Microbiology Test (6-10)

Restriction Enzymes

(restriction endonucleases) bacterial enzymes produced as a protection mechanism to cut and destroy foreign cytoplasmic DNA that is most commonly a result of bacteriophage infection. Stewart Linn and Werner Arber discovered restriction enzymes in their 1960s studies of how E. coli limits bacteriophage replication on infection. Today, we use restriction enzymes extensively for cutting DNA fragments that can then be spliced into another DNA molecule to form recombinant molecules. Each restriction enzyme cuts DNA at a characteristic recognition site, a specific, usually palindromic, DNA sequence typically between four to six base pairs in length. A palindrome is a sequence of letters that reads the same forward as backward. (The word "level" is an example of a palindrome.) Palindromic DNA sequences contain the same base sequences in the 5ʹ to 3ʹ direction on one strand as in the 5ʹ to 3ʹ direction on the complementary strand. A restriction enzyme recognizes the DNA palindrome and cuts each backbone at identical positions in the palindrome. Some restriction enzymescut to produce molecules that have complementary overhangs (sticky ends) while others cut without generating such overhangs, instead producing blunt ends

Other Non-Cellular Infectious Agents

* Prions: stanly crusiner; infection protein particles that cause spongy form encephalopathy; mad cow disease and we get variant form as humans (jakobs disease) * Satellite viruses: piggy back; ride on the coat of other viruses, they don't have all of the gnome to take over the host cell so they piggy back so they can be reproduced (delta agent infects hepatitis B) * Viroids: naked infectious RNA strands or particles. Plant pathogens

Transport Mechanisms (Nutrient Absorption)

**PHOSPHOLIPID BILAYER=selective permeability lets nutrients in and out of cell** Passive: net movement of substances across the membrane but the movement from HIGH TO LOW (concentration); going **down or with concentration gradient; free flowing (easily passes through); does not require an expenditure energy (all work requires energy, but this does not require ATP) Active: Net movement of substances from LOW TO HIGH **against concentration gradient; requires a lot of energy (ATP); receptor carriers; energy ATP; channels (ION gated match the charge); pumps (sodium potassium pump)

Modes of Viral Multiplication: Bacteriophage vs. Enveloped Animal Virus

*Adsorption/Attachment: BAC-T attaches by tail fibers can attach to any cell wall; EAV attaches by spikes attaches to our cell membrane *Penetration: BAC-T tail fibers inject their genetic material inside of the cell; EAV lands on us and is then our cells swallow it by using a vacuole trying to protect us, can also fuse the lipid membrane of virus and swallow nucleocapsid *Uncoating/Unravelling: (Genetic material) BACT-Teither viral enzymes of host enzymes or both will unravel the genome to expose the nucleotides.; EAV viral/host enzymes or both ingest the outer covering to release the GM which is later unraveled. (UNCOAT AND UNRAVEL IS FOR EAV) * Synthesis: ** it is this phase where the viruses are the most similar (BAC-T vs EAV) the viral genome will hijack or take over the host cells machinery (nucleus) and directs it to suspend everything needed to carry out normal activity and start producing all viral parts. **EXCEPT on EAV they make all of the viral parts except for the envelope it comes from the host. * Assembly/maturation: BAC-T assemble parts or synthesize together to create a complete viral particle which then matures (Viron); the head (nucleocapsid); text says protein that creates the spikes will go and position itself along the host membrane to await release * Release: BAC-T mature virus gets out same way by bursting out (lysis); EAV nucleocapsid will fuse with spiked host membrane and then will bud off or get spit out (the opposite of how it got in)

Viruses

*Can infect ANY living cell* Elusive Virus, viron, viral particle (Acelular) They are an obligate intracellular parasite: must invade a hosts cell so that it can reproduce or replicate. It needs a host. Viron: mature viral particle ***Most viruses are SELF LIMITING (Self-limiting (a.k.a. self-recovering) is a term used in clinical medicine to refer to any disease whose natural history is to resolve without treatment.)***

Cytopathic Effects(Inclusion bodies, Syncytia, Latent/persistent infections, Transformation)

*Cell damage or effect due to viral invasion; microscopic view of damage* Syncytia (RSV repiratory syncytia virus) Large masses inside of the cell of multinucleated fused cells Inclusions: cellular debrie ( left over viral parts or damaged organelles) Transformation: normal genes/cells get converted to oncogenes; many cancers now related to prior viral infections Persistent/latent: dormant; when a virus enters the host and has activity but then goes dormant

Generation Time/Population Growth Curve

- **Generation Time= doubling time- amount of time needed/ required for a cell's population to double; GT will vary on conditions and types of organisms Lag, Log, Stationary, Death/decline - Lag: begins at inoculation; considered an adjustment period, cells acquiring nutrient and beginning metabolic activity and increasing in size; theres little is any actual cell division - **Log: most favorable conditions (optimal) cells have high nutrients increased metabolism and maximum exponential growth/division** if we have an infection or if you were trying to clean, it is the best phase of attack to KILL things - Stationary/Equilibrium phase: Mode of competition because there is a decrease in nutrients, decrease in oxygen supply, and waste is starting to become release **call is equilibrium bc number of cells living and dividing are relatively equal to the number of cells that are dying off - Death and decline: nutrients and oxygen=depleted; there is high metabolic waste, and the number of cells dying exponentially greatly outnumber any living (CHEMOSTAT- instrument that pumps a continuous supply of fresh nutrients into a growing cell culture line)

