Biochem Exam 2 review

• Enzymes are catalytically active biological macromolecules.
• Enzymes function as catalysts to speed up chemical reactions by lowering the activation energy.

Enzyme Components

• Cofactors are inorganic ions of a coenzyme that are required for enzyme activity.
• Coenzymes are organic molecules like heme groups, NAD, or FAD.
• Prosthetic groups are coenzymes of a metal ion or organic compound that is very tightly or covalently bound to the enzyme protein.
• An apo-enzyme is an enzyme missing a cofactor, the protein part of an enzyme is also known as an apoprotein.
• A holo-enzyme has all necessary subunits, prosthetic groups, and cofactors and can work on its own.

Enzyme Classification

• Enzymes are classified based on the type of reaction they catalyze.
• Oxidoreductases catalyze redox reactions.
• Transferases catalyze group transfer reactions.
• Hydrolases catalyze hydrolysis reactions, which involve the transfer of functional groups to water.
• Lyases facilitate the addition of groups to double bonds or the formation of double bonds by removing groups.
• Isomerases transfer groups within molecules to yield isomeric forms.
• Ligases form C-C, C-S, C-O, and C-N bonds via condensation reactions coupled with ATP cleavage or similar cofactors.

Enzyme Function

• Enzymes increase the rate of reaction and decrease activation energy, but do not shift equilibrium.

Hypotheses for Substrate Interaction

• Lock and Key: The active site and substrate have complementary fixed shapes.
• Induced Fit: The active site changes shape slightly to fit around the substrate, this is like a hand and a glove.
• Enzymes speed up reactions by lowering the activation energy.
• This is achieved by increasing the temperature, which increases the number of collisions among molecules.
• Enzymes lower the activation energy by stabilizing the transition state, which increases the rate.
• Delta G is the difference in energy from reactants to products and controls the equilibrium constant K.
• Enzymes do not lower delta G.
• Only activation energy is lowered.
• Transition state theory suggests that a transition state forms as the old bonds of the substrate(s) weaken and the new bonds of the product(s) begin to form.
• The energy of the reaction comes from the activation energy, which depends on the nature of the reacting species and the chemical bonds undergoing rupture.
• A transition-state analog resembles the transition-state structure of the normal enzyme-substrate complex and inhibits an enzyme's binding.
• Transition-state analogs are similar to substrates, but have altered structures and just block active sites and are very potent inhibitors.

Catalytic Machinery

• Catalytic triad: Serine is the nucleophile, histidine acts as the general base, and aspartate stabilizes the positive charge on histidine.
• Enzymes speed up reactions by lowering the activation energy.
• Enzymes do not change the reaction equilibrium.

Enzyme Kinetics

• The Michaelis-Menten equation is Vo = Vmax [S] / Km+[S] and is used to predict the rate of reaction for a one-substrate enzyme-catalyzed reaction.
• At low [S], Km >> [S] or [S] is insignificant, so Vo is directly proportional to [S].
• At high [S], [S] >> Km or Km is insignificant, so Vo is equal to Vmax.
• When Vo is one half of the Vmax, Km is equal to [S].
• Michaelis-Menten kinetics does not account for allosteric regulation; Michaelis-Menten kinetics is very simple, not regulated; Allosteric regulation has a sigmoid (s) shape.
• Km relates to the affinity of the substrate with the enzymes, and Vmax relates to the turnover number of the enzyme when the enzyme is saturated with substrates
• A low Km is desired for best results.
• Competitive inhibition: The inhibitor and substrate compete for the active site, the Km increases, and Vmax stays the same.
• Uncompetitive inhibition: The inhibitor binds to a place other than the active site. Both Vmax and Km decrease.
• Mixed inhibition: The inhibitor may bind to the enzyme on a site different than the active site, even if the enzyme already has a substrate.
• Km increases and Vmax decreases.

Carbohydrates

• Carbohydrates function as instant fuel and short-term energy storage, precursors for nucleic acids, structural support to bacteria, plants, and insects, and provide recognition signals for various biological processes.

Carbohydrate Types

• Monosaccharides
• Disaccharides: Two monosaccharides linked by a glycosidic bond
• Polysaccharides: Thousands to millions of monosaccharides linked by glycosidic bonds

Carbohydrate Families

• Aldose: Does not have a ketone C=O within the structure.
• Ketose: Has a ketone C=O within the structure.
• The cyclic forms of monosaccharides can be D-glucopyranose and D-fructofuranose, or alpha and beta configurations.
• The alpha and beta configuration occurs at carbon number 1 on the anomeric carbon.
• Anomeric carbon is one linked to O on the ring.
• D means OH is on the right, and L means OH is on the left.
• The next-to-last carbon determines the D and L configuration
• D is the dominant configuration.
• Epimers are monosaccharides that differ in configuration ONLY around ONE asymmetric carbon.
• Isomers are molecules with the same molecular formula but differ in the way their atoms are arranged, not just by one element like carbon in epimers.
• Mannose, glucose, and galactose are all epimers of each other.
• When two sugars get linked together in cyclic form, it forms a hemiacetal/ hemiketal
• Linking two sugars together to make a disaccharide creates an acetal or ketal.

