Cell Biology - Introduction & Chemistry of Life

Comprehensive practice flashcards covering course overview, characteristics of living organisms, biological hierarchy, properties of water, carbohydrates, lipids, nucleic acids, and protein structure and function based on Cell Biology lecture notes.

How is biology defined in its broadest sense according to the lecture notes?

Biology is the science of living things, or the science of life.

What are the 7 characteristics shared by all living organisms?

1. Cellular organization
2. Sensitivity to environment
3. Reproduction
4. Growth and development
5. Homeostasis
6. Energy utilization
7. Evolutionary adaptation

What are the key aspects of cellular organization in living organisms?

All living organisms are made of one or more cells, are both complex and highly ordered, and all cells come from pre-existing cells.

What is homeostasis, and why is it essential for cell function?

Homeostasis is the process by which organisms maintain relatively constant internal conditions that differ from their environment. It is essential because cells can only function properly within a specific range of conditions, such as proper temperature, pH, oxygen, sugar, and other chemicals.

Why is a virus classified as a non-living entity based on the characteristics of life?

A virus lacks cellular organization, sensitivity to the environment, homeostasis, energy utilization, and cannot reproduce, grow, or develop without a host cell.

What are the five levels of hierarchical organization at the cellular level, from simplest to most complex?

Atoms, molecules, macromolecules, organelles, and cells.

What are the four levels of organization at the organismal level?

Tissues, organs, organ systems, and organisms.

What are emergent properties in hierarchical biological organization?

Emergent properties result from the interaction of components and cannot be deduced by looking at the parts themselves. Life is an emergent property of organized chemistry inside the cell.

How do ionic bonds form, and what is a hydration shell?

Ionic bonds form by the attraction of oppositely charged ions created by the gain or loss of electrons (such as $\text{Na}^+$ and $\text{Cl}^-$). A hydration shell is a group of water molecules that surround and stabilize individual ions in an aqueous solution.

What is electronegativity, and how does it determine whether a covalent bond is nonpolar or polar?

Electronegativity is an atom's affinity for electrons. Equal sharing of valence electrons results in nonpolar covalent bonds, while unequal sharing (due to differences in electronegativity) creates polar covalent bonds with positive and negative poles.

What causes hydrogen bonding between water molecules?

The polarity of water causes cohesion, where the partial negative pole of an oxygen atom in one water molecule attracts the partial positive pole of a hydrogen atom in another water molecule.

How do acids and bases differ in their effect on hydrogen ion ($\text{H}^+$) concentration in a solution?

An acid increases proton ion ($\text{H}^+$) concentration ($[\text{H}^+] > [\text{OH}^-]$), while a base accepts protons (such as $\text{OH}^-$ combining with $\text{H}^+$) to decrease $\text{H}^+$ concentration ($[\text{H}^+] < [\text{OH}^-]$) and raise the pH.

Define hydrophobic, hydrophilic, and amphiphilic molecules.

Hydrophobic molecules are nonpolar and "water-fearing" (do not mix with water). Hydrophilic molecules are polar and "water-loving" (mix with water). Amphiphilic molecules possess both hydrophobic and hydrophilic regions.

How many covalent bonds can a carbon atom form, and what defines an organic molecule?

Carbon can form up to 4 covalent bonds. Organic molecules are defined as molecules that contain carbon atoms (with the exception of $\text{CO}_2$).

Compare dehydration synthesis and hydrolysis reactions in polymer metabolism.

Dehydration synthesis joins monomers into polymers by removing a molecule of water. Hydrolysis breaks down polymers into smaller molecules by adding a molecule of water.

What is the general empirical formula for carbohydrates, and why do they store energy?

The general empirical formula is $\text{C}_n\text{H}_{2n}\text{O}_n$ (a 1:2:1 ratio of carbon, hydrogen, and oxygen). Carbohydrates store energy within their abundant $\text{C-H}$ covalent bonds.

Define monosaccharides and disaccharides, and provide examples of disaccharides mentioned in class.

Monosaccharides are single sugar monomers (3 to 7 carbons long). Disaccharides consist of two monosaccharides linked by a covalent glycosidic bond formed via dehydration synthesis. Examples include Lactose, Maltose, and Sucrose.

What are oligosaccharides, and what is their primary cellular function?

Oligosaccharides are small chains of about 3 to 10 monosaccharides linked together. They function on cell surfaces as identification markers (such as glycolipids and glycoproteins determining blood types A, B, AB, and O).

List the primary energy storage and structural polysaccharides in plants and animals.

Energy storage: Plants use Starch; Animals use Glycogen. Structural support: Plants use Cellulose; Arthropods and fungi use Chitin.

Why can humans digest starch but not cellulose?

Starch is composed of $\alpha$-glucose monomers with $\alpha$ 1-4 linkages, which human enzymes can break down. Cellulose is composed of $\beta$-glucose monomers with $\beta$ 1-4 linkages, which human digestive enzymes cannot break down.

Contrast the linkages and branching in amylose, amylopectin, and glycogen.

Amylose has unbranched 1-4 linkages. Amylopectin has 1-4 linkages with 1-6 branched linkages approximately per 20 subunits. Glycogen has 1-4 linkages with 1-6 branched linkages approximately per 10 subunits.

What are the main chemical characteristics of lipids, and how does their energy content compare to carbohydrates?

Lipids are insoluble in water and hydrophobic due to a high proportion of nonpolar $\text{C-H}$ bonds. They yield $9\,\text{kcal/g}$ of energy compared to $4\,\text{kcal/g}$ for carbohydrates. They do not form polymers.

