Biochemistry Exam 2
How many H-bonds are there between A and T? G and C?
-2 hydrogen bonds between A & T. - 3 hydrogen bonds between G & C
Directionality of DNA/RNA backbone.
-5' end is different from 3' end -We read the sequence from 5' to 3'
What is complementarity of DNA strands? Be able to draw complementary sequences of the given ones obeying Watson-Crick base-pairing rule and 5'-3' directionality.
-A forms base-pair with T -G forms base-pair with C -2 H-bonds between A and T -3 H-bonds between G and C -Having sequence of one strand allows unambiguous re creation of the second complimentary strand -Two strands are antiparallel
Define the following words: Apoenzyme, coenzyme, holoenzyme, & prosthetic group.
-Apoenzyme: an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor -Coenzyme: a complex organic or metalloorganic molecule; Most are derived from vitamins -Holoenzyme: ApoEnzyme + Cofactor; the enzyme is complete and catalytically active -Prosthetic group:A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein
What happens to enzymes at high and low temperatures? pH?
-At high temperatures the enzyme gets denatured. -At low temperatures the enzyme becomes inactive
What factors affect DNA denaturation?
-Base composition of DNA: the more hydrogen bonds that need to be broken the higher the temperature will be for the DNA to be denatured (high GC-content increases Tm, or melting pt.) -Length of DNA fragment: ~Longer DNA has higher Tm ~Larger effect for shorter DNA fragments -pH and ionic strength: High salt concentration increases Tm
What happens to the UV absorbance by DNA upon denaturation? What is hyperchromic effect?
-Based on hyperchromic effect: the material's increasing ability to absorb light. The Hypochromic Effect describes the decrease in the absorbance of ultraviolet light in a double stranded DNA compared to its single stranded counterpart. -UV absorbance increases upon separation of DNA strands
What are fatty acids? What are the two main types of fatty acids that are present in living organisms (saturated vs. unsaturated)? What type are the double bonds in the unsaturated fatty acids.
-Carboxylic acids w/ hydrocarbon chains containing between 4 to 36 carbons -Almost all have an even # of carbons -Most are unbranched -Saturated: 0 double bonds between carbons in the alkyl chain -Monounsaturated: 1 double bond between carbons in the alkyl chain -Polyunsaturated: more than one double bond in the alkyl chain -most double bonds aren't conjugated (no Methylene group to separate) -Most double bonds are cis
What is the standard nomenclature of fatty acids? What does 18:1(delta9) mean? Be able to draw the structural formula given the standard name. Be able to name the fatty acid based off of a given structure.
-Chain length and the number of double bonds are separated by a colon -Positions of double bonds are specified relative to carboxyl carbon (numbered 1) by superscript numbers following ∆ 18:1(delta9): 18 carbons, 1 double bond at Carbon 9
How many strands are usually in DNA? In RNA?
-DNA: double-stranded -RNA: single-stranded
What is denaturation of DNA? What is the reverse process?
-Denaturation is the unraveling of the two complementary strands -Denaturation may be reversible: annealing
What happens with the activation energy during enzyme-catalyzed reaction?
-Enzymes increase reaction rates (k) by decreasing activation energy ΔG‡ -Slow reactions are characterized by high activation energy (ΔG‡) that must be surmounted during the reaction
Why it is harder to melt DNA with higher GC-content?
-It increases the melting point because GC have 3 hydrogen bonds between them, which takes more energy or higher temps. to break all those bonds.
Define the following: Michaelis constant Km, turnover number kcat, initial reaction velocity Vo, maximum reaction velocity Vmax
-Km: Michaelis constant (concentration of the substrate at which velocity is 50% of the maximum) - an approximate measure of substrate's affinity for enzyme (only when k2<<k-1) -kcat or turnover number: how many substrate molecules can one enzyme molecule convert per second when the enzyme is saturated w/substrate -Vmax: maximum velocity of the reaction; the fastest speed that the reaction can theoretically occur -Initial velocity (V0) = Tangent to each curve taken at time 0
Biological roles & composition of structural lipids.
-Lipids that do not contain fatty acids: cholesterol, terpenes, etc. -Lipids that contain fatty acids (complex lipids), can be further separated into: -Storage lipids -Membrane lipids (Structural lipids) -Double layer of lipids: central feature of most biomembranes -amphipathic: 1 end is hydrophobic (non-polar tails) & the other is hydrophilic (polar head) -Variability comes from: Various backbones, Various fatty acids that can be attached, Various head groups
What are the biological roles and composition of lipids?
