Bacterial Metabolism, Enzymes, and Genetics Flashcards

Comprehensive vocabulary flashcard set covering bacterial metabolism, enzyme kinetics and regulation, cellular respiration, photosynthesis, gene expression, DNA replication, and bacterial genetics.

Metabolism

The sum of all chemical reactions taking place within an organism, composed of catabolism and anabolism.

Catabolism

Metabolic reactions that break down complex molecules into simpler ones, releasing energy ("cut apart").

Anabolism

Metabolic reactions that build complex molecules from simpler precursors, requiring energy ("add together").

Reactants

Substances present at the start of a chemical reaction, written to the left of the yield arrow.

Products

Substances present at the end of a chemical reaction, written to the right of the yield arrow.

Collision Action

The requirement that reactant molecules must collide with sufficient kinetic energy to break existing bonds so new bonds can form.

Biological Catalyst

An agent, such as an enzyme, that increases chemical reaction rates in cells without being consumed or altered by the reaction.

Enzyme

A large protein molecule that functions as a biological catalyst to accelerate specific biochemical reactions.

Activation Energy

The minimum amount of energy required to initiate a chemical reaction.

Substrate

The specific reactant molecule upon which a particular enzyme acts.

Active Site

The specialized pocket or groove on an enzyme's surface into which the substrate fits and where the catalytic reaction occurs.

Enzyme Specificity

The property of an enzyme to bind only to specific substrates due to complementary active site geometry and charge.

Induced Fit Model

The concept that initial substrate binding induces a slight conformational change in the enzyme to produce an optimal fit.

Denaturation

The unravelling or unfolding of a protein's specific three-dimensional structure, leading to loss of biological function.

Optimum Temperature

The specific temperature at which a given enzyme exhibits its maximum catalytic activity.

Optimum pH

The specific pH value at which an enzyme maintains proper charge interactions and functions at peak efficiency.

Enzyme Saturation

The condition occurring at high substrate concentrations when all enzyme active sites are continuously occupied, causing reaction rate to plateau.

Competitive Inhibition

Inhibition of enzyme activity caused by an inhibitor molecule competing directly with substrate for the active site.

Noncompetitive Inhibition

Inhibition caused by an inhibitor binding to an allosteric site, altering the enzyme shape so substrate cannot fit into the active site.

Allosteric Site

An alternate regulatory binding site on an enzyme distinct from the active site.

Feedback Inhibition

A regulatory control mechanism where the end product of a metabolic pathway noncompetitively inhibits the pathway's first enzyme.

Precursor Molecules

Small carbon intermediate compounds generated during catabolism that are assembled into macromolecules during anabolism.

Reducing Power

The stored energy held in reduced electron carriers such as $\text{NADH}$ and $\text{FADH}_2$ in the form of high-energy electrons.

Oxidation

The loss of electrons or hydrogen atoms from a molecule during a chemical reaction.

Reduction

The gain of electrons or hydrogen atoms by a molecule during a chemical reaction.

Redox Reaction

A coupled oxidation-reduction reaction where electron loss by one compound is coupled to electron gain by another.

OIL RIG Mnemonic

A memory tool standing for "Oxidation Is Loss, Reduction Is Gain" of electrons or hydrogen atoms.

Nicotinamide Adenine Dinucleotide ($\text{NAD}^+$)

A positively charged coenzyme that functions as an electron carrier in cellular metabolic pathways.

NADH

The reduced form of $\text{NAD}^+$ carrying two high-energy electrons and one proton ($\text{NADH} + \text{H}^+$).

Flavin Adenine Dinucleotide (FAD)

An uncharged coenzyme electron carrier involved in redox steps of cellular respiration.

FADH2

The reduced form of FAD carrying two complete hydrogen atoms (two electrons and two protons).

Adenosine Triphosphate (ATP)

The primary energy currency of the cell, composed of adenine, ribose, and three negatively charged phosphate groups.

Substrate-Level Phosphorylation

ATP synthesis achieved by the direct transfer of a high-energy phosphate group from an organic substrate to ADP.

Oxidative Phosphorylation

ATP production driven by energy released from redox reactions in an electron transport chain via chemiosmosis.