Describe the chemical composition of a triglyceride molecule.

A triglyceride is composed of one glycerol backbone attached to three fatty acid hydrocarbon chains (commonly even-numbered chains of 14 to 20 carbons) via ester linkages.

Distinguish between saturated and unsaturated fatty acids regarding chemical bonds, melting point, and origin.

Saturated fatty acids have no double bonds between carbons, a higher melting point, and are usually of animal origin. Unsaturated fatty acids contain one or more double bonds between carbons, a lower melting point, and are usually of plant origin.

Explain the structural difference between cis and trans fatty acids and the health risk associated with trans fats.

Natural unsaturated fatty acids have double bonds in a cis configuration, creating a kink/angle. Trans fatty acids are partially hydrogenated, straight molecules that elevate LDL ("bad") cholesterol and lower HDL ("good") cholesterol, increasing the risk of coronary heart disease.

Describe the structural components of a phospholipid and explain its amphiphilic behavior.

A phospholipid consists of a glycerol backbone, two nonpolar hydrophobic fatty acid tails, and one polar hydrophilic charged phosphate head group (often linked to choline, ethanolamine, or serine). It is amphiphilic, forming micelles or lipid bilayers in water.

How do unsaturated fatty acids affect cell membrane fluidity?

Unsaturated fatty acid tails contain double bonds that create kinks, preventing tight packing between the tails and making the plasma membrane more fluid.

What is the general structure of a steroid, and what role does cholesterol play in membrane fluidity at different temperatures?

Steroids consist of a 4-carbon ring structure. At body temperature, cholesterol lowers membrane fluidity; at lower temperatures, it increases membrane fluidity to prevent the membrane from solidifying.

What three components make up a nucleotide monomer?

A pentose sugar (ribose or deoxyribose), a phosphate group attached at C-5', and a nitrogenous base attached at C-1'.

Compare the structural differences between DNA and RNA regarding sugar type, nitrogenous bases, and strand structure.

DNA contains deoxyribose sugar (H at C-2'), thymine (T), and is double-stranded. RNA contains ribose sugar (OH at C-2'), uracil (U) instead of thymine, and is single-stranded.

Classify the five nitrogenous bases into purines and pyrimidines.

Purines (double-ring): Adenine (A) and Guanine (G). Pyrimidines (single-ring): Cytosine (C), Thymine (T, DNA only), and Uracil (U, RNA only).

What bond links nucleotides in a nucleic acid backbone, in what direction does it run, and what are the base pairing rules in DNA?

Nucleotides are linked by phosphodiester bonds between C-5' and C-3' of adjacent sugars running in a 5' to 3' direction. Complementary base pairing in DNA connects Adenine (A) to Thymine (T) via 2 hydrogen bonds, and Guanine (G) to Cytosine (C) via 3 hydrogen bonds.

Name three functional types of RNA and their roles in the cell.

1. Messenger RNA (mRNA): Transfers genetic information from DNA to the ribosome.
2. Ribosomal RNA (rRNA): Structural component of ribosomes with catalytic function.
3. Transfer RNA (tRNA): Carries amino acids to the ribosome.

Name three cellular nucleotides that do not form polymers and state their functions.

1. Adenosine triphosphate (ATP): Primary energy currency of the cell.
2. Nicotinamide adenine dinucleotide (NAD) & 3. Flavin adenine dinucleotide (FAD): Electron carriers for cellular reactions.

Describe the generic chemical structure of an amino acid.

An amino acid consists of a central $\alpha$-carbon bonded to an amino group ($\text{-NH}_2$ or $\text{-NH}_3^+$), a carboxyl group ($\text{-COOH}$ or $\text{-COO}^-$), a single hydrogen atom ($\text{-H}$), and a variable side chain ($\text{R}$ group).

How is a peptide bond formed between two amino acids?

A peptide bond is formed via dehydration synthesis between the carboxyl group of one amino acid and the amino group of an adjacent amino acid, creating a polypeptide chain running from N-terminus to C-terminus.

What is the difference between a polypeptide and a protein?

A polypeptide is an unbranched polymer of amino acids linked by peptide bonds. A protein consists of one or more folded polypeptides that possess a specific 3D shape and biological function.

Define the primary, secondary, tertiary, and quaternary levels of protein structure.

Primary: Unique sequence of amino acids linked by peptide bonds. Secondary: Local folding (alpha-helix or beta-pleated sheet) formed by hydrogen bonds between atoms of the peptide backbone. Tertiary: 3D structure formed by interactions between amino acid side chains (R groups). Quaternary: Arrangement of two or more polypeptide subunits in a functional protein.

List four types of bonds or interactions between side chains (R groups) that stabilize tertiary protein structure.

1. Hydrogen bonds
2. Ionic bonds (between opposing charges)
3. Disulfide bridges (covalent bonds between cysteine residues)
4. Hydrophobic interactions / Van der Waals attractions

Name six biological functions of proteins and provide an example for each.

1. Enzyme catalysis (Amylase)
2. Defense (Antibodies)
3. Transport (Membrane transport proteins)
4. Support (Keratin, collagen, fibrin)
5. Motion (Actin and myosin filaments)
6. Regulation (Hormones such as insulin)

What is protein denaturation, what environmental factors cause it, and what is its consequence?

Denaturation is the permanent disruption of secondary, tertiary, and quaternary bonds in a protein caused by extreme temperature, pH changes, high salt concentration, organic solvents, or detergents. The protein loses its 3D shape and biological function permanently.