AP Biology 1.5-1.6: Nucleic Acids and Proteins

Protein

A protein is a functional polypeptide or group of polypeptides with a specific three-dimensional shape. Proteins perform structural, catalytic, regulatory, transport, defense, storage, and contractile functions.

What common structural feature do all proteins share?

All proteins are polymers of amino acids arranged in a specific linear sequence. Their sequence and interactions determine their final shape and function.

Enzyme

An enzyme is a biological catalyst, usually a protein, that increases the rate of a biochemical reaction without being consumed. Its active site binds particular substrate molecules, giving the enzyme specificity.

How do catabolic and anabolic enzymes differ?

Catabolic enzymes help break larger substrates into smaller products, whereas anabolic enzymes help build more complex molecules from smaller substrates. Both increase reaction rates.

What are hormones, and what is one protein-hormone example?

Hormones are chemical signaling molecules secreted by endocrine cells that regulate physiological processes such as growth, metabolism, and reproduction. Insulin is a protein hormone that helps regulate blood glucose concentration.

What determines whether an amino acid is acidic, basic, polar, or nonpolar?

The chemical nature of its variable side chain, or R group, determines its classification. The R group also strongly influences how the amino acid interacts with water and other parts of a protein.

Amino acid

An amino acid contains a central $α$ carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group. Amino acids are the monomers that form proteins.

How do hydrophobic and hydrophilic amino acids tend to be distributed in a soluble globular protein?

Nonpolar, hydrophobic side chains tend to be buried in the protein interior away from water. Polar or charged, hydrophilic side chains tend to be exposed on the surface.

How are amino acids distributed in a protein embedded in a lipid bilayer?

Nonpolar side chains tend to face the hydrophobic interior of the lipid bilayer. Polar or charged side chains are more favorable in aqueous regions or in channels exposed to water.

Essential amino acid

An essential amino acid is one that an organism cannot synthesize in sufficient amounts and must obtain from its diet. Humans require nine essential amino acids; the exact list can vary among organisms.

Which amino acid side chains are examples of basic, positively charged groups?

Lysine and arginine have positively charged side chains under typical biological conditions, so they are classified as basic amino acids.

What structural feature makes proline unusual among the common amino acids?

Proline's side chain bonds back to its amino group, creating a ring. This restricts backbone flexibility and can disrupt or bend regular secondary structures.

Peptide bond

A peptide bond is a covalent amide linkage between the carboxyl group of one amino acid and the amino group of another. It forms through a dehydration reaction that releases $H_2O$.

What are the products of joining amino acids by peptide bonds?

Short chains are called peptides, and longer amino-acid polymers are called polypeptides. A polypeptide has an N-terminus with a free amino group and a C-terminus with a free carboxyl group.

How does a polypeptide differ technically from a functional protein?

A polypeptide is simply a polymer of amino acids. A protein is a polypeptide or collection of polypeptides that folds into a distinct functional structure and may include non-peptide prosthetic groups.

Post-translational modification

A post-translational modification is a chemical or structural change made to a polypeptide after translation, such as cleavage or phosphorylation. These changes can be required for the protein to become functional.

Primary protein structure

Primary structure is the unique linear sequence of amino acids in a polypeptide. It is determined by the nucleotide sequence of the gene encoding the protein.

How can a single nucleotide substitution cause a major change in protein function?

A nucleotide substitution can change a codon and replace one amino acid in the primary sequence. That substitution may alter folding at every higher structural level, as in sickle-cell hemoglobin.

What molecular substitution causes the altered hemoglobin associated with sickle-cell disease?

At position 6 of the $β$ chain, valine replaces glutamate. The resulting change in side-chain properties promotes hemoglobin fiber formation, distorting red blood cells.

Secondary protein structure

Secondary structure is the local folding of a polypeptide backbone into patterns such as an $α$-helix or a $β$-pleated sheet. Hydrogen bonds between backbone carbonyl oxygen atoms and backbone N–H groups stabilize these patterns.

What stabilizes an $α$-helix, and how many amino acid residues occur per turn?

Backbone hydrogen bonds stabilize the helix, generally between a carbonyl group and the N–H group about four residues farther along the chain. An $α$-helix contains approximately $3.6$ residues per turn.

β-pleated sheet

A $β$-pleated sheet is a secondary structure in which extended polypeptide segments align parallel or antiparallel and are stabilized by hydrogen bonds between their backbones. R groups project above and below the sheet.

Tertiary protein structure

Tertiary structure is the overall three-dimensional conformation of one polypeptide chain. It results primarily from interactions among R groups, including hydrophobic interactions, ionic attractions, hydrogen bonding, and disulfide bonds.

Which interactions commonly stabilize tertiary protein structure?

Hydrophobic side chains tend to cluster in the interior, while hydrogen bonds and ionic attractions form among suitable side chains. Cysteine side chains can form covalent disulfide bonds in the presence of oxygen.

