bio unit 1

5 kingdom hierarchy basis

Differences and similarities in morphological and nutritional characteristics.

Binomial nomenclature format

Genus and species, such as Homo sapiens.

Monera characteristics

Prokaryotic and unicellular without a membrane-bound nucleus.

Protista characteristics

Polyphyletic 'grab bag', mostly unicellular with a nucleus.

Fungi characteristics

Uni- or multicellular eukaryotes that cannot produce their own food.

Plantae characteristics

Multicellular, non-mobile photosynthetic organisms.

Animalia characteristics

Multicellular, mobile heterotrophic organisms.

Genetic translation workflow

DNA uses RNA to translate information into proteins.

Mutation occurrence

Occur randomly only in non-essential areas.

Ribosome gene sequence comparison

More similar sequences mean more closely related organisms.

The 3 domain classification system

Bacteria, Archaea, and Eukarya.

3 domain classification basis

Similarities and differences in molecular information.

Eukarya and Archaea shared traits

Cytoskeleton and phagocytosis genes.

Shared features of all cells

Cell membrane, cytosol, ATP, DNA, and ribosomes.

Eukaryote physical traits

Multicellular, Linear DNA in a nucleus, 80S ribosomes, and endomembrane system.

Prokaryote physical traits

Unicellular, Circular DNA in a nucleoid, 70S ribosomes, and no membrane-bound organelles.

Domain Bacteria cell walls

Made of peptidoglycan.

Domain Archaea cell walls

Made of pseudopeptidoglycan.

Domain Eukarya cell walls

Cellulose, hemicellulose, pectin, chitin, etc.

Why prokaryotes are small

Surface area to volume ratio decreases as the cell doubles in size.

Why eukaryotes can be large

The endomembrane system supports large protein generation.

Horizontal gene transfer

Occurs when a gene from one species becomes part of the genome in another species.

Eukarya origin

Eukarya emerged from archaea but holds genetic info from bacteria because of horizontal gene transfer.

Endosymbiotic theory

Some eukaryotic organelles were originally independent prokaryotic cells.

Origin of mitochondria and chloroplasts

Formed when two organisms formed a mutually beneficial and permanent relationship.

Evolution of eukaryotes

Life started out prokaryotic and eukaryotes evolved as a hybrid between Bacteria and Archaea.

Endosymbiosis host cell

An anaerobic Archaea-like prokaryote from ~1.5 billion years ago.

Endosymbiosis endosymbiont

A Bacteria-like prokaryote efficient at aerobic respiration.

Endosymbiosis mutual benefits

Archaea received energy (ATP) and bacteria received nutrients.

Evolution of the endomembrane system

Host cells used excess energy from endosymbiosis to evolve an endomembrane system.

Evidence for endosymbiotic theory

Mitochondria and chloroplasts match prokaryote size, have circular dsDNA, and divide by binary fission.

Organelle ribosomes

Mitochondria and chloroplasts have ribosomes more similar to modern bacterial ribosomes than eukaryotic ribosomes

Animal vs plant cell shared features

Both have a nucleus, mitochondria, microtubes, plasma membrane, and endomembrane system

Plant cell unique features

Plants have chloroplasts, a central vacuole, and a cell wall of cellulose

Classification by energy source

Phototrophs, chemotrophs, chemoorganotrophs, and chemolithotrophs

Autotroph vs heterotroph carbon sources

Autotrophs acquire carbon on their own; heterotrophs acquire carbon from other organisms.

Phototrophs

use sunlight

chemotrophs

use chemicals

chemoorganotrophs

use organic sources

chemolithotrophs

use non-organic sources

Biological system

An open thermodynamic system that continually exchanges both energy and matter with its surroundings.

Open system

A system that exchanges both energy and matter with its surroundings.

Closed system

A system that exchanges energy, but not matter, with its surroundings.

Isolated system

A system that exchanges neither energy nor matter with its surroundings.

First law of thermodynamics

Energy cannot be created or destroyed; it can only change location or transform from one form to another.

Molecular potential energy

Stored chemical energy that is higher in molecules containing a large proportion of non-polar covalent bonds.

Electrochemical gradient energy

Potential energy stored due to a solute concentration difference across a biological membrane, which can perform work when allowed to flow down the gradient.

Enthalpy ($H$)

The sum of all kinetic and potential energy contained within a thermodynamic system.

Exothermic reaction

A chemical reaction that releases heat to its surroundings, resulting in a negative change in enthalpy ($\Delta H < 0$).

Endothermic reaction

A chemical reaction that absorbs heat from its surroundings, resulting in a positive change in enthalpy ($\Delta H > 0$).

Spontaneous reaction

An energetically favorable reaction that can occur under given conditions without requiring a continuous input of energy.

Entropy ($S$)

A measure of how dispersed or spread out the energy of a system and its surroundings is, expressed in $J\,mol^{-1}\,K^{-1}$.