Aerobic Respiration

A metabolic pathway converting glucose into $\text{CO}_2$, $\text{H}_2\text{O}$, and ATP using $\text{O}_2$ as the final electron acceptor.

Glycolysis

A cytoplasmic pathway ("sugar splitting") that breaks one glucose molecule into two pyruvates, yielding a net $2\text{ ATP}$ and $2\text{ NADH}$.

Pyruvate

The three-carbon organic product formed at the conclusion of glycolysis.

Pyruvate Oxidation

The linking step converting each pyruvate into acetyl-CoA, producing $\text{CO}_2$ and $\text{NADH}$.

Acetyl-CoA

A two-carbon acetyl group linked to Coenzyme A that enters the Krebs cycle.

Krebs Cycle

A cyclic pathway that oxidizes acetyl-CoA to yield $\text{CO}_2$, $\text{NADH}$, $\text{FADH}_2$, and ATP via substrate-level phosphorylation.

Oxaloacetate

The four-carbon molecule that combines with acetyl-CoA to initiate each cycle of the Krebs pathway.

Electron Transport Chain (ETC)

A series of membrane-embedded protein complexes that transfer electrons to generate a proton gradient.

Chemiosmosis

The movement of hydrogen ions down their electrochemical gradient across a membrane through ATP synthase to generate ATP.

Proton Motive Force

An electrochemical gradient of hydrogen ions ($\text{H}^+$) established across a membrane by electron transport.

ATP Synthase

The membrane enzyme complex that catalyzes ATP synthesis from ADP and phosphate using energy from proton movement.

Final Electron Acceptor

The terminal substance that accepts low-energy electrons at the end of an electron transport chain.

Anaerobic Respiration

Respiration utilizing an inorganic final electron acceptor other than oxygen, such as $\text{NO}_3^-$, $\text{SO}_4^{2-}$, or $\text{CO}_3^{2-}$.

Fermentation

An anaerobic catabolic pathway consisting of glycolysis plus additional reactions that re-oxidize $\text{NADH}$ to $\text{NAD}^+$, yielding $2\text{ ATP}$.

Lactic Acid Fermentation

A fermentation process in which pyruvate is directly reduced to lactic acid to regenerate $\text{NAD}^+$.

Alcohol Fermentation

A two-step fermentation pathway converting pyruvate to acetaldehyde and then ethanol, producing $\text{CO}_2$ gas.

Propionibacterium Fermentation

Fermentation carried out by Propionibacterium producing $\text{CO}_2$ and propionic acid used in Swiss cheese.

Lactic Acid Microbes

Microorganisms such as Aspergillus, Lactobacillus, and Streptococcus that perform lactic acid fermentation.

Saccharomyces Fermentation

Alcoholic fermentation by yeast (Saccharomyces) generating $\text{CO}_2$ and ethanol for wine and beer.

Clostridium Fermentation

Fermentation performed by Clostridium species producing organic solvents like acetone and isopropanol.

Deamination

The enzymatic removal of an amino group ($-\text{NH}_2$) from an amino acid before it enters catabolic pathways.

Beta-Oxidation

The catabolic breakdown of fatty acids into two-carbon acetyl-CoA molecules for entry into the Krebs cycle.

Chlorophyll

A green pigment molecule used by photosynthetic organisms to capture light energy.

Thylakoid

A cellular membrane structure containing embedded photosystems where light-dependent photosynthetic reactions occur.

Photosystem

A light-harvesting matrix composed of chlorophyll and pigment molecules organized within a protein matrix.

Cyclic Photophosphorylation

A photosynthetic pathway where excited electrons leave chlorophyll and return to the same reaction center after producing ATP.

Noncyclic Photophosphorylation

Photosynthesis where electrons flow from water to $NADP^+$, generating ATP, NADPH, and releasing $O_2$ gas.

Carbon Fixation

The process of converting inorganic carbon dioxide gas into organic carbon compounds during the Calvin-Benson cycle.

Calvin-Benson Cycle

The light-independent pathway of photosynthesis that uses ATP and NADPH to construct glyceraldehyde 3-phosphate and glucose.

Ribulose Bisphosphate (RuBP)

The five-carbon acceptor molecule that combines with $\text{CO}_2$ at the start of the Calvin-Benson cycle.