Competitive vs Noncompetitive Inhibitors/ Repressors vs Inducers

- Competitive: a molecule similar enough to a substrate (mimic molecule) that it can compete with the substrate for binding to the active/catalytic site by just blocking the substrate from binding; if mimic molecule gets there first it will have no reaction. - Noncompetitive: a repressor molecule binds to enzyme at an allosteric/ regulatory site (somewhere other than active site) site and still blocks substrate binding by altering the shape of the active site (conformational change= site changes shape). - Inducer: stimulates enzyme synthesis by supplying enough inducer molecules or substrates; binds at regulatory to prevent repressors from binding - Repressors: ceases enzyme synthesis by providing appropriate concentration of particular amino acids

Enumeration of bacteria(Indirect/Direct)

- Enumeration: quantify; to put into numbers; count number of organisms in a culture sample (Plate count) - Direct: plate count/ pour plate; spread plate; microscopic count (cytometer-thick specialized slide that has wells in order to help separate and count) Flocytometry uses a funnel to count - Indirect: Estimation of cells are perceived in a given sample; turbidity - more turbid is more microbes; does not use a number; spectrophotometer: measueres the amount of cells, based on turbidity, by the amount of light that passes through the sample.

Chromosome (Prokaryotes vs Eukaryotes)

- Eukaryotes: typically liner, multiple distinct chromosomes. Many eukaryotic cells contain two copies of each chromosome (diploid- two complete sets, one from each parent) Length of the chromosome is longer than the cell, therefore they must be tightly packed; DNA supercoiling- DNA twisted tightly to fit inside cell (nucleus). Histones (DNA binding proteins) help to fold DNA and combo of DNA and these proteins= chromatin. Topoisomerases help maintain structure of supercoiled chromosomes - Prokaryotes: usually circular, and usually only contain a single chromosomes within nucleoid. Because there's only one copy of the genes, they are haploid. Topoisomerases also help supercoiling DNA (DNA gyrase found in bacteria and some archaea- help prevent overwinding DNA(top.)) Some parts are packed tighter than others, making parts more accessible to enzymes for gene expression

Exergonic vs. Endergonic Rxns

- Exergonic: reactions that are spontaneous and release energy; reactions that release energy outwardly; typically due to bond breakage (covalent bonds) providing temporary energy to turn ADP into ATP (catabolic) - Endergonic: require energy to proceed; chemical reactions that take in and expend energy; and atp> adp+Pi (anabolic )

Enzyme Classes (6 Common)

- Hydrolases: *hydrolytic RXN; breakdown of a covalent bond using water (phosphatase) - Lyases: breakdown of a covalent bond without water or oxidation (decarboxylase); split bonds without water - Ligases: Formation of a covalent bond between two large molecules; join molecules or substrates by condensation or dehydration synthesis - Transferases: transfer of functional group from one molecule to another (Kinase); will remove, add, and or relocate functional groups from one substrate/molecule to another (when we add a phosphate group to ADP we get ATP); (NH2-Amine group; to relocate is transamination, remove is deamination). - Isomerase: rearrangement of bonds within a molecule (mutase); converts molecules to there isomeric form; isomers- mirror images of one another; same chemical formula, but are structurally different (C6H12O6 are glucose and fructose) - Oxidoreductase: transfer of electrons; results in a change in oxidation state (dehydrogenase); oxidation reduction reactions

Reaction Types

- Hydrolysis: polymers are broken into monomers; water molecule as reactant; during reaction polymer is broken into two parts- one with hydrogen from water and there other with hydroxide left over from water (lose an electron=oxidized and gained an electon=reduced **check photos); energy is made during split and it will fuel ADP+Pi= ATP; exergonic because it releases energy outwardly - Condensation/Dehydration Synthesis: Monomers join to make polymers; synthesis of polymers will produce water; In this chemical reaction, monomer molecules bind end to end in a process that results in the formation of water molecules as a byproduct Transfer: parts of molecules are transferred between one another; bonds are broken to release part and bonds are formed between released part and another molecule; very complex chemical process; ADD (-ation) Remove( de-) relocate (trans-)

WRITTEN QUESTION 1. Draw & describe a typical growth curve for microorganisms; include the 4 phases and describe what's happening in each.

- Lag: begins at inoculation; considered an adjustment period, cells acquiring nutrient and beginning metabolic activity and increasing in size; theres little is any actual cell division - **Log: most favorable conditions (optimal) cells have high nutrients increased metabolism and maximum exponential growth/division** if we have an infection or if you were trying to clean, it is the best phase of attack to KILL things - Stationary/Equilibrium phase: Mode of competition because there is a decrease in nutrients, decrease in oxygen supply, and waste is starting to become release **call is equilibrium bc number of cells living and dividing are relatively equal to the number of cells that are dying off - Death and decline: nutrients and oxygen=depleted; there is high metabolic waste, and the number of cells dying exponentially greatly outnumber any living (CHEMOSTAT- instrument that pumps a continuous supply of fresh nutrients into a growing cell culture line)

Microbial Nutrition

- Macronutrients: most abundant element in cells is hydrogen (H), followed by carbon (C), oxygen (O), nitrogen (N), phosphorous (P), and sulfur (S) are macronutrients, and they account for about 99% of the dry weight of cells.; (Organic molecules -> carbs, proteins, lipids,**nucleic acid; they are required in large amounts to these microbes - Micronutrients: sodium (Na), potassium (K), magnesium (Mg), zinc (Zn), iron (Fe), calcium (Ca), molybdenum (Mo), copper (Cu), cobalt (Co), manganese (Mn), or vanadium (V), are required by some cells in very small amounts and are called micronutrients or trace elements; needed in small amounts; TRACE ELEMENTS: zinc, Mg, Mn, Fe; microminerals usually aid in protein structure and function (enzymes) cause most enzymes are protein in nature. - Essential: All of these elements are essential to the function of many biochemical reactions, and, therefore, are essential to life.; THOSE THAT ARE REQUIRED BY THE CELL - The four most abundant elements in living matter (C, N, O, and H) - GROWTH FACTOR: essential molecules or nutrients required by the cell but must be obtained from an outside source (additional vitamins we take)

