B1.2 proteins | Quizlet

Define an amino acid.

An amino acid is an organic molecule with an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a variable R group attached to a central carbon.

State the number of amino acids commonly found in proteins.

There are 20 different amino acids commonly found in proteins.

Outline the general structure of an amino acid.

a amine group, an alpha carbon, a carboxyl group, a hydrogen, and an R group, the functional group.

amine group -NH2
carboxyl group -COOH

The nitrogen of the amine group is connected to an alpha carbon, which connects to the carbon of a carboxyl group, a hydrogen, and an R group.

Annotate a diagram of an amino acid showing the amino group, carboxyl group, R group, and central carbon.

The central carbon (C) is bonded to four groups: amino group (-NH₂), carboxyl group (-COOH), hydrogen (H), and the R group (variable side chain).

Define a polypeptide.

A polypeptide is a polymer of amino acids joined by peptide bonds, formed during translation in ribosomes.

Define a peptide bond.

A peptide bond is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another via condensation.

State the number of peptide bonds in a polypeptide with 10 amino acids.

There are 9 peptide bonds in a polypeptide made of 10 amino acids.

Outline the formation of a peptide bond.

A peptide bond forms through a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water.

Explain how a condensation reaction joins amino acids.

In a condensation reaction, a water molecule is removed as the amino group and carboxyl group form a peptide bond between amino acids.

Annotate a diagram showing peptide bond formation between two amino acids.

Show two amino acids joining via a peptide bond between the -COOH and -NH₂ groups, with H₂O as a byproduct.

Define the primary structure of a protein.

The primary structure is the linear sequence of amino acids in a polypeptide chain.

Explain the primary structure and how it is determined.

The primary structure of a protein is the specific linear sequence of amino acids in a polypeptide chain. This sequence is held together by peptide bonds, which form between the carboxyl group of one amino acid and the amino group of the next during condensation reactions.

The primary structure is determined by the genetic code:

• A gene’s DNA sequence is transcribed into mRNA, which is then translated by ribosomes into a chain of amino acids.

• Each codon (three-base sequence in mRNA) specifies one amino acid.

• The order of codons determines the order of amino acids, forming the unique sequence of each protein.

This sequence is critical because it dictates how the protein will fold into its secondary, tertiary, and possibly quaternary structures, ultimately determining the protein’s shape and function.

Define the secondary structure of a protein.

The secondary structure involves local folding into alpha helices or beta-pleated sheets stabilized by hydrogen bonds.

Explain the role of hydrogen bonding in secondary protein structures.

Hydrogen bonds form between the backbone amide and carbonyl groups, stabilizing the alpha helices and beta sheets.

Explain the formation and significance of α-helices and β-pleated sheets in secondary structure.

α-helices and β-sheets are regular structures formed by hydrogen bonding, contributing to protein stability and shape.

Define the tertiary structure of a protein.

The tertiary structure is the overall 3D shape of a polypeptide, determined by interactions among R groups.

Explain the importance of R groups in determining protein shape.

R-groups determine a protein’s shape, location, and interactions in the organism. Depending on their properties, R-groups can be charged, polar (hydrophilic), or nonpolar (hydrophobic). These characteristics influence how the protein folds, whether it is soluble in water, and where it is located in the cell — for example, whether it is embedded in a membrane (hydrophobic) or exposed to the cytoplasm (hydrophilic). These interactions are crucial for the protein’s structure and function.

Explain the types of bonding in tertiary structure (H-bonds, ionic, hydrophobic interactions, disulfide bridges).

Hydrogen bonds are between polar functional groups, hydrophobic interactions are betweenon polar functional groups, and disulfide bridges are covalent bonds between 2 sulfurs of the thiol group of two cystines, and ionic bond between two charged functional groups, very density to ph changes.

Explain the significance of tertiary structure in enzyme function.

The 3D shape allows the active site to form, enabling substrate binding and catalysis.

Define the quaternary structure of a protein.

Quaternary structure involves the assembly of multiple polypeptide subunits into a functional protein.

Explain how quaternary structure applies to hemoglobin.

Hemoglobin has four polypeptide chains with heme groups, enabling oxygen transport.

Distinguish between the primary and secondary structures of proteins.

• Primary structure is the linear sequence of amino acids in a polypeptide chain, held together by peptide bonds. It determines the protein’s overall structure and function and is unique to each protein.

• Secondary structure refers to the regular, repeating patterns formed by hydrogen bonds between the backbone atoms (not R-groups) of the polypeptide. Common forms include alpha-helices and beta-pleated sheets.

