IB Biology Unit 3

Mr. Rassmussen

What is a peptide bond?

A covalent bond that links amino acids together.

What is a dipeptide?

Two amino acids linked by a condensation reaction.

What is a polypeptide?

A chain of many amino acids linked together; polypeptides are the main components of proteins.

What are essential amino acids?

Amino acids the body cannot make and must obtain from the diet. Nine of the 20 amino acids are essential in humans.

What are non-essential amino acids?

Amino acids the body can synthesize through metabolic pathways.

What is denaturation?

A change in a protein's three-dimensional shape caused by disruption of bonds and interactions that maintain its structure.

What are globular proteins?

Water-soluble, compact, roughly spherical proteins suited to functions such as hormones and transport.

What are fibrous proteins?

Long, elongated proteins that mainly have structural roles.

What is a non-conjugated protein?

A protein made only of polypeptide components held together by interactions such as ionic bonds, hydrogen bonds, disulfide bonds, and hydrophobic interactions.

What are examples of non-conjugated proteins?

Insulin and collagen.

What is a conjugated protein?

A protein containing one or more non-polypeptide components in addition to its polypeptide chain.

What is an example of a conjugated protein?

Hemoglobin.

What is a catalyst?

A substance that increases the rate of a chemical reaction without being changed by the reaction.

What is an enzyme?

A biological catalyst made by living cells that speeds up chemical reactions.

What is an active site?

The specific region of an enzyme where the substrate binds.

What is a substrate?

The substance on which an enzyme acts during a chemical reaction.

What is induced-fit binding?

The process in which the enzyme and substrate change shape slightly as they bind, allowing a better fit.

What is metabolism?

The complex network of interdependent chemical reactions that occurs in living organisms.

What are catabolic reactions?

Reactions that break larger molecules into smaller molecules and release energy.

What are two examples of catabolic reactions?

Food digestion and cellular respiration.

What are anabolic reactions?

Reactions that build larger molecules from smaller molecules and require energy.

What are three examples of anabolic reactions?

Photosynthesis, protein synthesis, and DNA synthesis.

What is activation energy?

The energy needed to start a chemical reaction by helping break bonds in substrate molecules.

What are intracellular enzyme-catalyzed reactions?

Enzyme-controlled reactions that occur inside cells and catalyze metabolic pathways.

What are examples of intracellular enzyme-catalyzed reactions?

Glycolysis and the Krebs cycle.

What are extracellular enzyme-catalyzed reactions?

Reactions in which enzymes break down large macromolecules outside cells so their smaller products can enter cells.

What is an example of an extracellular enzyme-catalyzed reaction?

Chemical digestion in the gut.

What is a cyclical metabolic pathway?

A pathway in which each intermediate is the product of one reaction and the substrate of another, eventually regenerating a starting compound.

What are examples of cyclical metabolic pathways?

The Krebs cycle and the Calvin cycle.

What is a linear metabolic pathway?

A chain of reactions that converts starting substances into a final product.

What is an example of a linear metabolic pathway?

Glycolysis.

What is an allosteric site?

A site on an enzyme, separate from the active site, where a regulatory molecule can bind and change enzyme activity.

What is competitive inhibition?

Inhibition in which an inhibitor competes with the substrate for the enzyme's active site.

What is noncompetitive inhibition?

Inhibition in which an inhibitor binds to a site other than the active site and changes enzyme activity.

What is feedback inhibition?

A process in which the end product of a metabolic pathway inhibits an earlier enzyme in that pathway.

What is an example of feedback inhibition?

The pathway that produces isoleucine.

What is mechanism-based inhibition?

Inhibition in which an enzyme's reaction mechanism leads to its inactivation by an inhibitor.

How does penicillin inhibit bacterial enzymes?

Penicillin inhibits bacterial transpeptidases, interfering with the formation of bacterial cell walls and helping kill bacteria.

What is the basic structure of an amino acid?

A central carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R-group.

How is a peptide bond identified in a dipeptide?

It is the covalent bond between the carbon of one amino acid's carboxyl group and the nitrogen of the next amino acid's amino group.

How does a condensation reaction join two amino acids?

An OH is removed from the carboxyl group of one amino acid and an H from the amino group of the other. Water forms, and a peptide bond joins the amino acids.

Why are amino acids important in the diet?

They are needed to build proteins for growth, tissue repair, and the production of enzymes.

Why must essential amino acids come from food?

The body cannot synthesize them, so they must be obtained through the diet.

Why do vegan diets require careful planning?

They must provide all essential amino acids through foods such as beans, lentils, nuts, seeds, soy, and grains.

How many amino acids are coded for in the genetic code?

20 amino acids.

How long can a peptide chain be?

It can contain as few as a few amino acids or as many as thousands.

Can amino acids occur in any order in a peptide chain?

Yes. Amino acids can occur in different sequences, and the sequence influences the protein's shape and function.

What are examples of proteins made from polypeptides?

Insulin and collagen.

What happens to a protein when it is denatured?