Mutualism, Commensalism & Parasitism

- Mutualism: both organisms benefit from association - Commensalism: where one organism benefits and other is unaffected not benefited or harmed - Parasitism: one organism benefits and the other is harmed

Krebs Cycle (Citric Acid)

- Pyruvate cannot go straight to Krebs cycle, it is oxidized (loses an electron) through decarboxylation (loses a Carboxyl group - COOH- loses a gas and H gets picked up by NAD to make NADH); electrons are held in the covalent bonds; we are then left with two Carboxyl groups (Acetyl-CoA); To BEIGIN KREBS CYCLE 2 CARBON ACETYL COA COMBINES WITH 4 CARBON OXYLOACITATE TO MAKE CIRTIC ACID (CITRATE); Citric acid is already isomerized and loses a carboxyl group (CO2/NADH); in the next step it loses another carboxyl group to make succinyl CoA and then we go to succinic acid by pulling off the CoA and the energy to pull this off made our first ATP; in the next reactions succinicdehydrogenase (removes 2 hydrogens)and then comes FADH2 (the annoying twin) to make fumarate; then we have Malatedehydrogenase to take the hydrogens from malic acid to make NADH to make oxyloacetate **THIS IS CYCLICAL**; we have created 3 CO2 , 4 NADH, 1 FADH2, and 1 ATP in the Krebs Cycle, turns twice because we had 2 pyruvates from Glycolysis

Oxidation-Reduction Reactions (Redox)

- Redox reactions: aka oxidation-reduction reactions; elections can move from one molecule to another so oxidization and reduction occur together; reactions involving electron transfers; ATP is made in ETC with redox reactions; fuel the majority of ATP production; oxidoreductase enzyme involved - ***OIL RIG= oxidation loses electron Reduction gains

Synergism & Antagonism

- Synergism: work together (two or more organisms) because they will benefit more because they work together - Antagonism: two or more organisms working against one another (Microbial Antagonism)= when microbes fight for space, nutrients, oxygen

Metabolism

- The term used to describe ALL chemical reactions in a cell; Sum total of all (physical) and chemical reactions within a cell or organism; 2 types= catabolism & anabolism

Glycolysis

- does not require oxygen in both aerobic and anerobic respiration TCA= important part of aerobic respiration; energy production and ETC = produces most ATP important!; ends with 2 3-carbon pyruvates.; glycolysis is splitting of sugar; before it can make 2 pyruvate it must be primed; hexokinase (6 carbon sugar) adds phosphate from atp onto glucose (ATP>ADP) makes it Glucose -6- phosphate ; then we have PhosphoGlucose Isomerase (isomer= same formular but a different structure) makes it into Fructose 6- phosphate; Next we have Phosphofructosekinase (Kinase likes to add) that phosphorylates another PO4- to carbon number 1 (we already had one on the 6th carbon) which will make it Fructose 1,6-diphosphate (1 and 6 signify where the phosphate is on a 6 carbon sugar); Next we have Aldolase which will break think molecule into two parts (isomers) (molecule on right with carbon on the end gets converted in the pyruvate and its name is glyceraldehyde 3-phosphate; next this glyceraldehyde adds another phosphate to the 1st one but this phosphate does not come from atp it was floating in the system making it glyceraldehyde 1,3 diphosphate; It then loses that phosphate and it goes to ADP to make ATP (*SUBSTRATE-LEVEL PHOSPHORYLATION) name of new molecule is 3 phosphoglycerate; that phosphate relocated from the third carbon to the second making it 2-phosphoglycerate and we are going to remove water (H and OH) and new name is phosphoenolpyruvate (this is when you take the water out-dehydration synthesis); next the phosphate is removed to make plain pyruvate and that phosphate we lost goes to another ADP yielding 2 ATP in total BUT in the isomer we had from fructose earlier, it then uses it to make 2 more ATP making *4 GROSS ATP* and 2 pyruvates.; We only have 2 NET ATP, because the system has to repay the two that it used to prime glucose in the first part (has to have 2 ATP for glycolysis) and TWO NADH**

Catabolism (digestion)

- larger complex (polymer or organic) molecules are broken down into smaller, simpler ones (monomer or inorganic), releasing energy. Most, not all catabolic reactions are hydrolytic (involve hydrolysis (water is added to split bonds)

Anabolism

- small, simple molecules are assembled into larger, complex ones, using energy (monomer and inorganic to polymer and organic); remove or take away water to combine molecules; dehydrate synthesis/ condensation reaction; pull the hydrogen and OH from molecules and it pulls the water off; Endergonic reaction so it will have ATP-Pi is ADP.

Substrate

- what enzymes bind to in order to carry out functions; the sit where the enzyme and substrate bind is called the active site and here there are amino acids that help to carry out chemical reactions; the specific molecules upon which the enzyme reacts - Enzymes will have an active site (catalytic site), and regulatory site (allosteric)

Binary Fission

A form of asexual reproduction in which one cell divides to form two identical cells.

