BIO150: Content for Test 2

Antimicrobial Therapy, Genetics, & (A Little Bit of) Metabolism

Viability

trait of living cells that are capable of growth and division

Active Energy

obtained with active intervention; spend energy to make energy

Passive Energy

obtained by the flow of entropy; obtained without intervention

Adenosine Triphosphate (ATP)

energy currency of all life, produced by the metabolism, whether it is cellular respiration/aerobic or fermentation; contains energy stored in a high-energy bond between a molecule of uncharged adenosine diphosphate and a third phosphate group to generate adenosine triphosphate

Entropy (S)

the tendency of matter in the universe to become disorganized and pursue equilibrium (K)

Equilibrium (K)

equal concentration of solute/ions across the concentration gradient; a state where the rates of opposing processes are balanced, resulting in no net change over time

Metabolism

all processes that involve the transformation of energy in a living thing; the chemical processes that occur within a living organism in order to maintain life

Catabolism

type of metabolism in which bonds are broken to create energy; digestion; complete catabolism is referred to as mineralization

Anabolism

type of metabolism in which bonds are formed to create new bonds and construct structures

Mineralization

complete oxidation; breaking of every single bond and 100% oxidation of the reductant and completed in aerobic respiration

Fermentation

a process that takes place when mineralization of glucose is not possible because it lacks an electron transport system; a metabolic process in organisms that converts carbohydrates into chemical energy, without requiring oxygen

Reducing Equivalent Balance

a measure of the electron-donating capacity in biochemical reactions; concept that makes fermenters unable to release an electron from a bond without an ion to accept an electron

Electron Transport System (ETS)

process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient

Electricity

a form of energy resulting from the existence of charged particles (such as electrons or protons), either statically as an accumulation of charge or dynamically as a current; generated by the flow of electrons towards protons

Membrane Potential

the difference in chemical concentration across a membrane resulting from the electron transport system that acts like a charged battery

Coenzyme

small, non-protein organic molecules that facilitate biochemical reactions within living organisms; transports electrons from the reductant to the electron transport system

Oxidation-Reduction Reactions

electrons are transferred from a higher electron concentration to a lower concentration by moving from one atom to another

Reductant

electron donor; applies to glucose in aerobic respiration

Oxidant

electron accepter; applies to oxygen in aerobic respiration

Enzymes

catalytic proteins that aid chemical reactions, dependent on shape and particular bonding sites; a substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction

Ionic Bond

type of chemical bond in which atoms are attracted to one another due to opposite charges

Cellular Electricity

cells can generate electrical signals through processes like electron transfer, which is crucial for energy conversion; electron transfer only applies to respiration (aerobic and anaerobic), not fermentation

Photochemical Energy

energy that takes advantage of photons (light particles)

Active Site

the enzyme’s physical features that allows it to bind to the component(s) of the reaction

Spontaneous Reaction

a reaction that follows entropy and will occur at some point without intervention but can be sped up by the presence of an enzyme

Final/Terminal Electron Acceptor

the molecule at the end of the electron transport system that accepts the final electron; present in both aerobic and anaerobic respiration, although the identity of the acceptor varies by oxygen requirement

Genetic Material

inheritable information in the form of deoxyribonucleic acid (DNA) that codes for gene products/proteins; the blueprint of life

Deoxyribonucleic Acid (DNA)

a polymer composed of two antiparallel polynucleotide chains that coil around each other to form a double helix and carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses

Ribonucleic Acid (RNA)

a single-stranded polynucleotide chain, present in all living cells; principal role is to act as a messenger carrying instructions from DNA for controlling the synthesis of proteins

Genome

all the DNA in a living creature

Chromosome

a package of DNA containing part or all of the genetic material of an organise; the structure varies by type of living thing

Genes

a section of a strand of a chromosome that may code for a protein; coding genes are sequence of nucleotides in DNA that is transcribed to produce RNA which is translated into a protein by a ribosome

Protein

gene product or the product of gene expression; large biomolecules and macromolecules that comprise one or more long chains of amino acid residues; perform a vast array of functions within organisms

Messenger RNA (mRNA)

type of RNA generated from the process of transcription to copy the genetic code to form a protein

Transfer RNA (tRNA)

type of RNA used to transport amino acids to the ribosome and RNA complex to build a protein off the blueprint of mRNA by reading the mRNA codons

Ribosomal RNA (rRNA)

a type of non-coding RNA which is the primary component of ribosomes, essential to all cells

Duplication/Replication

an exact copy of all the DNA in preparation for cell division; a complimentary and semiconservative process that takes place wherever the DNA is (in the nucleus on eukaryotes; floating in the cytoplasm in prokaryotes)

Replication Bubble

“bubble” of DNA, opened by various enzymes to create access to the genome for transcription

Replication Fork

the structure of unzipped DNA that forms during DNA transcription and/or replication; one side of the DNA replication bubble

Helicase

unwinds the chromosomal structure and the twisting/helix structure of the DNA and unzips the hydrogen bonds between bases to generate a replication fork

Topoisomerase

relieves the supercoil torsion during the unwinding of DNA (after helicase does its job of unzipping DNA) by cleaving the DNA strand apart, relieving the tension, and cleaving the DNA strand back together

Single-Stranded Binding Proteins

holds the DNA strand open during replication to maintain the replication fork; DNA doorstops

RNA Primase

generates RNA primers along the strand of DNA to define the starting point of a gene; places one primer on the leading strand and multiple on the lagging strand

DNA Polymerase

the enzyme that generates the hydrogen bonds between the old strand and the base pairs of the new strand in the semiconservative process of DNA replication, prompted by primers placed by RNA primase and removes them as the strands are generated