-Membrane structure and integrity: Predominant structural components of all cellular membranes -Storage of energy: Reduced compounds have lots of available energy, Hydrophobic nature allows good packing -Insulation from environment (thermal and mechanical): Low thermal conductivity, High heat capacity (can "absorb" heat), & Mechanical protection (can absorb shocks) -Water repellant: Hydrophobic nature keeps surface of the organism dry, Prevents excessive wetting (birds), & Prevents loss of water via evaporation -Buoyancy control and acoustics in marine mammals: Increased density while diving deep helps sinking (just a hypothesis) & Spermaceti organ may focus sound energy: sound stun gun? -Enzyme cofactors: Coenzyme Q is for ATP synthesis in mitochondria and Vitamin K allows blood clot formation -Antioxidants: Vitamins E and K -Pigments: Color of tomatoes, carrots, pumpkins, & some birds -Signalling molecules: Steroid hormones (act body-wide), Paracrine hormones (act locally), Hormone precursors (Vitamins A and D), & Growth factors
What are the main types of RNA in living organisms?
-Messenger RNA or mRNA: carries genetic info from the storage place (nucleus) to the ribosome where proteins are being synthesized -Transfer RNA or tRNA: adaptor molecules which bring amino acids into the ribosome -Ribosomal RNA or rRNA: main part of the ribosome which synthesize all proteins -Micro RNAs or miRNA: for some regulatory function has been documented, for the majority - no -Small inhibitory RNAs or siRNA: gene regulation
What are the advantages of the enzymes over inorganic catalysts?
-Milder reaction conditions (cell environment: 37˚C, pH~7.0) -Higher reaction rates (in a biologically useful timeframe) -Capacity for regulation (control of biological pathways) -Greater reaction specificity (no side products)
What are the three main classes of carbohydrates?
-Monosaccharide: one unit only (simple sugars) -Oligosaccharide (mostly Disaccharides) short chains of monosaccharide units joined by glycosidic bonds -Polysaccharides: more than 20 monosaccharide units
What components are nucleotides made of?
-Pentose Sugar: ribose or deoxyribose -Nitrogenous base: Adenine, Thymine, Cytosine, Guanine, Uracil -Phosphate group: mono-, di-, or triphosphate
Triacylglycerols as the main storage form of fatty acids. Which tryacylglycerols are called oils and which ones are called fats?
-Simplest lipids constructed from fatty acids -Result of esterification of glycerol with three fatty acids molecules -Unlike fatty acids they are non-polar Less soluble in water than fatty acids due to the lack of charged carboxylate group -Solid triacylglycerols are called fats -Liquid triacylglycerols are called oils
What are diastereomers? Examples? (e.g. mannose and galactose)
-Stereoisomers that aren't mirror images of each other -differ at one chiral center, and same molecular formulas -different physical properties
What are the factors that can affect activity of enzymes?
-Temperature -pH -Ionic strength -Presence of cofactors & prosthetic groups
What are enzymes?
-They are biological catalysts (i.e. they increase reaction rates w/o being used up). -They are proteins:Some RNA molecules (ribozymes) can also catalyze chemical reactions -Enzymes can use cofactors: Metal ions, Coenzymes (derived from vitamins), & Prosthetic group (coenzyme that is covalently attached)
What happens to reaction velocity at [S]>>Km? At [S]<<Km? At [S]=Km?
-[S] >> Km, V0 = Vmax: velocity does NOT depend on [S] -[S] << Km, V0 = Vmax[S]/Km: linear dependency -[S] = Km, V0 = 0.5Vmax
What are the mechanisms of Chymotrypsin and Transpeptidase? What is nucleophilic attack? What is the nucleophile in the reaction and what is the leaving group? What is the most important catalytic residue in chymotripsin which gives name to the whole class of proteases?
1) Substrate Binding 2) Nucleophilic Attack: Ser195 (most important catalytic residue) & His 57 generate an alkoxide ion (nucleophile) on Ser 195, which attacks the peptide carbonyl on the substrate. The carbonyl becomes negatively charged that is short lived because its stabilized by h-bonding in the oxyanion hole. 3) Substrate Cleavage: An amino leaving group leaves due to the negatively charged carbonyl collapsing back into a double bond, displacing the amino group which is protonated by His 57. 4) Water comes in 5) Water attacks 6) Break off from the enzyme 7) Product Dissociates
What are Watson-Crick base pairs?
