Biochemistry (Chapter 2b)

What is biochemistry, and how are compounds classified?

Biochemistry is the study of the chemical composition and reactions of living matter. Chemicals are classified as inorganic or organic. Inorganic compounds include water, salts, and many acids and bases; organic compounds include carbohydrates, lipids, proteins, and nucleic acids.

What are the major properties of water that make it important to life?

Water is the most abundant inorganic compound in cells and has high heat capacity, high heat of vaporization, polar solvent properties, reactivity, and cushioning ability.

What are high heat capacity and high heat of vaporization?

High heat capacity allows water to absorb or release large amounts of heat with little temperature change. High heat of vaporization means evaporation requires a large amount of heat, making evaporation useful for cooling.

Why is water an important solvent and transport medium?

Because water is polar, it dissolves and dissociates ionic substances and forms hydration layers around charged molecules such as proteins. It is the body's major transport medium.

How is water involved in chemical reactions and cushioning?

Water participates in hydrolysis and dehydration synthesis reactions. It also cushions organs from trauma; for example, cerebrospinal fluid cushions nervous system organs.

What are salts?

Salts are ionic compounds that dissociate into separate ions in water: cations are positively charged and anions are negatively charged.

What are electrolytes, and why are ions important?

Ions in solution are electrolytes because they conduct electrical current. Ions such as sodium, potassium, calcium, and iron have specialized body functions, and ionic balance is important for homeostasis.

What are acids and bases?

Acids are proton donors that release H+ in solution. Bases are proton acceptors that take up H+; bases may also release OH− in solution.

What are examples of important acids and bases in the body?

Important acids include hydrochloric acid (HCl), acetic acid, and carbonic acid (H2CO3). Important bases include bicarbonate (HCO3−) and ammonia (NH3).

What does pH measure?

pH measures the concentration of hydrogen ions [H+] in a solution and ranges from 0–14. More H+ means greater acidity and a lower pH.

Why is the pH scale logarithmic?

Each change of one pH unit represents a 10-fold change in H+ concentration. For example, pH 5 is 10 times more acidic than pH 6.

What are the acidic, neutral, and basic pH ranges?

Acidic = pH 0–6.99 with high H+. Neutral = pH 7 with equal H+ and OH−. Basic/alkaline = pH 7.01–14 with low H+.

What is a neutralization reaction?

An acid and a base react together in a displacement reaction to form water and a salt. Example: NaOH + HCl → NaCl + H2O.

What are the major properties of carbon in organic molecules?

Carbon is electroneutral, shares electrons rather than gaining or losing them, and can form four covalent bonds. Major carbon-containing organic compounds are carbohydrates, lipids, proteins, and nucleic acids.

What are monomers and polymers?

Monomers are small building blocks that can join to form larger molecules called polymers.

What is the difference between dehydration synthesis and hydrolysis?

Dehydration synthesis joins monomers by removing water. Hydrolysis breaks molecules apart by adding water.

What are the major monomer → polymer relationships?

Carbohydrates: monosaccharides → polysaccharides. Proteins: amino acids → polypeptides/proteins. Nucleic acids: nucleotides → DNA or RNA. Lipids do not form true polymers.

What are carbohydrates and their three classes?

Carbohydrates contain C, H, and O, usually with H and O in a 2:1 ratio. They include monosaccharides (one sugar), disaccharides (two sugars), and polysaccharides (many sugars).

What are monosaccharides?

Simple sugars with 3–7 carbons and the general formula (CH2O)n. Important examples include glucose, fructose, galactose, ribose, and deoxyribose.

What are disaccharides?

Double sugars formed by dehydration synthesis of two monosaccharides. Important examples are sucrose, maltose, and lactose. Example: glucose + fructose → sucrose + water.

What are the major polysaccharides?

Starch = carbohydrate storage in plants; glycogen = carbohydrate storage in animals; cellulose = indigestible structural carbohydrate in plants. formed by dehydration synthesis of monomers

What are the main characteristics and types of lipids?

Lipids contain C, H, and O and sometimes P, and they are insoluble in water. Major types are triglycerides, phospholipids, steroids, and eicosanoids.

What are triglycerides made of and what are their functions?

Triglycerides contain one glycerol and three fatty acids joined by dehydration synthesis. Their major functions are energy storage, insulation, and protection.

How do saturated and unsaturated fatty acids differ?

Saturated fatty acids have only single carbon bonds, contain the maximum number of H atoms, are relatively straight, and tend to be solid at room temperature. Unsaturated fatty acids have one or more double bonds that create kinks and tend to be liquid at room temperature.

What are examples of saturated and unsaturated fats?

Saturated fats include animal fats and butter. Unsaturated fats include plant oils such as olive oil. The slides also identify trans fats as modified unsaturated fats and omega-3 fatty acids as "heart healthy."

What is the structure of a phospholipid?

A phospholipid contains glycerol, two fatty acids, and a phosphorus-containing group. Its polar hydrophilic head is attracted to water, while its nonpolar hydrophobic tails repel water.

Why are phospholipids important?

Their hydrophilic heads and hydrophobic tails allow them to form bilayers, making phospholipids important components of cell membranes.

What are steroids, and why is cholesterol important?

