Amino acids and proteins

icer215's version from 2016-08-24 03:56


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Watson and Crick are credited with discovering this dogma
central dogma molecular biology explains the flow of genetic information. DNA to RNA to Protein. DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes
ribosomes serve as factories in the cell where the information is ‘translated’ from a code into the functional product.
DNA and RNAare made up of nucleotides
Proteinsare made up of amino acids
ReplicationDNA copies itself
TranscriptionDNA can be copied into RNA
Translationthe information in RNA to synthesize a protein in a process
DNA-RNA-Proteinreplication-transcription-translation. linear polymers. this means that each individual unit, or monomer, is only attached to, at most, two other units
Reverse Transcription information flows backward from RNA to DNA
Reverse Transcriptaseis an enzyme that generates complementary DNA or cDNA from a RNA template. needed for the replication of retroviruses, including HIV
Retroviruses use the enzyme to reverse transcribe their RNA genomes back into DNA, which is then integrated into the host genome and replicated along with it.


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Noncoding RNA (ncRNA)a functional RNA molecule that skips this last step of being translated into a protein and can directly perform functions within the cell as a RNA molecule
Epigeneticsis the study of heritable changes in gene activity that are not caused by changes in DNA sequence. DNA sequence can be modified resulting in a different phenotype without changes to the underlying DNA sequence
Amino acids that have an amino group bonded directly to the alpha-carbon are referred to as alpha amino acids
alpha amino acid has a carbon atom, called an alpha carbon; bonded to a carboxylic acid; an amino; a hydrogen atom; and an R group that is unique for every amino acid.
Chirality refers to a molecule that has optical activity, so amino acids are optically active molecules. The only exception is glycine, the simplest amino acid
L and D amino acids are mirror images of each other and are non-superimposable on each other, just like our left and right hands.
L-Amino Acidssymbol indicates counterclockwise rotation of the plane. more commonly found in nature than D-amino acids. found in proteins, whereas D-amino acids cannot
D-Amino Acids symbol indicates clockwise rotation of the plane
Absolute configuration at the alpha positionR vs S, D vs L
R” symbol indicates right. R is assigned clockwise in decreasing priority when looking down the bond.
“S” symbol indicates left. S is assigned counterclockwise.
R and SThey are assigned by decreasing atomic number


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Amino acids as dipolar ionsLow pH, High pH, pH
Low pH cationic form
High pHanionic form
pH pI = zwitterion form (neutral)
Isoelectric point is the point along the pH scale where the amino acid has a net zero charge.
Alkylgly, ala, val, leu, ile, met, pro. non-polar and hydrophobic
Aromaticphe and trp. non-polar and hydrophobic
Neutraltyr, ser, thr, cys, gln, asn. polar and hydrophilic
Acidic glu and asp. polar and hydrophilic
Peptide bonds are covalent bonds formed by the nucleophilic addition-elimination reaction between the carboxylic group of one amino acid and the amino group of another amino acid. join amino acids together
Acidic amino acidthe R group contains a carboxylic acid. Loses protons, becomes negatively charged
Basic amino acidthe R group has an amine group (contains nitrogen). Binds protons, gaining positive charge
Sulfur linkagecysteine and cysteine


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Disulfide bonda covalent bond linking two thiol (—SH) groups. bond between cysteine is crucial in the formation of complex proteins such as insulin receptors
Peptide linkagepolypeptides and proteins
Peptide bonda covalent bond linking a carboxyl group with an amino group, releasing a water molecule as a byproduct
Polypeptide chaina series of amino acids linked by peptide bonds. The different ends of the polypeptide chain (N-terminus and C-terminus) cause polarity in the molecule
Hydrolysishydro+water and lysis= unbind.The addition of a water molecule will break the peptide bond, causing release of free energy.
Cysteineside chain with the thiol group
cystine2 cysteines forming a disulfide bond
PrimaryLinear amino acid sequences in the polypeptide chain liked by covalent bonds. Sequences are read from the N-terminus to the C-terminus
SecondaryLinked by hydrogen bonds. Alpha helix and Beta sheets
Alpha helixcoiled loosely in a clockwise direction, like a spring
Beta sheets (strand)folded in a way such that they lie anti-parallel to each other