Central Dogma of Biology

The fundamental principle describing the flow of genetic information: DNA to RNA to Protein.

Gene Expression

The process where genetic instructions encoded in DNA are transcribed into RNA and translated into functional proteins.

Bacterial Chromosome

A single, circular, double-stranded supercoiled DNA molecule carrying essential genes required for cell survival.

Plasmid

A small, circular, extrachromosomal DNA molecule carrying nonessential beneficial genes such as toxin production or drug resistance.

Nucleotide

The monomer building block of nucleic acids, consisting of a five-carbon sugar, a phosphate group, and a nitrogenous base.

Antiparallel Strands

The arrangement of double-stranded DNA where one strand runs in the $5'$ to $3'$ direction and the complementary strand runs $3'$ to $5'$.

Complementary Base Pairing

Specific hydrogen bonding rules between nucleic acid bases: Adenine pairs with Thymine (or Uracil), and Guanine pairs with Cytosine.

Gene

A specific sequence of DNA nucleotides that codes for a specific amino acid sequence in a protein.

Semiconservative Replication

The DNA replication mechanism where each generated daughter molecule contains one intact parent strand and one newly synthesized strand.

Origin of Replication (OoR)

A specific nucleotide sequence on DNA where double strands separate to initiate replication.

Replication Bubble

The open region of unwound DNA formed at an origin of replication where bidirectional copying occurs.

Replication Fork

The Y-shaped structure formed at the boundary of a replication bubble where unwinding occurs.

Helicase

The enzyme that unzips double-stranded DNA by breaking hydrogen bonds between nitrogenous base pairs.

Topoisomerase II (DNA Gyrase)

The enzyme that relaxes supercoiling and relieves mechanical stress on DNA ahead of replication forks by creating temporary cuts.

Single-Stranded Binding Proteins (SSBP)

Proteins that bind to separated single strands of DNA to prevent hydrogen bonds from reforming double-stranded DNA.

Primase

The enzyme that synthesizes short RNA primers required for DNA polymerase to initiate nucleotide addition.

DNA Polymerase III

The main enzyme complex that adds complementary DNA nucleotides in the $5'$ to $3'$ direction during replication.

DNA Polymerase I

The enzyme whose exonuclease activity removes RNA primers and replaces them with newly synthesized DNA nucleotides.

DNA Ligase

The enzyme that joins Okazaki fragments by sealing gaps in the sugar-phosphate backbone.

Sliding Clamp

A protein factor that holds DNA Polymerase III securely attached to the template strand during nucleotide polymerization.

Leading Strand

The new DNA strand synthesized continuously in the $5'$ to $3'$ direction toward the advancing replication fork.

Lagging Strand

The new DNA strand synthesized discontinuously in short fragments away from the replication fork.

Okazaki Fragments

Short segments of DNA synthesized discontinuously on the lagging template strand.

Transcription

The process of synthesizing a complementary single-stranded RNA molecule using a DNA template strand.

RNA Polymerase

The primary enzyme that binds DNA, separates strands, and builds an RNA transcript in the $5'$ to $3'$ direction.

Promoter

A specific DNA sequence upstream of a gene where RNA polymerase binds to initiate transcription.

Messenger RNA (mRNA)

The type of RNA that carries protein-building genetic instructions from DNA to the ribosome.

Transfer RNA (tRNA)

An RNA molecule featuring an anticodon and amino acid attachment site that delivers amino acids during translation.

Ribosomal RNA (rRNA)

The RNA component that combines with proteins to construct functional ribosomal subunits.

Translation

The cytoplasmic process of decoding an mRNA nucleotide sequence into a specific sequence of amino acids to form a protein.

Codon

A three-nucleotide sequence on mRNA that codes for a specific amino acid or translation stop signal.

Anticodon

A triplet sequence of nucleotides on a tRNA molecule complementary to a specific codon on mRNA.

Start Codon

The mRNA triplet AUG that initiates translation and specifies the amino acid methionine.

70S Ribosome

The prokaryotic protein synthesis complex composed of a large $50S$ subunit and a small $30S$ subunit.

Silent Mutation

A base substitution mutation in DNA that alters a codon but does not change the specified amino acid.

Horizontal Gene Transfer

The transfer of genetic material between organism cells independently of vertical parent-to-offspring reproduction.