Leading Strand

strand of DNA in DNA replication that is built continuously; needs just one primer as the 5’ to 3’ orientation follows the replication fork

Lagging Strand

strand of DNA in DNA replication that is built discontinuously and in Okazaki fragments due to its orientation; 5’ to 3’ orientation does not follow the replication fork

Okazaki Fragments

fragments of DNA formed during the replication that generates the lagging strand in a discontinuous fashion

DNA Ligase

enzyme that binds the DNA back together after topoisomerase cuts the DNA strand to relieve torsion and binds the Okazaki fragments (on the lagging strand) to one another to create a new, continuous, complimentary strand

Mutation

any change in the DNA base pairs; the vast majority are caused by errors performed by DNA polymerase

Single-Base Substitution/Point Mutation

specific type of mutation in which one base pair is erroneously changed; caused by DNA polymerase

Transcription

forming a complimentary RNA copy of a particular gene for protein production; process of copying the information from DNA into RNA to express certain genes

RNA Polymerase

places the complimentary base pairs to generate messenger RNA (but does not form the hydrogen bonds that DNA polymerase forms) during transcription

Endoplasmic Reticulum

a continuous membrane system that forms a series of flattened sacs within the cytoplasm of eukaryotic cells and serves multiple functions, being important particularly in the synthesis, folding, modification, and transport of proteins

Translation

translating the genetic language of nucleotides (RNA which is transcribed from DNA) into amino acids to build a protein by using a ribosome as the translational machine

Codon

unit of three base pairs in RNA that codes for a particular amino acid; every possible three-base combination of the four RNA bases generates a codon

Amino Acid

basic unit of a protein, held together by peptide bonds; twenty different types of amino acids

Induction

the process where specific signals, such as hormones or other molecules, stimulate the synthesis of proteins in cells; enhances cellular protein synthesis while inhibiting protein breakdown, allowing for increased levels of specific proteins when needed

Repression

lack of protein production that ensures that unnecessary proteins are not produced, conserving cellular resources; suppression of protein synthesis, often through the action of repressor proteins that inhibit gene expression

Peptide Bond

bond that exists between amino acids to create an amino acid chain that becomes a protein

Hydrogen Bond

bond that holds two complimentary base pairs together in a DNA double helix; unzipped during replication and transcription

Covalent Bonds

a type of chemical bond that involves the sharing of electron pairs between atoms; exists in DNA as it links nucleotides together in a single strand of DNA; form between the phosphate group of one nucleotide and the sugar of the next, creating a sugar-phosphate backbone that is crucial for the structural integrity of the DNA molecule (also called phosphodiester bonds)

Ribosome

ribonucleoprotein particle found in all cells that synthesizes proteins by translating genetic information encoded in messenger RNA; creates peptide bonds between amino acids

Affinity

refers to the strength of attraction between two molecules, such as an antigen and an antibody or a receptor and its ligand

R Group

a crucial component of amino acids that defines their unique properties; in the structure of an amino acid, the R group is attached to the central carbon atom and varies among different amino acids, influencing their behavior and function in proteins

Polar R Group

carries a slightly negative charge and slightly positive charge, just like water, making it hydrophilic and therefore likely to exist on the outside of a protein, towards the cellular fluid

Nonpolar R Group

does not react with the charges present in water, making it react like a fat; balls up away from the cellular fluid

Amino Acids: how do acids and bases react to one another?

acids love bases; acids hate acids, and bases hate bases

Amino Acids: how do polar and nonpolar react to one another?

polar loves polar, and nonpolar loves polar

Repulsion

refers to the strength of opposition between two molecules, like how two negative charges oppose one another

Frameshift Mutation

 a genetic mutation caused by insertions or deletions of nucleotides that change the reading frame of a DNA sequence

Mutagen

stimuli that causes a mutation

Post-Translational Folding

choreographed, ordered series of folds due to interactions between pairs of amino acids (repulsions and affinities); must fold in the correct order to generate a function protein/enzyme

Denaturation

the alteration of its three-dimensional structure, rendering it unable to perform its biological function; the protein’s chain of amino acids stays intact, but the intricate folds and coils that give the protein its working structure unravel

Renaturation

the reverse of denaturation 

Antibiotic Resistance (AMR)

ability to survive elevated/increasing concentrations of one or more antibiotics over time

Transformation

direct uptake of bacterial DNA as a DNA repair mechanisms under stressful conditions

Transduction

phage mediated transfer of bacterial DNA from one cell to another; can be general or specialized

-cillin Antibiotics

narrow spectrum, bactericidal antibiotics that oppose the cell wall by breaking up the existing tetrapeptide X-links and/or bacteriostatic, preventing additional X-link formation by binding to tetrapeptidease (beta lactams) and produced by fungi

-sporin Antibiotics

narrow spectrum, bactericidal antibiotics that oppose the cell wall by breaking up the existing tIsoniazid

Metronidazole/Flagyl

antibiotic that makes use of oxygen and free radicals to damage DNA of the targeted microbe; drug of choice for treatment of anaerobic infections and only works on organisms incapable of efficiently detoxifying oxygen free radicals

Isoniazid

synthetic bactericidal antibiotic; “pro-drug” activated by a Mycobacterial enzyme, Emthambutol, that inhibits enzymes necessary for cell wall synthesis

Quinolones

bacteriostatic antibiotics that are semi-synthetic quinine derivatives that are particularly good to treat UTIs but has multiple side effects, including severe tendonitis

Vancomycin

antibiotic that is naturally produced by soil bacterium and was hailed as the last defense against MRSA until Vancomycin Resistant Enterococcus