Chapter 5 Macromolecules and Biological Concepts

Flashcards covering proteins, nucleic acids, water properties, biological levels of organization, evolutionary mechanisms, scientific methodology, and chemical principles from Chapter 5 lecture notes.

Protein composition

Polymers composed of amino acid monomers linked together sequentially by covalent peptide bonds.

Origin of the term amino acid

Derived from its core molecular structure, which contains both a basic amino group ($\text{NH}_2$) and an acidic carboxyl group ($\text{COOH}$).

Amino group chemical behavior in water

Acts as a base in aqueous solutions, accepting a proton ($\text{H}^+$) from water to form a positively charged group ($\text{NH}_3^+$).

Carboxyl group chemical behavior in water

Acts as an acid in aqueous solutions, donating a proton ($\text{H}^+$) to water to form a negatively charged group ($\text{COO}^-$).

Central alpha carbon (\alpha-carbon) attachments in amino acids

Four covalent attachments bonded to the central carbon: an amino group, a carboxyl group, a single hydrogen atom, and a variable R-group.

Carbon atom valence bonding capacity

Capable of forming up to $4$ stable covalent bonds with other atoms due to its four valence electrons.

Number of standard biological amino acids

There are $20$ standard amino acids commonly utilized by living organisms to construct functional proteins.

Distinguishing structural feature of individual amino acids

The unique physical, chemical, and structural properties of the variable side chain known as the R-group.

Three primary chemical classifications of amino acid R-groups

Categorized based on side chain polarity and charge into fully charged (acidic or basic), partially charged (polar uncharged), and nonpolar (hydrophobic).

Mechanism behind fully charged R-groups

Occurs when acidic side chains donate protons or basic side chains accept protons in aqueous solution, resulting in net negative or positive electrical charges.

Significance of a full positive charge on an R-group

Indicates that the functional group acted as a base in a neutral, water-filled environment by gaining a proton.

Hydrophilic vs. hydrophobic R-group behavior

Hydrophilic R-groups contain polar or ionic bonds that interact favorably with water, whereas hydrophobic R-groups consist primarily of nonpolar bonds ($\text{C-H}$) that avoid interaction with water.

Sulfhydryl functional group composition

A functional group consisting of a sulfur atom bonded directly to a hydrogen atom ($\text{-SH}$).

Primary biological role of antibodies

Specialized defense proteins that identify and bind to foreign invaders to protect organisms from pathogen infection.

Primary biological role of enzymes

Biological catalysts that dramatically accelerate biochemical reaction rates, enabling cellular metabolic reactions, energy extraction, and biomolecule synthesis.

Role of proteins in cell motility and signaling

Function as contractile motor components for cell movement and serve as transmembrane receptors or extracellular chemical messengers for cell-to-cell communication.

Peptide bond

A specialized covalent amide linkage formed between the carboxyl carbon of one amino acid and the amino nitrogen of a second amino acid.

Functional groups involved in peptide bond formation

The carboxyl group ($\text{-COOH}$) of one amino acid reacts with the amino group ($\text{-NH}_2$) of an adjacent amino acid through a dehydration reaction.

Direction of polypeptide chain elongation

New amino acids are strictly appended to the free carboxyl terminus ($\text{C-terminus}$) of a growing polypeptide chain.

Peptide bond structural rigidity

Exhibits partial double-bond character due to electron resonance, which restricts free rotation around the backbone linkage.

Primary structure of a protein

The unique, linear arrangement and sequence of amino acids linked together by covalent peptide bonds.

Directional convention for writing amino acid sequences

Conventionally written from the free amino terminus ($\text{N-terminus}$) to the free carboxyl terminus ($\text{C-terminus}$).

Polypeptide vs. oligopeptide definition

An oligopeptide is a short chain containing fewer than $50$ amino acids, whereas a polypeptide is a longer amino acid polymer containing $50$ or more units.

Two primary types of protein secondary structure

The coiled, spring-like $\alpha$-helix and the folded, pleated sheet known as the $\beta$-pleated sheet.

Depiction of secondary structures in structural biology

Visually rendered using stylized ribbon diagrams to display local folding patterns along the polypeptide backbone.

R-group compatibility with secondary structures

Steric hindrance, physical bulk, and electrical charges of R-groups determine whether local backbone regions can adopt stable $\alpha$-helices or $\beta$-sheets.

Peptide backbone groups involved in secondary structure folding

Precise spatial alignment between carbonyl oxygen ($\text{C=O}$) and amide hydrogen ($\text{N-H}$) groups along the main peptide backbone.

Chemical bonding stabilizing protein secondary structure

 stabilized by hydrogen bonds formed between partial positive charges on $\text{N-H}$ groups and partial negative charges on $\text{C=O}$ groups on the polypeptide backbone.

Bonds maintaining protein primary structure

Covalent peptide bonds connecting consecutive amino acid residues in a linear chain.

Interactions stabilizing protein tertiary structure

Overall three-dimensional conformation stabilized by hydrogen bonds, ionic bonds, hydrophobic interactions (van der Waals forces), and covalent disulfide bridges between variable R-groups.