AT/GC
What makes DNA more stable under physiological conditions compared to RNA?
Ability to hydrogen bond. Hydrolsis accelerated by enzymes DNAses
Describe the 4 main types of catalytic mechanisms: acid-base catalysis, covalent catalysis, metal-ion catalysis, and electrostatic catalysis
Acid-base catalysis: give and take protons Covalent catalysis: a transient covalent bond btwn enzyme & substrate that changes reaction paths; requires a nucleophile on the enzyme (can be a reactive serine, thiolate, amine, or carboxylate) Metal ion catalysis: use redox cofactors, pKa shifters; involves a metal ion bound to the enzyme, interacts w/substrate to facilitate binding, & participates in oxidation reactions Electrostatic catalysis: preferential interactions with TS
What are aldoses and ketoses
Aldose: carbohydrate with an aldehyde functional group Ketose: carbohydrate with a ketone
CHAPTER 10: LIPIDS
CHAPTER 10: LIPIDS
CHAPTER 6: ENZYMES
CHAPTER 6: ENZYMES
CHAPTER 7: CARBOHYDRATES
CHAPTER 7: CARBOHYDRATES
CHAPTER 8: NUCLEOTIDES AND NUCLEIC ACIDS
CHAPTER 8: NUCLEOTIDES AND NUCLEIC ACIDS
What happens with Km and Vmax upon inhibition by each of the above inhibitors?
Competitive: Mixed: Apparent decrease in Vmax, Apparent change in Km, Lineweaver-Burk Plot lines intersect left from the Y-axis Uncompetititive: do not change Km
Types of reversible enzyme inhibitors: competitive, uncompetitive and mixed inhibitors.
Competitive: inhibit substrate binding but do not affect catalysis -Bind to the active site -Compete with the substrate for binding -Inhibit binding of the substrate -Do not affect catalytic function ~Changes in kinetic parameters -No change in Vmax -Apparent increase in Km (decrease in specificity) -Lineweaver-Burk Plot: lines intersect at Y-axis Mixed: inhibit substrate binding and inhibit catalytic function. -Bind to enzyme with or without bound substrate -Bind to regulatory site -Inhibit substrate binding -Inhibit catalytic function ~Changes in kinetic parameters -Apparent decrease in Vmax -Apparent change in Km -Lineweaver-Burk Plot: lines intersect left from the Y-axis Non-competitive: do not affect substrate binding, but inhibit catalytic function -Bind only to ES complex -Do not bind to the active site of the enzyme -Do not affect substrate binding -Inhibit catalytic function ~Changes in kinetic parameters Apparent decrease in Vmax Apparent decrease in Km No change in Km/Vmax Lineweaver-Burk Plot: lines are parallel
Structural formula of glyceraldehyde (monosaccharide)
D form, and is the only aldotriose
D- and L-stereoisomers of monosaccharides. Which of the two types are the predominant in living organisms?
D stereoisomers are the most common
What can cause DNA denaturation?
Denaturation can be induced by high temperature, or change in pH
What are the ways to lower the activation energy in chemical reactions?
Enzyme uses the binding energy of substrates to organize the reactants to a fairly rigid ES complex -Entropy cost is paid during binding -Rigid reactant complex transition state conversion is entropically OK
How do enzymes work? Define the following: Substrate, product, enzyme's active site, activation energy, transition state.
Enzymes act by binding substrates into their active sites. -Substrate: Molecule acted upon by an enzyme -Active site: Pocket on enzyme where reactions occur -General enzymatic reaction: E + S <-> ES <-> EP <-> E + P -Enzymes increase reaction rate by lowering activation energy
Is the chemical equilibrium affected during enzyme-catalyzed reaction?
Enzymes do not affect equilibrium (ΔG)
What happens with the rates of forward and reverse reactions during enzyme catalysis?
Enzymes equally increase reaction rates of both forward and reverse reactions
Conformations of fatty acids: straight vs. kinked conformation. What causes kinked conformation in the fatty acid?
Fatty acids become kinked due to presence of cis double bonds.
Structural formula of fructose (monosaccharide)
Fructose is the ketose form of glucose
What are furanose and pyranose forms of monosaccharides?