Second law of thermodynamics

The law stating that the total entropy of the universe ($\Delta S_{\text{total}}$) always increases during any spontaneous process.

Condition for system entropy decrease

A system's entropy can decrease ($\Delta S_{\text{system}} < 0$) if the entropy of the surroundings increases by a greater magnitude.

Free energy ($G$)

The portion of a system's energy available to perform work under constant cellular temperature and pressure.

Exergonic reaction

A spontaneous reaction in which free energy is released ($\Delta G < 0$), leaving products with less free energy than reactants.

Endergonic reaction

A non-spontaneous reaction requiring an input of free energy, in which products have more free energy than reactants ($\Delta G > 0$).

Gibbs free energy equation (system terms)

$$\Delta G = \Delta H - T \cdot \Delta S_{\text{system}}$$

Gibbs free energy equation (total universe entropy)

$$\Delta G = -T \cdot \Delta S_{\text{total}}$$

Chemical equilibrium

The dynamic state where forward and reverse reaction rates are equal, resulting in constant substrate/product ratios and $\Delta G = 0$.

Standard free energy change ($\Delta G^\circ$)

The free energy change measured under standardized conditions ($25\,^\circ\text{C}$, $1\,\text{atm}$, and $1.0\,\text{M}$ reactant/product concentrations).

Cellular free energy equation

$$\Delta G = \Delta G^\circ + RT \ln\left(\frac{[\text{products}]}{[\text{reactants}]}\right)$$

Catabolism

Metabolic pathways that break down complex organic molecules into simpler ones, releasing energy.

Anabolism

Metabolic pathways that consume energy to synthesize complex cellular molecules from simpler precursors.

Connected reactions

Metabolic reaction sequences where the product of an initial reaction serves directly as the substrate for the next reaction.

Coupled reactions

Processes where an exergonic reaction (such as ATP hydrolysis) provides the free energy required to drive an endergonic reaction.

Biological composition of catalysts

Most biological catalysts are proteins (enzymes), while some are RNA molecules (ribozymes).

Three main categories of amino acid R-groups

Non-polar (hydrophobic), uncharged polar (hydrophilic), and charged polar (acidic/negatively charged or basic/positively charged).

Structural hierarchy: Peptide vs. Polypeptide vs. Protein

Peptide is a polymer of amino acids; polypeptide is a polymer with more than 10 amino acids; protein is one or more polypeptides folded into a functional 3D conformation.

Primary structure of a protein

The linear sequence of amino acids linked together by peptide bonds in a polypeptide chain.

Secondary structure of a protein

Local structural motifs, such as helices, sheets, and turns, formed primarily by hydrogen bonds along the peptide backbone.

Tertiary structure of a protein

The overall 3D shape of a single polypeptide chain resulting from interactions among the R-groups.

Quaternary structure of a protein

The multi-subunit spatial arrangement of more than one polypeptide chain, such as hemoglobin.

Activation energy ($E_a$ or \begin{equation*}\Delta G^{\ddagger}\end{equation*})

The initial amount of energy required to destabilize bonds in reactant molecules to initiate a chemical reaction.

Effect of biological catalysts on activation energy ($E_a$) and free energy change ($ $\Delta G$)

Catalysts lower the activation energy ($E_a$) of a reaction to speed up the rate, but do not alter the overall free energy change ($\Delta G$).

Induced fit model

Mechanism of enzyme action where substrate binding induces a conformational change in the active site, forcing reactants into the transition state.

Substrate orientation strategy in catalysis (e.g., Hexokinase)

The active site holds multiple substrates in precise alignment so their reactive functional groups can interact directly without bending or charging.

Charge interaction strategy in catalysis (e.g., Pepsin)

Active site amino acids alter the local chemical environment to generate reactive ions (like $\text{OH}^-$ from water) that break substrate bonds without forming a covalent intermediate.

Substrate strain / distortion strategy in catalysis (e.g., Trypsin)

An active site amino acid residue (e.g., serine) directly attacks the substrate to form a temporary covalent link, physically straining and cleaving the targeted bond.

$V_{\text{max}}$ in enzyme kinetics

The maximum rate of an enzymatic reaction achieved when the enzyme active sites are completely saturated with substrate.

Denaturation of enzymes

The loss of an enzyme's functional 3D structure caused by environmental factors like extreme pH or high temperature, which disrupt hydrogen and ionic bonds.

Reversible competitive inhibition

Inhibition where a molecule structurally similar to the substrate noncovalently binds to the active site, directly competing with the substrate.

Allosteric (non-competitive) regulation

Regulation where a molecule noncovalently binds to a site other than the active site, inducing a conformational change that alters substrate affinity.

Feedback inhibition

A regulatory mechanism in biochemical pathways where the end product of a pathway inhibits an enzyme operating early in the pathway.