Distinguish between fibrous and globular proteins with examples.

Fibrous and globular proteins differ in structure, solubility, and function. Fibrous proteins are long, thin, and usually insoluble in water, making them ideal for structural roles like support and strength. They have repetitive amino acid sequences and are very stable. Examples include collagen (in connective tissue), keratin (in hair and nails), and elastin (in skin).

In contrast, globular proteins are compact, spherical, and generally soluble in water, which suits them for metabolic and regulatory functions. Their structure is irregular and more easily affected by environmental changes. Examples include hemoglobin (oxygen transport), insulin (blood sugar regulation), and amylase (digestion).

Compare the properties of hemoglobin and collagen.

Hemoglobin is globular, soluble, and transports oxygen; collagen is fibrous, insoluble, and provides structural support.

Compare the solubility of fibrous vs. globular proteins.

• Fibrous proteins are generally insoluble in water. Their structure consists of long, linear chains with repetitive amino acid sequences and extensive hydrophobic R-groups, which form tight intermolecular bonds. This gives them a structural role (e.g., collagen, keratin).

• Globular proteins, on the other hand, are usually soluble in water. Their compact, spherical shape results from folding that positions hydrophilic R-groups outward (toward the aqueous environment) and hydrophobic R-groups inward. This makes them well-suited for metabolic roles, such as enzymes or hormones.

Define a fibrous protein.

A fibrous protein is long, insoluble, and provides structural support (e.g., keratin, collagen).

Define a globular protein.

A globular protein is compact, soluble, and typically involved in metabolic functions (e.g., enzymes, hormones).

Distinguish between a polypeptide and a protein.

A polypeptide is a single amino acid chain; a protein may consist of one or more polypeptides with functional structure.

Describe the process of protein synthesis from amino acids.

Proteins are synthesized by ribosomes via translation, linking amino acids in a sequence determined by mRNA.

Explain the role of chaperone proteins in folding.

Chaperone proteins assist in proper folding of new polypeptides and prevent aggregation.

Define denaturation.

Denaturation is the loss of a protein's shape and function due to disruption of its structure (e.g., by heat or pH).

Describe how temperature affects protein structure (denaturation).

High temperatures increase kinetic energy, breaking the weak bonds that maintain a protein’s shape. This disrupts:

• Secondary structure: hydrogen bonds between backbone atoms (C=O and N–H).

• Tertiary structure: interactions between R-groups, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

This causes denaturation, where the protein unfolds and loses its functional shape. The primary structure (amino acid sequence) stays intact, but function is lost—often irreversibly.

Describe how pH affects protein structure (denaturation).

Changes in pH affect protein structure by altering the charges on R-groups, disrupting bonds that maintain the tertiary and sometimes secondary structure:

• Ionic bonds between oppositely charged R-groups are especially sensitive to pH.

• Extreme pH can also affect hydrogen bonding by adding or removing protons (H⁺), disturbing polar interactions.

This causes denaturation, where the protein unfolds and loses its specific 3D shape and function. The primary structure remains unchanged, but the protein often becomes nonfunctional.

Evaluate the impact of pH change on protein structure and function.

Changes in pH can disrupt structural bonds, altering shape and inactivating proteins like enzymes.

Predict the effect of high fever on enzyme structure.

A high fever can denature enzymes by disrupting their tertiary structure, reducing catalytic activity.

List four functions of proteins in the body.

1. Enzymes → Speed up chemical reactions (e.g., digestion).

2. Structure → Support cells/tissues (e.g., collagen, keratin).

3. Transport → Carry molecules (e.g., hemoglobin for oxygen).

4. Movement → Enable muscle contraction (actin/myosin).

5. Immunity → Antibodies fight infections.

6. Hormones → Regulate body processes (e.g., insulin).

7. Signaling → Cells communicate via receptor proteins.

8. Balance → Maintain pH and fluid levels (e.g., albumin).

9. Energy → Backup fuel source when needed.

10. DNA Control → Regulate gene activity (transcription factors).

11. Clotting → Stop bleeding (e.g., fibrinogen).

12. Senses → Detect light, taste, etc. (e.g., rhodopsin).

State one example each of a fibrous and a globular protein.

Fibrous: collagen; Globular: hemoglobin.

Outline how the structure of collagen supports its function.

Collagen has a triple helix structure, providing tensile strength for connective tissues.

Outline the role of proteins in cell signaling.

