resuspend in buffer 4. dialysis to change solvent |
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Chromatography
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1. beads or cellulose fibers to wash protein solution through column
2. eluate collected and assayed for protein |
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Ion-exchange chromatography
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separates based upon protein charge
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Gel filtration chromatography
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uses porous resin and separtes based upon proetin size
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Affinity chromatography
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attach ligand to matrix and greatly purifies
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Electrophoresis
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separates proteins based upon migration in electric field
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PAGE
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polyacrylamide gel electrophoresis: separates based on size and charge
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SDS-PAGE
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uses sodium dodecyl sulfate and 2-mercaptoethanol and separates based on size
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Edman degradation
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1. PITC reagent reacts with free N-terminus to form PTC-peptide
2. treat with trifluoroacetic acid and cleave last amino acid 3. analyze by chromatography 4. good for large small amino acid residues |
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If protein is greater than 50 amino acid residues, must use...
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proteases or chemical reagents to cleave bonds
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Cleaves to carboxyl side of lysine and arginine
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trypsin
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Cleaves at aromatic and bulk nonpolar side chains
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chymotrypsin
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Cleaves to carboxyl side of glutamate and aspartate
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Staphylococcus aureus V8 protease
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G-actin and F-actin are...
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microfilaments
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Microtubules act as...
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tracks for kinesin
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Microfilaments constantly...
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shrink and grow by adding or losing actin monomers from ends
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Microfilament length can be controlled by...
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capping proteins
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Newly formed actin filaments have...
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bound ATP
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Keratin is composed of...
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2 helices forming coiled-coil and 2 coiled-coils forming protofibril
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Protofibrils group to form...
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microfibril intermediate filament
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Many microfibrils forms a...
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macrofibril
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Macrofibrils in hair are held together by...
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hydrogen bonds and disulfide bonds between cysteins
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Perms reduce...
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disulfide bonds, changes the curl, and reforms disulfide bonds
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The most abundant protein in vertebrates
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collagen
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Collagen is present in...
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connective tissue, tendons, blood vessels, cornea
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Collagen is strengthened by...
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cross-linking of lysines and hydroxyproline, a modified amino acid with extra -OH
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Hydroxyproline is made by...
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post-translational modification requiring vitamin C
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Vitamin C deficiency can lead to...
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weakened collagen (scurvy)
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Defective gene of forming vitamin C is...
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pseudogene
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