Mechanism of ionic bonding in tertiary protein structure

Electrostatic attractions that form between fully charged, oppositely acting acidic and basic R-group side chains.

Disulfide bridge

A strong covalent bond formed when the sulfhydryl ($\text{-SH}$) groups of two cysteine amino acid residues undergo oxidation.

Protein denaturation

The structural unfolding or disruption of a protein's native three-dimensional conformation, leading to complete loss of biological activity without breaking primary peptide bonds.

Requirements for protein quaternary structure

Requires two or more separate polypeptide chains (subunits) binding together via hydrogen bonds, ionic interactions, hydrophobic forces, or disulfide bonds.

Central paradigm of protein structure and function

Structure drives function; the explicit three-dimensional spatial arrangement of a protein directly determines its biological capability.

Full names of DNA and RNA

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

Nucleic acid

A macromolecular polymer composed of nucleotide monomers joined in a linear chain by covalent phosphodiester bonds.

Three components of a nucleotide monomer

Consists of a phosphate group, a five-carbon pentose sugar, and a nitrogen-containing nitrogenous base.

Nucleoside composition

A molecular subunit composed solely of a nitrogenous base covalently linked to a pentose sugar, lacking any phosphate group.

Phosphodiester bond

The covalent linkage that connects adjacent nucleotides by joining the sugar of one nucleotide to the phosphate group of another.

Specific groups involved in a phosphodiester bond

Forms between the phosphate group on the $5'$ carbon of one sugar and the hydroxyl ($\text{-OH}$) group on the $3'$ carbon of the adjacent sugar.

Directional polarity of nucleic acid strands

The strand ends are chemically distinct, possessing a free $5'$ phosphate group at one end and a free $3'$ hydroxyl ($\text{-OH}$) group at the other end.

Four nitrogenous bases of DNA

Cytosine ($\text{C}$), Thymine ($\text{T}$), Guanine ($\text{G}$), and Adenine ($\text{A}$).

Sugar-phosphate backbone composition

The structural framework of a nucleic acid strand, formed by alternating pentose sugar and phosphate units linked via phosphodiester bonds.

Two primary structural differences between RNA and DNA

RNA utilizes ribose sugar instead of deoxyribose and incorporates the pyrimidine base uracil ($\text{U}$) instead of thymine ($\text{T}$).

Chemical difference between ribose and deoxyribose sugars

Ribose possesses a hydroxyl group ($\text{-OH}$) on its $2'$ carbon atom, whereas deoxyribose has a hydrogen atom ($\text{-H}$) at the $2'$ position.

Functional impact of the 2' hydroxyl group in RNA

Enhances the chemical reactivity and catalytic potential of RNA, but drastically decreases its intrinsic molecular stability compared to DNA.

Complementary base pairing rules in DNA

Adenine specifically forms two hydrogen bonds with Thymine ($\text{A-T}$), and Cytosine forms three hydrogen bonds with Guanine ($\text{C-G}$).

Antiparallel orientation of DNA strands

The two complementary strands of the double helix run in opposite chemical directions ($5' \rightarrow 3'$ relative to $3' \rightarrow 5'$).

Stem-loop structure in RNA

A secondary structure formed when a single-stranded RNA folds back on itself, creating a region of double-stranded stem base pairing topped by an unpaired loop.

Pyrimidine bases

Cytosine ($\text{C}$), Thymine ($\text{T}$), and Uracil ($\text{U}$).

Ring structure of pyrimidines

Characterized by a single six-membered aromatic ring containing carbon and nitrogen atoms.

Purine bases

Adenine ($\text{A}$) and Guanine ($\text{G}$).

Ring structure of purines

Characterized by a bicyclic structure composed of a six-membered ring fused to a five-membered ring.

Relative cellular stability of RNA vs. DNA

RNA is chemically transient and degrades rapidly inside cells, whereas DNA is highly stable and persistent for long-term genetic storage.

Chemical bond within a water molecule

A polar covalent bond formed between oxygen and each hydrogen atom.

Cause of polarity in water molecule covalent bonds

Oxygen's high electronegativity pulls shared electrons closer to its nucleus, creating a partial negative charge ($\delta^-$) on oxygen and partial positive charges ($\delta^+$) on the hydrogens.

Chemical bonding between adjacent water molecules

Intermolecular hydrogen bonds formed between partial negative charges on oxygen atoms and partial positive charges on hydrogen atoms of neighboring molecules.

Four emergent properties of water

Cohesive and adhesive behavior, ability to moderate temperature, expansion upon freezing, and versatile solvent capabilities.

Cohesion in water

The hydrogen-bond-mediated attraction between identical water molecules, which generates exceptionally high surface tension.

Surface tension

A physical property that measures how difficult it is to stretch, deform, or break the surface layer of a liquid.

Adhesion in water

The physical attraction and hydrogen bonding between water molecules and other polar or charged surfaces.

Transpiration

The physiological process by which plants pull water upward from roots through xylem tissue, sustained by water cohesion and adhesion to plant cell walls.

Kinetic energy

The fundamental energy of motion possessed by moving particles, molecules, or objects.

