Chapter 3 Nucleic Acids, Proteins, and Enzymes



Chapter 3- Nucleic Acids, Proteins, and Enzymes

Concept 3.1 Nucleic Acids Are Informational Macromolecules

________________are polymers specialized for storage, transmission, and use of ________________ information.

________________ = deoxyribonucleic acid

________________ = ribonucleic acid

Monomers: ________________

Nucleotide: Pentose sugar + N-containing base + ________________group

________________: Pentose sugar + N-containing base

Bases:

Pyrimidines—________________rings

Purines—________________rings

Sugars:

DNA contains ________________

RNA contains ________________

Nucleotides bond in ________________reactions to form ________________linkages.

Nucleic acids grow in the ________________direction.

Complementary base pairing:

________________and thymine always pair (A-T)

________________and guanine always pair (C-G)

Base pairs are linked by ________________bonds.

There are so many hydrogen bonds in DNA and RNA that they form a fairly strong attraction, but not as strong as ________________bonds.

Thus, base pairs can be separated with only a ________________amount of energy.

RNA is usually ________________-stranded, but may be folded into 3-D structures, by hydrogen bonding.

Folding occurs by ________________base pairing, so structure is determined by the order of bases.

DNA—two polynucleotide strands form a “________________” that twists into a ________________helix.

Sugar-phosphate groups form the sides of the ladder, the hydrogen-bonded bases form the rungs.

DNA is an informational molecule: genetic information is in the sequence of base pairs.

DNA has two functions:

________________

Gene ________________—base sequences are copied to RNA, and specify amino acids sequences in proteins.

DNA replication and transcription depend on the base pairing:

5′-TCAGCA-3′

3′-AGTCGT-5′

3′-AGTCGT-5′ transcribes to RNA with the sequence 5′-_____________-3′.

________________—complete set of DNA in a living organism

________________—DNA sequences that encode specific proteins and are transcribed into RNA

Not all genes are ________________in all cells of an organism.

DNA base sequences reveal ________________relationships.

Closely related living species should have more ________________base sequences than species that are more distantly related.

Scientists are now able to determine and compare entire genomes of organisms to study evolutionary ________________.

Concept 3.2 Proteins Are Polymers with Important Structural and

Metabolic Roles

Major functions of proteins:

________________—catalytic proteins

• ________________proteins (e.g., antibodies)

• _____________and regulatory proteins—control physiological processes

• Receptor proteins—receive and respond to molecular signals

Storage proteins store amino acids

• ________________proteins—physical stability and movement

• Transport proteins carry substances (e.g., ________________)

• Genetic regulatory proteins regulate when, how, and to what extent a gene is ________________

Protein monomers are ________________.

Amino and carboxylic acid functional groups allow them to act as both acid and base.

The ________________differs in each amino acid.

Only 20 amino acids occur extensively in the proteins of all organisms.

They are grouped according to properties conferred by the R groups.

Cysteine side chains can form covalent bonds—a ________________________________, or disulfide bond.

Amino acids are linked in condensation reactions to form ________________linkages or bonds.

Polymerization takes place in the amino to carboxyl direction.

________________structure of a protein—the sequence of amino acids

+________________structure—regular, repeated spatial patterns in different regions, resulting from hydrogen bonding

• α (________________) helix—right-handed coil

β (________________) pleated sheet—two or more polypeptide chains are extended and aligned

________________structure—polypeptide chain is bent and folded; results in the definitive 3-D shape

The outer surfaces present functional groups that can interact with other molecules.

Interactions between R groups determine tertiary structure.

• Disulfide bridges hold a folded polypeptide together

• ________________bonds stabilize folds

Hydrophobic side chains can aggregate

van der Waals interactions between hydrophobic side chains

• Ionic interactions form salt bridges

Secondary and tertiary protein structure derive from primary structure.

________________—________________or ________________are used to disrupt weaker interactions in a protein, destroying secondary and tertiary structure.

The protein can return to normal when cooled—all the information needed to specify the unique shape is contained in the primary structure.

Factors that can disrupt the interactions that determine protein structure (denaturing):

________________

Concentration of ________________

High concentrations of ________________substances

________________substances

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions

Living systems depend on reactions that occur spontaneously, but at very _______________rates.

________________are substances that speed up reactions without being permanently altered.

No catalyst makes a reaction _____________that cannot otherwise occur.

Most biological catalysts are proteins (enzymes); a few are RNA molecules (ribozymes).

In some exergonic reactions there is an energy barrier between reactants and products.

An input of energy (the ________________ or Ea) will put reactants into a transition state.

Enzymes ________________the activation energy—they allow reactants to come together and react more easily.

Example: A molecule of sucrose in solution may hydrolyze in about 15 days; with sucrase present, the same reaction occurs in 1 second!

Enzymes are highly specific—each one catalyzes only one chemical reaction.

Reactants are ________________: they bind to a specific site on the enzyme—the ________________.

Specificity results from the exact 3-D shape and chemical properties of the active site.

The enzyme–substrate complex (ES) is held together by hydrogen bonding, electrical attraction, or ________________covalent bonding.

The enzyme is ________________changed at the end of the reaction.

Enzymes may use one or more mechanisms to catalyze a reaction:

Inducing strain—bonds in the substrate are stretched, putting it in an unstable transition state.

Some enzymes require ions or other molecules in order to function:

________________—inorganic ions

________________add or remove chemical groups from the substrate. They can participate in many different reactions.

Prosthetic groups (non-amino acid groups) permanently bound to their enzymes.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes

Enzyme-catalyzed reactions are part of metabolic pathways—the product of one reaction is a substrate for the next.

________________—the maintenance of stable internal conditions

Cells can regulate metabolism by controlling the ___________of an enzyme.

Cells often have the ability to turn synthesis of enzymes off or on.

Chemical inhibitors can bind to enzymes and _____________reaction rates.

Natural inhibitors regulate metabolism; artificial inhibitors are used to treat ________________, kill pests, and study enzyme function.

Irreversible inhibition—inhibitor covalently binds to a side chain in the active site. The enzyme is permanently inactivated.

Reversible inhibition (more common in cells):

A __________inhibitor competes with natural substrate for active site.

A ________________inhibitor binds at a site distinct from the active site—this causes change in enzyme shape and function.

________________regulation—non-substrate molecule binds a site other than the active site (the allosteric site)

The enzyme changes ________________, which alters the chemical attraction (affinity) of the active site for the substrate.

Allosteric regulation can ________________or inactivate enzymes.

Protein ________________are enzymes that regulate responses to the environment by organisms.

They are subject to allosteric regulation.

The active form regulates the activity of other enzymes, by ________________allosteric or active sites on the other enzymes.

Metabolic pathways:

The first reaction is the ________________step—other reactions then happen in sequence.

Feedback inhibition (end-product inhibition)—the final product acts as a ____________inhibitor of the first enzyme, which shuts down the pathway.

________________affects enzyme activity:

Acidic side chains generate H+ and become ________________.

Basic side chains attract H+ and become ________________.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes

Example:

glutamic acid—COOH glutamic acid—COO– + H+

The law of mass action—the higher the H+ concentration, the more reaction is driven to the ________________to the less hydrophilic form.

This can affect enzyme shape and function.

Protein tertiary structure (and thus function) is very sensitive to the concentration of H+ (pH) in the environment.

All enzymes have an ________________pH for activity.

________________affects enzyme activity:

Warming increases rates of chemical reactions, but if temperature is too high, non-covalent bonds can break and ________________enzymes.

All enzymes have an ________________temperature for activity.

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