Its three-dimensional shape changes, it loses its function, and it may become insoluble and form a precipitate.

How can temperature cause protein denaturation?

High temperatures disrupt interactions that maintain a protein's shape, changing its structure and potentially its active site.

How can pH cause protein denaturation?

Extreme acidic or basic conditions disrupt interactions within a protein, changing its shape and potentially its function.

How do R-groups affect polypeptide properties?

R-groups may be hydrophobic or hydrophilic. Hydrophilic R-groups may be polar or charged and can be acidic or basic.

What determines a protein's three-dimensional shape?

The sequence of amino acids and the precise position of each amino acid within the structure.

Why can proteins have precise and repeatable structures?

Their amino acid sequences and interactions determine how they fold into particular three-dimensional shapes.

What is the primary structure of a protein?

The specific sequence of amino acids joined by peptide bonds.

What is the secondary structure of a protein?

Local folding of a polypeptide chain, such as alpha helices and beta-pleated sheets, stabilized by hydrogen bonds.

What is the tertiary structure of a protein?

The overall three-dimensional folding of a single polypeptide chain, maintained by interactions between its R-groups.

What is the quaternary structure of a protein?

The arrangement of two or more polypeptide chains that form a functional protein.

What bonds hold amino acids together in primary structure?

Peptide bonds.

What bonds stabilize secondary protein structure?

Hydrogen bonds.

What interactions help stabilize tertiary protein structure?

Hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions between R-groups.

What is required for quaternary protein structure?

Two or more polypeptide chains associate to form one protein.

How are protein form and function related?

A protein's specific three-dimensional shape determines how it interacts with other molecules and allows it to perform its function.

Why is insulin a globular protein?

It is compact and folded into a roughly spherical shape, which suits its role as a hormone that regulates blood glucose.

Why is collagen a fibrous protein?

Its long, strong, rope-like structure makes it suitable for supporting tissues such as skin, tendons, and ligaments.

What is enzyme specificity?

An enzyme catalyzes a particular reaction because its active site has a shape and chemical properties suited to its substrate.

Why do living organisms need many different enzymes?

Enzymes are specific to particular reactions, so different metabolic reactions require different enzymes.

How does molecular motion affect enzyme activity?

Molecules move constantly because of kinetic energy, causing substrates to collide with enzyme active sites.

How does a successful substrate-active site collision affect enzyme activity?

If the substrate binds successfully, an enzyme-substrate complex forms and the reaction can occur.

What happens when successful enzyme-substrate collisions become more frequent?

The rate of enzyme activity increases, provided conditions are suitable.

How are active-site structure and enzyme-substrate specificity related?

The active site has a specific three-dimensional shape complementary to its substrate, allowing the enzyme to bind and catalyze a particular reaction.

How does denaturation affect an enzyme's active site?

Denaturation changes the active site's shape, preventing the substrate from binding properly and reducing or stopping enzyme activity.

How does temperature affect enzyme activity?

Activity generally increases as temperature rises toward an optimum because molecules move faster. Above the optimum, denaturation can cause activity to decrease sharply.

How does pH affect enzyme activity?

Each enzyme has an optimum pH. More acidic or more basic conditions can change the active site's shape and reduce activity or denature the enzyme.

How does increasing substrate concentration affect enzyme activity?

The rate generally increases because more substrate molecules can collide with active sites, until the enzymes become saturated and the rate levels off.

How does increasing enzyme concentration affect enzyme activity?

If enough substrate is available, increasing enzyme concentration generally increases the reaction rate because more active sites are available.

Why is enzyme activity affected by both pH and temperature?

Both factors affect molecular motion and the interactions maintaining enzyme structure, including the shape of the active site.

Why is heat generation inevitable during metabolism?

Metabolic reactions do not transfer energy with 100% efficiency, so some energy is released as heat instead of being used for useful work.

Which animals use metabolic heat to help maintain a constant body temperature?

Mammals, birds, and some other animals.

How does a competitive inhibitor interact with an enzyme?

It competes with the substrate for the active site and prevents some substrate molecules from binding.

How can increased substrate concentration affect competitive inhibition?

Increasing substrate concentration can reduce the inhibitor's effect because the substrate is more likely to occupy the active site.

What are statins, and how do they act as enzyme inhibitors?

Statins are competitive inhibitors of an enzyme involved in cholesterol production.

How does a noncompetitive inhibitor interact with an enzyme?

It binds to a site other than the active site, changing the enzyme's activity.

Can increased substrate concentration overcome noncompetitive inhibition?

No. The inhibitor does not compete for the active site, so adding more substrate does not overcome the inhibition.

What is the key difference between competitive and noncompetitive inhibition?

Competitive inhibitors bind to the active site and compete with the substrate; noncompetitive inhibitors bind elsewhere and alter enzyme activity.

How can you distinguish competitive from noncompetitive inhibition using substrate concentration?

If increasing substrate concentration reduces inhibition, it suggests competitive inhibition. If inhibition remains despite increasing substrate concentration, it suggests noncompetitive inhibition.