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Tertiaryis folded into a final 3-D shape
Ionic interactionsbetween amino acids (e.g. lysine and aspartic acid)
Hydrogen bonds are present to hold nitrogen or oxygen atoms to hydrogen atoms
Van der Waals dispersion forces hold some amino acids with large hydrocarbon groups together.
ProlinePlays an important role in alpha helices of membrane proteins. Usually exposed at the surface of globular proteins, displaying hydrophobic spots. Induces a 30° kink for structural purposes
CystineForms disulfide bonds and Poor at hydrogen bonding
Hydrophobic bondingBonding occurs between non-polar molecules that usually form in the core of the protein and Allows folding of water soluble, globular proteins
Quaternaryproteins are formed by subunits, which are held by the same bonds that hold together tertiary structure proteins
ElectrophoresisA technique that separates and identifies different charged particles using the electric field
Different types of electrophoresisagarose gel and SDS-PAGE
Agarose gel electrophoresis a nontoxic technique that separates nucleic acids (DNA/RNA). The negatively-charged property of nucleic acids allows for movement towards the cathode (positive charge side). This method also allows for the identification of sizes of particles.


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SDS-Polyacrylamide gel electrophoresis separates proteins based on mass, not charge. SDS (sodium dodecyl sulfate) neutralizes the charges in the particles. The lighter the particle, the faster it moves through the gel.
examples of non-enzymatic proteins are receptors, ion channels, transport proteins, motor proteins and antibodies
Transport proteinsHigh concentration of transport proteins = high affinity for certain molecules. Low concentration = low affinity. Hemoglobin works as a crucial transport protein in a human body by delivering oxygen to muscle tissues
Immune systemAntibodies are part of the adaptive immune system. Their function is to find foreign antigens (e.g. viruses) and to target them for destruction
Motor proteins produce forces and allow for cellular motility
Myosin generates forces by contracting muscles
Kinesin is for intracellular transport
Dynein is for intracellular transport and provides motility of cilia
Catalystincreases the rates of chemical reactions by reducing the activation energy (Ea), but does not get consumed in the process
Acid/base catalysisenzymes act as an acid or a base. acid works as a proton donor and the base works as a hydroxide ion (proton acceptor). By transferring a proton or a hydroxide ion, chemical reactions can be catalyzed for faster effects.
Covalent catalysisthe formation of covalent bonds with an active site or with a cofactor reduces energy for transition reactions along the way. These bonds will be broken for the reuse of the enzyme for more chemical reactions.
Electrostatic catalysisthe formation of ionic bonds with intermediates stabilizes the transition states in chemical reactions


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Ionic bondscan be from partial ion charges or acidic or basic side chains from amino acids (e.g. glutamic acid) or cofactors (e.g. Zn)
OxidoreductasesOxidation Of A Hydrogen
TransferasesMove A Functional Group From A Donor Molecule To An Acceptor Molecule
HydrolasesCouple Breaking A Bond With Hydrolytic Cleavage
LyasesBreaking A Bond With Elimination To Form A Double Bond (or Ring) Or Adding To A Double Bond
IsomerasesAlter The Geometry Or Structure Of The Reactant Molecule
LigasesCouple Forming A Bond (joining Two Molecules) With Atp Hydrolysis
Enzymesreduce the activation energy (Ea) of a reaction.
Reduction of Eaincreases the rate of the reaction.
The idea of saturation kineticsis that as the concentration of substrate increases, so does the rate of reaction.
Enzymes do not effect theKeq, ΔG, and thermodynamics of a reaction
Enzymes do effectThe rate constant (k). Rate = k[A][B]. The kinetics of a reaction. Think saturation kinetics (mentioned earlier). The reserve reaction. Enzymes speeds up both reverse and forward reactions – thus no change in equilibrium.