Steroids consist of four interlocking rings. Cholesterol is an important steroid used to make vitamin D, steroid hormones, and bile salts, and it is also part of the plasma membrane.

What are proteins made of, and what are their general functions?

Proteins are polymers of amino acids joined by peptide bonds and contain C, H, O, N, and sometimes S and P. Their functions include structural support, catalysis, transport, contraction, communication, and defense.

What are examples of major protein functions?

Structural proteins such as collagen provide support; enzymes catalyze reactions; hemoglobin transports oxygen; actin and myosin produce contraction; receptors participate in communication; antibodies provide defense.

What is the basic structure of an amino acid?

Each amino acid contains an amine group, an acid/carboxyl group, and an R group. The R group differs among the 20 types of amino acids.

What are peptide bonds?

Peptide bonds are covalent bonds that join amino acids together. They form by dehydration synthesis and can be broken by hydrolysis.

What are the four levels of protein structure?

Primary = amino acid sequence. Secondary = local folding into alpha helices or beta pleated sheets. Tertiary = interactions that create the overall 3-D shape of one polypeptide. Quaternary = interaction of two or more polypeptide chains.

How do fibrous and globular proteins differ?

Fibrous proteins are strandlike, water-insoluble, stable, and mainly structural; examples include keratin, elastin, and collagen. Globular proteins are compact, water-soluble, sensitive to environmental changes, and commonly functional; examples include antibodies, hormones, enzymes, and molecular chaperones.

What is protein denaturation?

Denaturation occurs when a globular protein unfolds and loses its functional 3-D shape. Changes in pH or temperature can cause it. Mild denaturation may be reversible, while extreme changes can make it irreversible.

What is activation energy?

Activation energy is the initial energy needed to begin a chemical reaction and break or form bonds.

How do enzymes speed up reactions?

Enzymes act as catalysts by lowering the activation energy barrier, allowing reactions that would eventually occur to happen more quickly.

What are a substrate, active site, and enzyme-substrate complex?

The substrate is the reactant an enzyme acts on. It binds to a specific region called the active site, forming an enzyme-substrate complex.

What is induced fit?

When a substrate binds, the enzyme changes slightly so chemical groups in the active site are positioned more effectively to catalyze the reaction.

What happens during the enzyme catalytic cycle?

Substrate binds to the active site → enzyme-substrate complex forms → reaction occurs → product is released → enzyme remains unchanged and can be used again.

How does substrate concentration affect enzyme activity?

Increasing substrate concentration can increase reaction rate until all enzyme active sites are occupied. At this point the enzyme is saturated, and adding more substrate will not increase the rate; more enzyme is needed.

How do temperature and pH affect enzyme activity?

Each enzyme has an optimal temperature and optimal pH at which its shape and activity are best. Moving too far from these conditions decreases enzyme activity and may cause denaturation.

What are cofactors and coenzymes?

Cofactors are nonprotein helpers required by some enzymes. They may be inorganic, such as metal ions, or organic. An organic cofactor is called a coenzyme; vitamins can act as coenzymes.

How do competitive and noncompetitive inhibitors differ?

Competitive inhibitors bind to the enzyme's active site and compete with the substrate. Noncompetitive inhibitors bind elsewhere, change the enzyme's shape, and make the active site less effective.

What is feedback inhibition?

The end product of a metabolic pathway inhibits an earlier enzyme in the pathway. In the slide example, isoleucine binds to an allosteric site on the first enzyme, making its active site unavailable and stopping further isoleucine production.

How can phosphorylation control enzymes and proteins?

Protein kinase uses ATP and transfers a phosphate group to a protein, producing ADP and a phosphorylated protein. Protein phosphatase removes the phosphate group. Adding or removing the phosphate can regulate protein activity.

What are nucleic acids made of?

Nucleic acids contain C, H, O, N, and P and are polymers made from nucleotide monomers. Each nucleotide contains a nitrogenous base, a pentose sugar, and a phosphate group.

What are the two major types of nucleic acids?

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

What is the structure and function of DNA?

DNA is a double-stranded double helix located mainly in the nucleus. It contains the genetic blueprint for synthesis of proteins and uses deoxyribose sugar and the bases A, G, C, and T.

Which DNA bases are purines and pyrimidines, and how do they pair?

Purines: adenine (A) and guanine (G). Pyrimidines: cytosine (C) and thymine (T). Complementary pairing: A pairs with T, and G pairs with C.

How does RNA differ from DNA?

RNA is usually single-stranded, contains ribose instead of deoxyribose, uses uracil instead of thymine, and is active mostly outside the nucleus in protein synthesis.

What are the three major types of RNA?

Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA); together they carry out DNA's instructions for protein synthesis.

What is ATP and what is its main function?

ATP (adenosine triphosphate) captures energy released from glucose breakdown and provides immediate usable energy to power cellular reactions.

What is the structure of ATP?

ATP is an adenine-containing RNA nucleotide with two additional phosphate groups, giving it three phosphate groups total.

What happens when ATP loses phosphate groups?

Loss of the terminal phosphate converts ATP → ADP and releases usable energy. Loss of another phosphate converts ADP → AMP.

What three types of cellular work can ATP drive?

Transport work: ATP activates membrane transport proteins. Mechanical work: ATP helps contractile proteins produce movement. Chemical work: ATP provides energy for energy-requiring chemical reactions.