Distinction between temperature and heat

Temperature measures the average kinetic energy of molecules within a body, whereas heat is the total thermal energy transferred from one body to another.

Specific heat

The quantity of heat required to raise or lower the temperature of $1\,\text{g}$ of a given substance by $1\,^\circ\text{C}$.

Specific heat capacity of liquid water

Defined as $1\,\text{cal}/(\text{g}\cdot^\circ\text{C})$, which is unusually high compared to most other common liquids.

Mechanism of water temperature resistance

Its high specific heat requires substantial heat input to disrupt extensive hydrogen bonds before individual water molecules can accelerate and increase kinetic energy.

Heat of vaporization

The specific quantity of heat energy that $1\,\text{g}$ of a liquid must absorb to transition from liquid state into gas.

Evaporative cooling mechanism

Cooling of a surface that occurs as high-kinetic-energy molecules evaporate into gas, leaving behind molecules with lower average kinetic energy.

Structural cause of ice floating on liquid water

As water freezes, stable hydrogen bonds lock molecules into a spacious, fixed crystalline lattice, spreading molecules further apart and reducing solid density below liquid density.

Ecological significance of floating ice

Prevents bodies of water from freezing solid from the bottom up, insulating liquid water beneath and preserving aquatic life during freezing conditions.

Biological levels of organization (smallest to largest)

Cell, tissue, organ, organ system, organism, population, community, ecosystem, biome, biosphere.

Population (ecological definition)

A localized group of organisms belonging to the same species that inhabit a specific geographic area at the same time.

Community (ecological definition)

An interacting assemblage of diverse populations of different species coexisting within a shared environment, excluding abiotic components.

Ecosystem vs. community distinction

An ecosystem encompasses both the living biological community and all non-living abiotic factors (light, soil, water) interacting within an area.

Emergent property

A novel capability or complex characteristic that appears at higher organization levels due to the specific arrangement and interactions of simpler lower-level components.

Relationship between biological structure and function

Structure describes physical form and chemical composition, while function describes biological duty; structural design directly determines functional possibilities.

Three domains of biological classification

Domain Bacteria, Domain Archaea, and Domain Eukarya.

Structural features of Domain Bacteria

Unicellular prokaryotes featuring cell walls constructed with peptidoglycan and membrane lipids composed of unbranched fatty acid chains.

Structural features of Domain Archaea

Unicellular prokaryotes possessing unique membrane lipids with isoprenoid chains, lacking peptidoglycan, and frequently adapted to extreme environments.

Domain Eukarya composition

Unicellular and multicellular organisms constructed from eukaryotic cells with membrane-enclosed organelles and a nucleus, subdivided into protists, fungi, plants, and animals.

Central Dogma of molecular biology

The directional pathway of genetic information transfer within cells, summarized as $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$.

Gene expression

The cellular process in which genomic instructions encoded in DNA are converted into functional cellular products such as proteins.

Transcription phase of gene expression

The biological synthesis of a complementary messenger RNA (mRNA) copy using a specific genomic DNA sequence as a template.

Translation phase of gene expression

The ribosomal process where nucleotide codons in mRNA are decoded to build a specific sequence of amino acids into a protein.

Biological evolution

Heritable changes in the genetic composition and allele frequencies of a biological population over successive generations.

Gene flow

The movement and incorporation of alleles between different populations due to the migration of breeding individuals.

Genetic mutations

Heritable changes in the nucleotide sequence of genomic DNA that generate novel genetic variations within a population.

Genetic drift

Fluctuations in allele frequencies within a population caused by chance events, bottlenecks, or founder effects rather than natural selection.

Natural selection

An evolutionary process where individuals with favorable heritable traits survive and reproduce at higher rates, increasing adaptive trait frequency in subsequent generations.

Sequential steps of the scientific method

Make observations, conduct research, formulate a hypothesis, test via controlled experimentation, analyze collected data to draw conclusions, and communicate findings.

Inductive vs. deductive scientific reasoning

Inductive reasoning synthesizes general principles from specific empirical observations, whereas deductive reasoning applies general premises to logically derive specific predictions.

Controlled experiment

An experimental setup designed to isolate the effect of a single independent variable by keeping all other environmental and procedural variables strictly constant.

Independent vs. dependent variable

The independent variable is the specific factor manipulated by the researcher, while the dependent variable is the measured outcome that responds to changes.

Null hypothesis purpose

Establishes a baseline default hypothesis claiming no statistically significant difference, correlation, or effect exists between tested experimental groups.

Hypothesis vs. prediction distinction

A hypothesis provides a plausible, testable explanation for an observed phenomenon, whereas a prediction outlines a specific observable result expected during testing.

Octet rule

A chemical principle stating that atoms interact by gaining, losing, or sharing electrons to achieve a complete outer valence shell of $8$ electrons.

Isotope

Variants of a chemical element that possess the identical atomic number (protons) but differ in neutron count, resulting in distinct atomic masses.

Ion

An atom or bound group of atoms that has acquired a net electrical charge through the gain or loss of one or more valence electrons.