Mutations (Common Types)

A mutation is a heritable change in the DNA sequence of an organism. The resulting organism, called a mutant, may have a recognizable change in phenotype compared to the wild type, which is the phenotype most commonly observed in nature. A change in the DNA sequence is conferred to mRNA through transcription, and may lead to an altered amino acid sequence in a protein on translation. Because proteins carry out the vast majority of cellular functions, a change in amino acid sequence in a protein may lead to an altered phenotype for the cell and organism. Point mutations may have a wide range of effects on protein function. As a consequence of the degeneracy of the genetic code, a point mutation will commonly result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change. This change would have no effect on the protein's structure, and is thus called a silent mutation missense mutation results in a different amino acid being incorporated into the resulting polypeptide. The effect of a missense mutation depends on how chemically different the new amino acid is from the wild-type amino acid. The location of the changed amino acid within the protein also is important. For example, if the changed amino acid is part of the enzyme's active site, then the effect of the missense mutation may be significant. Many missense mutations result in proteins that are still functional, at least to some degree. Sometimes the effects of missense mutations may be only apparent under certain environmental conditions; such missense mutations are called conditional mutations. Rarely, a missense mutation may be beneficial. Under the right environmental conditions, this type of mutation may give the organism that harbors it a selective advantage. nonsense mutation, converts a codon encoding an amino acid (a sense codon) into a stop codon (a nonsense codon). Nonsense mutations result in the synthesis of proteins that are shorter than the wild type and typically not functional. Because codons are triplets of nucleotides, insertions or deletions in groups of three nucleotides may lead to the insertion or deletion of one or more amino acids and may not cause significant effects on the resulting protein's functionality. However, frameshift mutations, caused by insertions or deletions of a number of nucleotides that are not a multiple of three are extremely problematic because a shift in the reading frame results. Because ribosomes read the mRNA in triplet codons, frameshift mutations can change every amino acid after the point of the mutation. The new reading frame may also include a stop codon before the end of the coding sequence. Consequently, proteins made from genes containing frameshift mutations are nearly always nonfunctional.

Obligate vs. Facilitative

Aerobe: - Obligate has to have normal oxygen in order to thrive - Facultative: can grow both with or without oxygen Anaerobe: - Obligate: has to be oxygen free to thrive - Faculative: I can let a little oxygen but too much is deadly

Aerobic vs Anaerobic Respiration

Aerobic = with Oxygen Anaerobic = without Oxygen (Lactic acid is byproduct) living things produce chemical energy by degrading sugar molecules (e.g. glucose) through aerobic respiration and anaerobic respiration. Aerobic respiration uses oxygen, hence, the term "aerobic". It has three major steps. First, it begins with glycolysis wherein the6-carbon sugar molecule is lysed into two 3-carbon pyruvatemolecules. Next, each pyruvate is converted into acetyl coenzyme A to be broken down to CO2 through the citric acid cycle. Along with this, the hydrogen atoms and electrons from the carbon molecules are transferred to the electron-carrier molecules, NADH, and FADH2. Then, these electron carriers shuttle the high-energy electrons to the electron transport chain to harness the energy and synthesize ATP. The final electron acceptor in the chain is oxygen. As for anaerobic respiration, this form of respiration does not require oxygen. However, it is similar to aerobic respiration in a way that the electrons are passed along the electron transport chain to the final electron acceptor. In anaerobic respiration, the bottom of the chain is not oxygen but other molecules, for example, sulfate ion (SO4-2) or nitrate ion (NO3-).

WRITTEN QUESTION 2. Give in your detail the process of Aerobic Cellular Respiration, (including Glycolysis, Krebs & ETC); what are the main inputs and output products?

Aerobic cellular respiration begins with the lengthy process of glycolysis with the first 5 steps being the investment phase where glucose is changed into fructose-1,6-biphosphate through three enzymatic reactions- 1st is phosphorylation at C-1, 2nd isomerization and 3rd phosphorylation at C-6 with help of Hexokinase, phosphoglucose isomerase and phosphofrucktokinase-1 respectively and 2 ATP molecules are consumer at 1st and 3rd reaction. Now, phospho-1,6-bisphosphate cleaves into two C-3 molecules that are glyceraldehyde 3-phosphate and dihydroxyacetone phosphate with the help of Aldolase enzme and these two molecules converts into one another with the help of triose phosphate isomerase enzyme. The next phase is the pay off phase and this phase has remaining 5 steps, two molecules of glyceraldehyde-3-phosphate changed into 2 molecules of pyruvate with production of 4 ATP molecules and 2 NADH also. 6th step,Glyceraldehyde-3-phosphate convert into 1,3-bisphosphoglycerate and also two molecules of NADH with help of Glyceraldehyde-3-phosphate dehydrogenase. Next step is formation of 3-phosphoglycerate with two ATP molecules with the help of phosphogkycerate kinase enzyme. 8th step is formation of 2-phosphogkycerate with the help of dismutase enzyme, in next step this changes into phosphoenolpyruvate with the help of enolase enzyme and in the final step, phosphoenolpyruvate changes into pyruvate and 2 ATP also formed with the help of pyruvate kinase enzyme. In glycolysis 2 ATP molecules are consumed with the production of 4 ATP, 2 NADH and 2 pyruvate molecules per molecule of glucose. The formed pyruvate can be used as a precursor in the citric acid cycle. Pyruvate cannot go straight to Krebs cycle, it is oxidized (loses an electron) through decarboxylation (loses a Carboxyl group - COOH- loses a gas and H gets picked up by NAD to make NADH); electrons are held in the covalent bonds; we are then left with two Carboxyl groups (Acetyl-CoA); To BEIGIN KREBS CYCLE 2 CARBON ACETYL COA COMBINES WITH 4 CARBON OXYLOACITATE TO MAKE CIRTIC ACID (CITRATE); Citric acid is already isomerized and loses a carboxyl group (CO2/NADH); in the next step it loses another carboxyl group to make succinyl CoA and then we go to succinic acid by pulling off the CoA and the energy to pull this off made our first ATP; in the next reactions succinicdehydrogenase (removes 2 hydrogens)and then comes FADH2 (the annoying twin) to make fumarate; then we have Malatedehydrogenase to take the hydrogens from malic acid to make NADH to make oxyloacetate **THIS IS CYCLICAL**; we have created 3 CO2 , 4 NADH, 1 FADH2, and 1 ATP in the Krebs Cycle, turns twice because we had 2 pyruvates from Glycolysis The final step of aerobic respiration is the ETC. The hydrogen carriers (NADH and FADH2) are oxidised and release high energy electrons and protons. The electrons are transferred to the electron transport chain, which consists of several transmembrane carrier proteins. As electrons pass through the chain, they lose energy - which is used by the chain to pump protons (H+ ions) from the matrix. The accumulation of H+ ions within the intermembrane space creates an electrochemical gradient (or a proton motive force). Chemiosmosis allows the electons to move in a gradient down the chain. Oxygen acts as the final electron acceptor, removing the de-energised electrons to prevent the chain from becoming blockedThe accumulation of H+ ions in the intermembrane space creates an electrochemical gradient (or a proton motive force) H+ ions return to the matrix via the transmembrane enzyme ATP synthase (this diffusion of ions is called chemiosmosis). As the ions pass through ATP synthase they trigger a phosphorylation reaction which produces ATP (from ADP + Pi) Total yeild of ATP is 38 for prokaryotes and 36 for Eukaryotes.