Quaternary protein structure

Quaternary structure is the arrangement and interaction of multiple polypeptide subunits in one functional protein. Noncovalent interactions between subunits commonly stabilize this level.

Disulfide bond

A disulfide bond is a covalent $S-S$ linkage formed when two cysteine sulfhydryl groups are oxidized. It can stabilize tertiary structure within one chain or connect separate polypeptide chains.

How does protein shape relate to protein function?

A protein's three-dimensional shape positions chemical groups to create specific binding sites and reactive environments. Altering the shape can prevent an enzyme from binding its substrate or otherwise eliminate function.

Denaturation

Denaturation is the disruption of a protein's higher-order structure by conditions such as extreme temperature, pH, or chemicals, usually without breaking its peptide bonds. Loss of shape often causes loss of function.

Why can denaturation sometimes be reversible but sometimes irreversible?

If the primary sequence remains intact and the denaturing condition is removed, a protein may refold and regain function. Irreversible changes occur when aggregation or chemical damage prevents the native conformation from being restored.

What role do molecular chaperones play in protein folding?

Chaperones associate with newly synthesized or damaged polypeptides and help them fold correctly, often by preventing inappropriate aggregation. They generally dissociate after the target protein reaches its proper conformation.

How does a protein's amino-acid sequence determine its final conformation?

The sequence determines the positions of nonpolar, polar, charged, and cysteine side chains. Their resulting interactions with one another and the surrounding solvent drive the polypeptide toward a particular three-dimensional structure.

Why can sequence comparison of cytochrome $c$ provide evidence about evolutionary relationships?

Cytochrome $c$ performs an essential role in electron transport, so much of its sequence is conserved. Fewer amino-acid differences between species generally indicate a more recent common ancestry, assuming comparable evolutionary rates.

Nucleic acid

A nucleic acid is a polymer of nucleotides that stores, transmits, or helps express genetic information. The two major types are DNA and RNA.

Nucleotide

A nucleotide consists of a nitrogenous base, a five-carbon pentose sugar, and one or more phosphate groups. Nucleotides polymerize to form DNA or RNA.

How do the sugars in DNA and RNA differ chemically?

RNA contains ribose, which has an $-OH$ group at the $2'$ carbon. DNA contains deoxyribose, which has $H$ rather than $-OH$ at the $2'$ carbon.

Purine versus pyrimidine

Purines have two fused nitrogen-containing rings; adenine and guanine are purines. Pyrimidines have one ring; cytosine, thymine, and uracil are pyrimidines.

Phosphodiester linkage

A phosphodiester linkage connects the $5'$ phosphate of one nucleotide to the $3'$ hydroxyl group of the next sugar. These linkages create the directional sugar-phosphate backbone of a polynucleotide.

How do DNA and RNA differ in bases, strand structure, and primary roles?

DNA contains A, T, G, and C and is typically a double-stranded genetic information store. RNA contains A, U, G, and C, is usually single-stranded, and participates in protein synthesis and gene regulation.

DNA double helix

DNA consists of two antiparallel polynucleotide strands twisted into a double helix. Sugar-phosphate backbones face outward, while complementary nitrogenous bases face inward and are held together by hydrogen bonds.

What does antiparallel mean for the two strands of DNA?

The strands run in opposite chemical directions: one strand runs $5' \to 3'$ while the other runs $3' \to 5'$. This orientation is a consequence of the directional phosphodiester backbone.

What is the DNA complementary base-pairing rule?

Adenine pairs with thymine, and guanine pairs with cytosine. Thus, the complementary strand to $5'$-AATTGGCC-$3'$ is $3'$-TTAACCGG-$5'$ when written antiparallel to the original.

What is the significance of complementary base pairing during DNA replication?

Each parental DNA strand serves as a template for synthesis of a complementary strand. Each daughter DNA double helix therefore contains one parental strand and one newly synthesized strand.

Genome

An organism's genome is its complete set of genetic material. It includes genes that encode proteins as well as genes that produce functional RNA molecules.

How are DNA, chromatin, and chromosomes related in eukaryotic cells?

DNA associates with histone proteins to form chromatin. Chromosomes are highly organized structures made from chromatin and contain many genes.

What roles do mRNA, rRNA, and tRNA play in protein synthesis?

mRNA carries genetic instructions from DNA to a ribosome. rRNA forms a major structural and functional component of ribosomes, while tRNA uses complementary base pairing to deliver the amino acid specified by an mRNA codon.

How is an RNA sequence transcribed from a DNA template different from a DNA complementary sequence?

RNA uses uracil in place of thymine and contains ribose rather than deoxyribose. For example, a DNA template sequence $3'$-AATTGCGC-$5'$ produces complementary RNA $5'$-UUAACGCG-$3'$.

Codon

A codon is a sequence of three bases in mRNA that specifies one amino acid or a termination signal during translation. Ribosomes read successive codons to direct polypeptide synthesis.