Anomers

• Anomers are isomeric forms of monosaccharides which differ only at the hemiacetal carbon.
• Beta goes into cellulose, and alpha goes into starch.
• In cyclization, O turns into OH at the anomeric carbon.
• Anomeric carbon is involved in cyclization and can turn into alpha (OH on bottom) or beta (OH on top).
• Anomeric center is important to the reactivity of carbohydrates.
• It is the site at which ring-opening occurs, becoming the carbonyl group.

Sugars

• Reducing sugars are aldoses that give away an OH and non-reducing sugars are ketoses because they can't give away an OH.
• Aldehyde on carbon 1 is important for reducing sugars.
• Ketone group on carbon 2 is important for nonreducing sugars.
• Carbon 1 gets oxidized and turns into COOH, and Fehling's reagent is reduced
• Sugars exist in cyclic and linear form at equilibrium.
• Carbonyl carbon (C1) must be free to reduce.
• The two types of glycosidic bonds are O-linked glycosidic bonds and N-linked glycosidic bonds.
• The linkage is to the anomeric carbon.
• Homopolysaccharides are are one monosaccharide type, and heteropolysaccharides are different types.
• Alpha-1,4 linkages are in chains, and alpha-1,6 linkages are branched.
• Biological roles include: energy storage, structural support, cell signaling, lubrication, and protection, and intermediates in metabolic pathways
• Chitin makes up an insect skeleton.
• Cellulose is structural.
• Amylose and amylopectin are starch in plant cells and help with energy storage.
• Peptidogylgen makes up cell walls in bacteria.
• Cellulose contains the bond type of beta-1,4, which is why humans can't consume it.
• Humans lack the specific enzyme to break the bond.

Nucleic Acids

Functions

• Nucleic acids function for DNA and RNA.
• DNA stores genetic information.
• RNA helps to synthesize proteins.
• The basic backbone has ribose sugars, and linking sugars use a phosphodiester bond and are negatively charged.
• Nucleic acids are on the inside.
• DNA has long-term storage.
• mRNA helps proteins from the nucleus reach the cytoplasm.
• DNA and RNA are nucleic acids, nucleosides, and nucleotides which are building blocks.
• Some nucleic acids, such as ribozymes, can act as catalysts in a variety of biochemical reactions, such as RNA splicing, peptide bond formation, and RNA polymerization.
• DNA contains hereditary information that determines an organism's traits.
• It stores the 4 nitrogenous bases A, T, G, and C.
• RNA helps the building blocks of cells and perform a wide range of functions, including catalysis, transport, and signaling.
• Protein synthesis involves the conversion of the genetic information stored in DNA into an RNA molecule (messenger RNA or mRNA), which is then translated by the ribosomes into a specific sequence of amino acids that make up a protein.

Backbone

• The basic backbone structure of DNA and RNA has a nitrogenous base, a five-carbon sugar, and a phosphate group
• A nucleotide (-ate) has three components of a nitrogenous base, pentose sugar, and one or more phosphates.
• A nucleoside (-ine) is the molecule without the phosphate, but has a nitrogenous base and a pentose sugar.
• DNA has adenine, guanine, cytosine, and thymine.
• RNA has uracil instead of thymine.
• The difference between a ribose sugar and a deoxyribose sugar is the presence or absence of a hydroxyl (-OH) group on the 2' carbon of the sugar molecule.
• The ribose has an (OH) hydroxyl group in the 2' sugar, while a deoxyribose does not and instead has one less oxygen atom.
• The linkage is a N-linked glycosidic bond between ribose and pyrimidines or purines
• This is because of the phosphate group.
• Chargaff's rule says that in any DNA, G = C and A = T.
• The base pairing in DNA is the same as Chargaff's rule, so G = C and A = T.
• DNA strands are complementary and antiparallel.
• 10 base pairs = 1 turn; single base pair = 3.4 angstroms; 10 base pairs = 34 angstroms
• DNA strands are complementary and antiparallel.

Properties

• Tm is the midway point and is the point where 50% of the DNA is denatured.
• Can be determined by change in viscosity or change in absorption.
• More G/C content = higher Tm because has 3 H bonds and is harder to break
• More A/T content = lower Tm because only has 2 H bonds and is easier to break
• DNA supercoiling helps two strands unwind and is also helpful for transcription and replication.
• DNA supercoiling is the twisting and coiling of the double-stranded DNA molecule upon itself.
• It is an important structural feature of DNA and is essential for its proper functioning in a cell.
• One of the major functions of DNA supercoiling is to compact the DNA molecule into a small space within the cell.
• It also helps regulate gene expression
• Introns are transcribed but are not translated. They are matured RNA and not coded for DNA. Introns are removed before they are translated.
• DNA annealing is the process in which to complementary strands come together to form a double-stranded molecule.