After Glycolysis and Krebs...

After both we have 3 CO2, 10 NADH, 2 FADH2, 4 NET* ATP

Genetics/Genome

All the genetic information in a cell is found in the form of DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). A gene is the segment of DNA which gives instructions for the formation of gene products, and the whole genetic information of a cell comprises the genome. The DNA is packaged in chromosomes.

Overall Yeild of ATP (Prokaryotes vs Eukaryotes)

CHEMIOSMOS: the electron carriers (NADH and FADH2) take their electrons and protons to the ETC to cash in for ATP Molecules - For each NADH it creates roughly 3 ATP for each FADH2 it yields 2 ATP- 10*3 and 2*2 is 34 ( ***Total yield of ATP glycolysis-ETC there are 38 atp for prokaryotes and 36 for Eukaryotes for Aerobic Respirations. Because of the cell wall in prokaryotes and eukaryotes in mitochondria (cell wall doesn't require as much energy as it does to travel through mitochondria).

How Viruses Are Classified and Named

Chemical content/composition, genetic core, structural makeup, and host relationship (plant virus vs animal virus),**Disease type (respiratory virus)

Cofactor Vs Coenzyme

Cofactors: an inorganic molecule necessary for an enzyme to function; A cofactor is a non-protein chemical compound. It is bound to the protein and it is needed in the biological activity of the protein. Another term for them are 'helper molecules' because they help in the biochemical transformations. There are two types of cofactors: CoenzymesProsthetic groups Coenzymes are cofactors that are bound to an enzyme loosely.Prosthetic groups are cofactors that are bound tightly to an enzyme. As additional information, an enzyme can be without a cofactor, and this is called apoenzyme. An enzyme is considered complete if it has the cofactor and it is called a holoenzyme. Coenzyme: an organic molecule necessary for an enzyme to function; A coenzyme, on the other hand, is a small, organic non-protein molecule. It carries chemical groups between enzymes. It is not regarded as a part of the enzyme's structure. Vitamins are good examples of a coenzyme. They carry chemical groups between the enzymes. Another term for them is cosubstrates. Cofactors serve the same purpose as coenzymes, as they regulate, control, and adjust how fast these chemical reactions would respond and take effect in our body. The big difference is that coenzymes are organic substances, while cofactors are inorganic.

ATP (adenosine triphosphate)

Composed of a sugar ribose, nitrogenous base adenine, and a chain of three phosphate groups bonded to it; A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the "energy currency" of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms ATP (Figure 8.3). Adding a phosphate group to a molecule, a process called phosphorylation, requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. Thus, the bonds between phosphate groups (one in ADP and two in ATP) are called high-energy phosphate bonds. When these high-energy bonds are broken to release one phosphate (called inorganic phosphate [Pi]) or two connected phosphate groups (called pyrophosphate [PPi]) from ATP through a process called dephosphorylation, energy is released to drive endergonic reactions - ATP is energy for the cell- has 3 phosphayte groups which is done through dephosphorylation; Substrate level phosphorylation - The removal/cleave of a phosphate from a substrate/molecule and directly adding to ADP to yield ATP (***GLYCOLYSIS AND KREBS); Chemiosmosis is a series of enzyme driven reactions that carry or pass electrons down a chain to generate energy used to make ATP (oxidative-phosphrylation= a bunch of enzyme carriers that throw the electrons like a hot potato and whoever is stuck with it they get reduced -high energy to low energy) - Photophosphorylation- involves photosynthesis, use of radiant or light energy to make ATP (plants do this)

Vectors (ex. Plasmids & Bacteriophages)

DNA molecules that carry DNA fragments from one organism to another. Plasmids used as vectors can be genetically engineered by researchers and scientific supply companies to have specialized properties. Some plasmid vectors contain genes that confer antibiotic resistance; these resistance genes allow researchers to easily find plasmid-containing colonies by plating them on media containing the corresponding antibiotic. The antibiotic kills all host cells that do not harbor the desired plasmid vector, but those that contain the vector are able to survive and grow. Some phage vectors can hold larger inserts than most plasmids, allowing the cloning of large eukaryotic genes and their regulatory elements. The larger insert size also reduces the total number of clones needed for a DNA library to contain the entire genome from a species.