Furanose: 5 membered oxygen containing ring Pyranose: 6-membered oxygen containing ring
Structural formula of galactose (monosaccharide)
Galactose is an epimer of glucose at C4-atom
What are reducing sugars? Which chemical group(s) in monosaccharide make them reducing?
Glucose -An aldehyde group makes a sugar a reducing sugar
What are glycerophopholipids? What components are they composed of? How many fatty acids are typical in glycerophospholipids? Are these fatty acids saturated or unsaturated? What are head groups? Are they charged or not? Are they polar or not?
Glycerophopholipids are: Primary constituents of cell membranes and are derivatives of L glycerol-3-phosphate They are made of: 2 fatty acids that are attached to L-glycerol-3-phosphate via ester linkages with hydroxyls on 1st and 2nd carbons (diacylglycerol) Typically: unsaturated fatty acids are connected to Carbon 2 Head groups: Highly polar phosphate group may be further esterified by an alcohol - such substituent groups
What are enzyme inhibitors?
Inhibitors are compounds that decrease enzyme's activity
What is initial velocity of the enzyme-catalyzed reaction?
Initial velocity (V0) = Tangent to each curve taken at time 0
What are reversible and irreversible enzyme inhibitors?
Irreversible inhibitors: -Chemically react with the enzyme -Cause irreversible inactivation of the enzyme -Destroy functional group in the active site -One inhibitor molecule can permanently shut off one enzyme molecule -Usually powerful toxins -Could be used as drugs Reversible inhibitors: -Bind to and can dissociate from the enzyme -Structurally similar to substrates or products -Could be used as drugs to slow down particular enzyme
Structural formula of dihydroxyacetone (monosaccharide)
Is the only ketotirose
Why is lactose a reducing sugar, while sucrose is not?
Lactose does not have a hemiacetal group.
Structural formula of mannose (monosaccharide)
Mannose is an epimer of glucose at C2-atom
What happens with the melting points of fatty acids as the number of double bonds in them increases (assumin that the number of carbons is the same)?
Melting point decreases. -It takes less thermal energy to disrupt disordered packing of unsaturated fatty acids. Thus, Unsaturated fatty acids have a lower melting point
What are the cofactors that can help enzymes catalyze their reactions?
Metal ions, coenzymes, and prosthetic groups.
What are epimers? Examples? (e.g. glucose and galactose)
Monosaccharides that differ only in the configuration around one Carbon atom
What are the functions on nucleotides in biological systems?
Nucleotide functions: -Energy for metabolism (ATP) -Enzyme cofactors (NAD+) -Signal transduction (cAMP) -Building blocks for nucleic acids Nucleic acid functions: -Storage of genetic information (DNA) -Transmission of genetic information (mRNA) -Processing of genetic information (ribozymes) -Protein synthesis (tRNA and rRNA)
What's the difference between nucleoside and nucleobase?
Nucloeside is just the nitrogenous base and and the pentose sugar. -Nucleobase: either purine or pyrimidine; Nitrogen containing heteroaromatic molecules --Planar or almost planar structures --Absorb UV light around 250-270 nm
What is backbone of nucleic acid? What nucleotide components it is made of?
Phosphates + Sugars = Backbone -DNA: A & T, G & C -RNA: A & U, G & C
What are phosphodiester bonds?
Phosphodiester bonds link successive nucleotides in linear polymers - nucleic acids (2 types): DNA - deoxyribose RNA - ribose
What is Chargaff's rule?
Purines pair with pyrimidines: A pairs with T/U - 2 H-bonds G pairs with C - 3 H-bonds
Two main types of nucleobases: purines and pyrimidines. What are the most common nucleobases from each class?
Purines: Adenine & Guanine Pyrimidines: Cytosine, Uracil, & Thymine Both Are: -Good H-bond donors and acceptors -Neutral molecules at pH 7.0
What is in common and what is different between DNA and RNA?
Similarities: Differences: -Contains ribose sugar instead of deoxyribose -Contains uracil bases instead of thymine -More complex structures -Mostly single stranded RNA
What factors affect solubility and melting points of fatty acids?
Solubility in water (typically poor): -Decreases as the chain length increases -Increases as the number of double bonds increases Melting Point: -Unsaturated fatty acids of the same lengths are oily liquids -Decreases as the chain length decreases -Decreases as the number of double bonds increases
What's the difference between storage and structural polysaccharides
Starch (energy storage in plants): 2 homopolysaccharides of glucose-amylose (long & unbranched α1-->4 linked) & amylopectin (branched at α1-->6 every 24-30) Glycogen (energy storage in animal liver & muscles): homopolysaccharide of glucose Cellulose: linear homopolymer of glucose; most abundant polysaccharide in nature Chitin (component in exoskeletons): linear homopolymer
What are lipids?