Proteins like hormones and receptors transmit signals across membranes and coordinate responses.

Proteins are essential in cell signaling. They act as receptors that detect signals, transducers that relay and amplify messages, and effectors that trigger responses. Some also function as transcription factors, altering gene expression. Together, these proteins help cells communicate and respond to their environment.

Outline the role of proteins in immune response.

Antibodies are proteins that recognize and bind to antigens to neutralize pathogens.

Explain the role of enzymes as proteins.

Enzymes are proteins that act as biological catalysts. They speed up reactions by lowering activation energy, work on specific substrates, and have an active site shaped by their 3D structure. Their function depends on conditions like temperature and pH, which can denature them.

Explain the role of protein hormones like insulin.

Insulin is a globular protein hormone that regulates blood glucose by promoting uptake into cells.

Explain why protein structure is essential to function.

The shape determines how a protein interacts with other molecules (e.g., substrate binding in enzymes).

Suggest how a mutation that changes one amino acid could affect protein function.

A single change may alter folding, disrupt active sites, or destabilize the protein, impairing function.

Justify why fibrous proteins are suited for structural roles.

Their long, stable, insoluble structure resists tension, making them ideal for support.

Justify why globular proteins are ideal as enzymes.

Globular proteins are ideal as enzymes because of their compact, spherical shape, which allows them to be soluble in water and function efficiently in aqueous environments, such as the cytoplasm or blood. Their tertiary structure creates a specific active site, where substrates bind with high specificity — a key feature for catalysis.

Additionally, the folding of R-groups in globular proteins enables the formation of a chemically reactive active site, allowing the enzyme to lower activation energy and speed up biological reactions. Their flexible structure also supports conformational changes needed for induced fit mechanisms.

Thus, globular proteins' solubility, structural specificity, and flexibility make them ideal for enzyme function in biological systems.

Evaluate the significance of protein structure in medical applications.

Understanding structure enables drug design, diagnosis of misfolding diseases, and targeted therapies.

Define oligopeptide.

An oligopeptide is a short chain of amino acids, typically between 2 and 20 residues long, joined by peptide bonds.

Compare the source of amino acids by plant and animal cells.

Animal cells can synthesize all non-essential amino acids and obtain essential ones from diet; plant cells can synthesize all amino acids from inorganic substances.

Define "essential" as related to dietary amino acids.

Essential amino acids are those that cannot be synthesized by the human body and must be obtained from the diet.

Define "non-essential" as related to dietary amino acids.

Non-essential amino acids are those that the human body can synthesize and do not need to be consumed in the diet.

Outline why vegan diets require attention to food combinations to ensure essential amino acids are consumed.

Vegan diets must combine different plant protein sources to ensure all essential amino acids are provided, as most plants are incomplete protein sources.

Outline why there is a limitless diversity of DNA base sequences.

DNA is made of four bases (A, T, C, G) that can be arranged in any order and length, allowing infinite combinations to code proteins.

Identify the "backbone" of a polypeptide.

The backbone of a polypeptide is the repeating sequence of nitrogen (N) from the amino group, alpha carbon (Cα), and carbon (C) from the carboxyl group.

Define "conformation" as related to protein structure.

Conformation refers to the specific three-dimensional shape of a protein that results from its amino acid sequence and folding.

Outline how a DNA sequence codes for a polypeptide that will repeatedly fold into the same precise, predictable protein conformation.

The DNA sequence determines the order of amino acids, which determines R-group interactions, leading to consistent folding and a predictable structure.

Identify the alpha-helix and beta-pleated sheet in images of protein structure.

Alpha-helices appear as spirals or coils, while beta-pleated sheets appear as flattened arrows or ribbons pointing in alternating directions.

Explain how the polarity and charge of amino acid R-groups determine whether they are classified as hydrophilic or hydrophobic, and how this influences protein structure.

Amino acids are classified based on the polarity and charge of their R-groups:

• Hydrophilic amino acids have polar or charged R-groups. They are attracted to water and are typically found on the outer surfaces of proteins in aqueous environments. These include:

  • Acidic (negatively charged),

  • Basic (positively charged),

  • Uncharged polar amino acids.

  In short, hydrophilic amino acids help proteins interact with water and other polar molecules, support solubility, and often play active roles in binding and catalysis.

• Hydrophobic amino acids have nonpolar R-groups, which are repelled by water. They tend to cluster in the interior of the protein, away from water, helping to stabilize the protein’s three-dimensional structure through hydrophobic interactions.