DNA vs RNA

DNA: deoxyribonucleic acid; The building blocks of nucleic acids are nucleotides. Nucleotides that compose DNA are called deoxyribonucleotides. The three components of a deoxyribonucleotide are a five-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base, a nitrogen-containing ring structure that is responsible for complementary base pairing between nucleic acid strands; The nitrogenous bases adenine (A) and guanine (G) are the purines; they have a double-ring structure with a six-carbon ring fused to a five-carbon ring. The pyrimidines, cytosine (C) and thymine (T), are smaller nitrogenous bases that have only a six-carbon ring structure. Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. The two DNA strands are antiparallel, such that the 3ʹ prime end of one strand faces the 5ʹ prime end of the other (3 and 5 prime represents the side of the pentose sugar); Phosphodiester bonds are what hold the NUCLEOTIDES toether on the same strand; hydrogen bonds hold the ANTIPARALELL backbones together (when it comes time to trancribe (dna to rna) we need a weak assosiation (hydrogen bonds) to break).; DNA stores the information needed to build and control the cell. The transmission of this information from mother to daughter cells is called vertical gene transfer and it occurs through the process of DNA replication. DNA is replicated when a cell makes a duplicate copy of its DNA, then the cell divides, resulting in the correct distribution of one DNA copy to each resulting cell. RNA: Structurally speaking, ribonucleic acid (RNA), is quite similar to DNA. However, whereas DNA molecules are typically long and double stranded, RNA molecules are much shorter and are typically single stranded. RNA molecules perform a variety of roles in the cell but are mainly involved in the process of protein synthesis(translation) and its regulation.; RNA is typically single stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group. The subtle structural difference between the sugars gives DNA added stability, making DNA more suitable for storage of genetic information, whereas the relative instability of RNA makes it more suitable for its more short-term functions. The RNA-specific pyrimidine uracil forms a complementary base pair with adenine and is used instead of the thymine used in DNA. Even though RNA is single stranded, most types of RNA molecules show extensive intramolecular base pairing between complementary sequences within the RNA strand, creating a predictable three-dimensional structure essential for their function; Cells access the information stored in DNA by creating RNA to direct the synthesis of proteins through the process of translation. Proteins within a cell have many functions, including building cellular structures and serving as enzyme catalysts for cellular chemical reactions that give cells their specific characteristics. The three main types of RNA directly involved in protein synthesis are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).

Codons (start vs stop)

Each amino acid is defined within the mRNA by a triplet of nucleotides called a codon. The relationship between an mRNA codon and its corresponding amino acid is called the genetic code. Whereas 61 of the 64 possible triplets code for amino acids, three of the 64 codons do not code for an amino acid; they terminate protein synthesis, releasing the polypeptide from the translation machinery. These are called stop codons or nonsense codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also typically serves as the start codon to initiate translation. The reading frame, the way nucleotides in mRNA are grouped into codons, for translation is set by the AUG start codon near the 5' end of the mRNA. Each set of three nucleotides following this start codon is a codon in the mRNA message. WE NEED TO KNOW: AUG- start UAA- stop UAG- stop UGA- stop

Factors that Affect Enzyme Function

Enzymes are subject to influences by local environmental conditions such as pH, substrate concentration, and temperature. Although increasing the environmental temperature generally increases reaction rates, enzyme catalyzed or otherwise, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, losing their three-dimensional structure and function. Enzymes are also suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature. Active-site amino-acid side chains have their own acidic or basic properties that are optimal for catalysis and, therefore, are sensitive to changes in pH. Another factor that influences enzyme activity is substrate concentration: Enzyme activity is increased at higher concentrations of substrate until it reaches a saturation point at which the enzyme can bind no additional substrate. Overall, enzymes are optimized to work best under the environmental conditions in which the organisms that produce them live. For example, while microbes that inhabit hot springs have enzymes that work best at high temperatures, human pathogens have enzymes that work best at 37°C. Similarly, while enzymes produced by most organisms work best at a neutral pH, microbes growing in acidic environments make enzymes optimized to low pH conditions, allowing for their growth at those conditions. Many enzymes do not work optimally, or even at all, unless bound to other specific nonprotein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Two types of helper molecules are cofactors and coenzymes. Cofactors are inorganic ions such as iron (Fe2+) and magnesium (Mg2+) that help stabilize enzyme conformation and function. One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn2+) to function.

Common Tools Used in the Genetic Engineering Process

Enzymes: - Restriction endonuclease Originates in bacterial cells Many different types exist Natural function is to protect the bacterium from foreign DNA (bacteriophage) Recognizes 4 to 10 base pairs (palindromic sequence) Cleaves DNA at the phosphate-sugar bond (sticky ends vs. blunt ends) Used in the cloning method Ex. EcoRI from Escherichia coli - Ligases: Link DNA fragments Rejoin the phosphate-sugar bonds Used in the cloning method • Reverse transcriptase - cDNA Converts RNA to DNA Ex. Complementary DNA (cDNA) Required for eucaryote gene expression mRNA to cDNA No introns are present Analysis of DNA • Electrophoresis Separation of DNA based on size Negative charge DNA (phosphate group) migrates to positive electrode Uses: Characterizing DNA fragment; Fingerprinting; Hybridization and probes; Sequencing; Polymerase Chain Reaction • Nucleic acid hybridization -Complementation- Complementary sites on two different nucleic acids bind or hybridize - DNA hybridize with DNA; DNA hybridize with RNA; RNA hybridize with RNA -Probes -Small stretches of nucleic acid with a known sequence called an oligonucleotide Single stranded; Detects specific nucleotide sequences in unknown nucleic acid samples -Southern Blot Method for detecting an unknown sample of DNA; Incorporates restriction endonuclease, electrophoresis, denaturing, probing, and visual detection. • Sequencing Provide the identity and order of nucleotides (bases); Common Method(Sanger Method) (Fig. 10.6) • Polymerase Chain Reaction (Fig 10.7): Specific amplification of DNA • Involves a denaturing, priming (annealing), and extension cycle • 30 cycles are sufficient for detection of DNA • Can be used to detect disease or infectious agents Cloning vectors Carry a significant piece of the donor DNA (gene of interest)/Table 10.1Readily accepted DNA by the cloning hostContain an origin of replicationContain a selective antibiotic resistant geneEx. Plasmids, phages • Recombinant Organisms/Genetically Modified • Modified bacteria and viruses • Transgenic plants • Transgenic animals