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Substratesbind to an enzyme at the active site
Enzyme-substrate complexWhen these two bind together, they make up this
Two theoriesdescribing how enzymes and substrates interact.
Theory 1Enzyme Specificity (lock-and-key model) – Certain enzymes bind specifically to specific substrates.
Theory 2Induced Fit – Enzymes and substrates will conform to each others’ shapes in order to bind together.
High heat and extreme pH (either very high or very low)decrease reactions because these denature enzymes. Enzymes are proteins, and proteins denature in the presence of high heat or extreme pH.
Extreme pH and heat decreasethe reaction rate, a continually higher substrate concentration will continue to increase the reaction until up to a certain point but will not decrease the reaction rate.
Comparativelyan enzymes structural strength (ability to prevent denaturing) is better for withstanding high heat than it is for withstanding extreme pH.
Enzymes are proteinsWell, most of them are. A small portion of them consist of RNA.
CofactorsAn inorganic molecule or a metal ion that certain enzymes use to catalyze a reaction/process. e.g. Zn2+, Fe2+ (alcohol dehydrogenase), Fe3+, Cu2+, Cu+, K+, Mg2+
CoenzymesThe non-protein chemical component of enzymes. Many are derived from vitamins. Needed for catalysis. Act as an intermediate carrier of electrons or specific atoms or function groups that transfer for an overall reaction. e.g. NAD, CoA, NADP, FAD, thiamine, B12
Water-soluble vitaminsVitamin B (1, 2, 3, 6, 12). Found in meat, eggs, fish, milk, and fresh vegetables


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Vitamin CFound in fruits and vegetables. Essential in small quantities for the body
Enzyme kinematicsReaction rate (V, for velocity) is the amount of product formed per unit time (mole/s). It depends on the concentration of substrate (S) and enzyme.
Amount of substrate= rate V (is directly proportional). Double the amount of the substrate doubles the reaction rate. However, there is only so much substrate that every active site is continuously occupied and adding more substrate doesn’t increase the reaction rate. At this time, the enzyme is said to be “saturated”
Vmax= reaction rate when the enzyme is saturated
Km= Michaelis constant = substrate concentration at which the reaction velocity is half its maximum = Vmax/ 2. Km is unique for each enzyme-substrate pair and gives information on the affinity of the enzymes for its substrate.
Competitive InhibitionThis type of inhibitor will compete with the substrate. It blocks off the enzyme at the active site. bind to the enzyme, they can be overcome by increasing the amount of substrates (higher concentration of substrates give substrates a higher chance of binding to the enzyme)
The reaction’s maximum velocity(Vmax, also known as the maximum reaction rate) is unchanged by competitive inhibition.


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A competitive inhibitor can bindto a substrate OR an enzyme. However, it cannot bind to both at the same time for any give substrate-enzyme complex. Each competitive inhibitor resembles the substrate that it’s responsible for competing with.
Allosteric enzymesTwo binding sites: one for the substrate of the enzyme and the other for effectors, which modulate the enzyme activity. Upon the binding of an effector, the enzyme changes its conformation
Effectors bondnon-covalently at the allosteric site and interact with the enzyme reversibly
Homotropic allosteric enzymeacts as both the substrate for the enzyme and the effector of the enzyme’s activity, affecting the catalytic activities
Heterotropic allosteric enzymeacts only as the effector that regulates the enzyme’s activity. It does not act as the substrate.
Covalently-modified enzymesBoth the active and the inactive form of enzymes are covalently and structurally modified by other enzymes
Glycogen phosphorylase has two typesA, the active form, and B, the inactive form.
ZymogenInactive enzyme precursor. Upon hydrolysis or change of configuration of the active site, the enzyme becomes active. Lysosomes play an important role in cleaving the site to activate the enzyme. Secreted by the pancreas to prevent the digestion of proteins in the cells