Structurally diverse class of organic molecules that are characterized by: -Low solubility in water -Good solubility in nonpolar solvents -Are relatively hydrophobic
Cyclization of monosaccharides: What is anomeric carbon? What are the α- and β-configurations of the anomeric carbon?
The carbon that is now a new chiral center that was involved in the carbonyl bond.
What feature determines whether a disaccharide is reducing or not?
The presence of a hemiacetal group. A hemiacetal is formed when an alcohol attacks an aldehyde. -The second monomer with the hemiacetal group is reducing. -Anomeric carbon (has the acetal) involved in the glycosidic linkage is non-reducing
Structural formula of ribose (monosaccharide)
The standard five-carbon sugar
Structural formula of glucose (monosaccharide)
The standard six-carbon sugar
What are trioses, tetroses, pentoses and hexoses?
Triose: 3 Carbons in carbohydrate backbone Tetrose: 4 Carbons in carbohydrate Pentose: 5 Carbons in carbohydrate Hexose: 6 Carbons in carbohydrate
What is a glycosidic bond? What groups and atoms from monosaccharides are involved in glycosidic bond formation?
Two monosaccharides joined together by an O-bond. They form when the anomeric carbon of one monosaccharide reacts with the carbon carrying a hydroxyl group from the the second monosaccharide.
What are the main features of DNA double helix.
Two strands are wound around the same axis, backbone is outside, nucleobases are inside, nucleobases from one strand base pair with nucleobases from the other one based on Chargaff's rule, two strands are antiparallel.
What are the 2 forms of the Michaelis-Menten equation? How are they interpreted?
V=Vmax*[S]/(Km+[S]) and V=kcat*[Etot]*[S]/(Km+[S]) in which Vmax is expressed as Vmax= kcat*[Etot]
What is maximum velocity of the enzyme-catalyzed reaction?
Vmax is the maximum velocity of the reaction. -A point is reached beyond which increases in V0 are vanishingly small as [S] increases. This plateau-like V0 region is close to the maximum velocity, Vmax.
Role of binding energy in catalysis?
Weak binding interactions between the enzyme and the substrate provide a substantial driving force for enzymatic catalysis. Prominent physical & thermodynamic factors contributing to activation energy: -Entropy (freedom of motion) of molecules in solution. -Solvation (H bonded water molecules surrounding substrate) -Distortion of substrate molecules -Proper alignment -Binding energy can be used to overcome all these but it is only one of several contributors to the overall catalytic mechanism
Structural formula of sucrose (disaccharide). What type of linkage does it have?
glycosidic bond (α 1-->4)
What's the nomenclature of nucleotides and nucleosides?
one-letter and three-letter codes for ribo and deoxyribo-nucleotides Adenine: -RNA: A, AMP, Adenylate (nucleotide), Adenosine (nucleoside) -DNA: A, dA, dAMP, Deoxyadenylate (nucleotide), Deoxyadenosine (nucleoside) Guanine: -RNA: G, GMP, Guanylate, Guanosine -DNA: G, dG dGMP, Deoxyguanylate, Deoxyguanosine Uracil: U, UMP, Uridylate, Uridine (nucleoside) Cytosine: -RNA: C, CMP, cytidylate, cytidine -DNA: C,dC, dCMP, deoxycytidylate , deoxycytidine Thymine: T, dT, dTMP, deoxythymidylate, deoxythymidine
What is the objective of study of kinetics?
study the rate at which compounds react and how different factions affect enzymatic reactions.
What are carbohydrates? What's their composition? What are their biological roles?
they are polyhydroxy aldehydes or ketones, or substances that yield such compounds upon hydrolysis. -Have empirical formula (CH2O)2 -produced from CO2 and H2O during photosynthesis Functions: -energy storage & energy source -structural component of cell walls in plants & bacteria & exoskeletons of arthropods
Interconversion of α- and β-anomers in aqueous solutions
α-configuration: when the hydroxyl group on the anomeric carbon is trans to the CH2OH group. β-configuration: when the hydroxyl group on the anomeric carbon is cis to the CH2OH group.