Protein and Fat Catabolism for Energy

Fats:The next favorite foods to make energy after sugars, are fats. Fats are stored in our fat cells as triglycerides, just like how glucose is stored as glycogen in our liver and muscles. Triglycerides are made of three saturated fatty acids. Remember a fatty acid is just a long chain of carbons with hydrogens attached. Fatty acids are always an even number of carbon atoms long. They can be 12, 14, 16, 18, 20, 24 carbons and so on. You'll never find a FA that's an odd number of carbons. What happens is that this fatty acid is broken up two carbons at a time which turns it into the two-carbon acetyl sugar. This is called a beta oxidation reaction. Then they are broken down in the krebs cycle as if they were sugars. We know a fatty acid is not a small molecule such as glucose which is 6 carbon atoms long. It's more like, say, 24 carbons long so that would form a whopping 12 acetyl sugars and since it was a triglyceride to begin with, there would be three fatty acids. Imagine that! The catabolism of a triglyceride will create 36 acetyl sugars at once and it will flood the system and they can't go through the krebs cycle fast enough so some of these acetyl sugars become keto acids. These tend to be formed when the body is breaking down fats faster than normal. Each gram of fat provides twice as much energy as carbs or protein. Anytime there's an increased rate of fat break down, there's more keto acids (aka ketone bodies). Note that since the fats are turned into acetyl sugars that enter the krebs cycle, that means they HAVE to have oxygen. Sugars are the only foods that can be broken apart without the need for oxygen. Catabolism of fat -> Formation of ketoacids ("ketone bodies") Proteins:Proteins are the least favorite food to use as energy but if the body needs to, it will. Proteinsare made up of amino acids so when they are digested, we are left with hundreds or thousands of amino acids. The picture to your right reminds you of what an amino acid looks like. It begins with a carbon atom, attached to one side is an amino group, on the other side is an acid group (COOH), third a hydrogen. Where they differ is what's attached in place of "R." In order to use amino acids as energy, you need to convert them to sugars. Sugars are made of carbon, hydrogen, and oxygen. Fats are mostly carbon and hydrogens. Amino acids have carbon atoms, hydrogen, oxygen and NITROGEN atoms. If we are going to turn amino acids into sugars, we have to remove this nitrogen to turn it into sugar. The process of removing that amino group is called deamination (taking away the amino group, NH2). When you remove that NH2, you actually form NH3(Ammonia). Then in your liver, this ammonia is turned into Urea which is basically a carbon and oxygen with two amino groups. Your liver releases this urea into the blood stream and is the major organic waste carried in our blood stream. When they clinically measure the amount of urea in your blood, that is commonly known as the BUN level. BUN stands for Blood Urea Nitrogen (Urea contains Nitrogen). This blood is then filtered by our kidneys and appears in our urine as the major organic waste of our urine. So we've explained how amino groups are removed so it doesn't have nitrogen so chemically we are left with carbons, hydrogens and oxygens like a sugar. What is this new amino-acid-minus-the-amine-group called? Now that it doesn't have the amino group, it's still an acid and it's called a keto acid (aka "ketone bodies"). The ketoacid can be reversibly formed into acetyl sugar. Amino Acids -> NH2 removed -> NH3 -> Urea is formed in liver and excreted in urine. When the body makes sugar that wasn't a sugar, such as ketoacids into acetyl sugars, that's known as gluconeogenesis. This name is generally reserved for proteins specifically. (ANABOLISM) Beta oxidation: processes where fatty acids are broken down to produce acetyl CoA

Biotechnology vs. Genetic Engineering

Genetic Engineering: Genetic engineering is a biotechnological application where the DNA or genes of organisms are manipulated according to the requirement. Genetic engineering has been utilizing mainly to benefit the needs of humans. In genetic engineering, an identified gene of other organisms that are responsible for a certain function is isolated, and it is introduced into another organism, let the gene express, and benefit from it. The introduction of foreign genes into an organism's genome is performed through the techniques of Recombinant DNA Technology (RDT); the first use of RDT was demonstrated in 1972. The organism to whom the gene has been introduced is called the genetically modified organism. Biotechnology:Biotechnology is one of the very highly productive applications of biology where organisms have been modified in order to gain financial benefits. However, with this definition, one might feel that the use of a circus elephant can be considered as an application of biotechnology, but it is not so. It is important to notice that biotechnology uses a biological system, product, derivative, or organism, in a technological aspect to benefit financially. The main streams that biotechnology touches are cell and tissue culture, genetic engineering, microbiology, embryology, molecular biology, and many others; In biotechnology, the organisms are not always modified to be different, but their natural processes are enhanced to get the optimum product. Hence, the organisms that are being used in biotechnology may not be in grave danger under natural conditions.

Ligases

Link DNA fragments (Olazaki fragments); rejoin phosphate sugar bonds; used in cloning method

Lytic vs. Lysogenic

Lytic cycle and the lysogenic cycle are two mechanisms of viral replication, which may occur interchangeably. The main difference between lytic cycle and lysogenic cycle is that lytic cycle destroys the host cell whereas lysogenic cycle does not destroy the host cell. Lytic Cycle: a type of a viral reproduction mechanism which results in the lysis of the infected cell. It occurs through five stages: adsorption, penetration, replication, maturation, and release. Virus may attach to the cell wall or the plasma membrane of the host cell. The attachment of the virus occurs to a specific receptor of the cell membrane, weakening the cell membrane. Virus produces a hole to penetrate its genetic material into the cytoplasm of the host. If the virus enters a permissive host, the viral DNA is replicated and produces viral proteins inside the host cell. Then, new viral particles are produced by the maturation of the proteins. The lysis of the host cell releases the viral particle from the cell. Lysogenic Cycle: is a viral reproduction mechanism in which the viral DNA is integrated into the host genome. The new set of genes in the host genome is called the prophage. Thereby, viral DNA becomes a part of the host genome. Once the host genome replicates, the viral genes are also replicated simultaneously. Since the host cell does not lyse, no symptoms of viral infection are shown in host.

Important Coenzymes of Cellular Respiration

NAD and FAD

Taxonomy of Viruses

Order (ends in virales), family (end in viridae and currently there are 97) , genus (genera will just end in virus); 7-9 viral order names but we need to know primary order 3** *Caudovirales *Nidovirales *Mononegavirales

Osmosis (Tonicity)

Osmosis: the movement of water molecules from a solution with a high concentration of water molecules to a solution with a lower concentration of water molecules, through a cell's partially permeable membrane **osmotic pressure= amount of pressure or force required to suspend or stop water flow (similar to equilibrium- no net exchange of water) - Passive; movement of water from high to low; in terms of cell we measure water concentration to solute - Tonicity: hypertonic (too much water in the cell, so water flows from the cell (shriveled) hypotonic (too much water outside of cell so water flows in (cell swells) Isotonic (equal amounts of solutue on both sides, cell looks normal (equilibrium)

Diffusion

Passive: moving solutes or substances; simple (passive) {does not require carrier protein because it is right size and ionic content and charge} vs. facilitated {requires specific helper proteins to move molecules from HIGH TO LOW - aka carrier proteins - specificity- meant for only certain things, saturation- all carrier molecules have bound to their substance, competition- 100 molecules but only 70 can bind so they compete with one another to bind}

Genes (Genotype vs Phenotype)

Segments of DNA molecules are called genes, and individual genes contain the instructional code necessary for synthesizing various proteins, enzymes, or stable RNA molecules. The full collection of genes that a cell contains within its genome is called its genotype. However, a cell does not express all of its genes simultaneously. Instead, it turns on (expresses) or turns off certain genes when necessary. The set of genes being expressed at any given point in time determines the cell's activities and its observable characteristics, referred to as its phenotype. Genes that are always expressed are known as constitutive genes; some constitutive genes are known as housekeeping genes because they are necessary for the basic functions of the cell. While the genotype of a cell remains constant, the phenotype may change in response to environmental signals (e.g., changes in temperature or nutrient availability) that affect which nonconstitutive genes are expressed. For example, the oral bacterium Streptococcus mutans produces a sticky slime layer that allows it to adhere to teeth, forming dental plaque; however, the genes that control the production of the slime layer are only expressed in the presence of sucrose (table sugar). Thus, while the genotype of S. mutans is constant, its phenotype changes depending on the presence and absence of sugar in its environment.

Virus Structure

Size range: varies from .2 Micrometers up to nanometers Viral components: Capsids: Protects genetic core. outer protein covering or shell of a virus; the subunits of the protein is called capsomers which vary in size and number. This shell is added to genetic core is the nucleocapsid (can be naked or enveloped -membrane lipid covering) The viral envelope is a small portion of phospholipid membrane obtained as the virion buds from a host cell. The viral envelope may either be intracellular or cytoplasmic in origin. **ENVELOPED HAPPENS WHEN RELEASED FROM HOSTS CELL **; attached to capsid is spikes (pointed or knobular) spikes are used for attachment or adhesion. In absence of spikes then the capsid itself will aid in attachment. Spikes or capsid provoke immune response; It is the capsid that determines viral shape-Helical (ribbon like) and Icosohedral (3-d shape 20 sided structure) Complex viruses (contains things more than common -spikes, nucleocapsid, envelope-) Ex. Retrovirus (retrovirus contains reverse transcriptase (enzyme) example is HIV Ex. BACT-T (bacteriophages- specifically infect bacterial cells)

Substrate-Level vs Oxidative Phosphorylation

Substrate level phosphorylation - The removal/cleave of a phosphate from a substrate/molecule and directly adding to ADP to yield ATP (***GLYCOLYSIS AND KREBS) Oxidative phosphorylation - the energy required for ATP synthesis comes from the oxidation of NADH and FADH2 in the electron transport chain.

DNA Replication

Synthesis of DNA (copying) from a DNA blueprint; DNA replication is a Semiconservative process (After replication completion the new DNA molecules contain one original parental strand and a new daughter strand resulting is two idental strands (1=leading {the strand in the template that gets synthesized in a continuous manner 5 prime to 3 prime direction} and 2= lagging -synthesized in a dicontinuous manner, in pieces/fragmets/gaps (Olcazaki fragments)-backwards orientation (5 to 3 prime; Leading =3 to 5 to lagging will me 5 to 3; we can only build new strands going 5 to 3 prime direction so on second strand is will be oposite (antiparell) Enzymes: Helicase- unwinds the two DNA strands to expose the nucleotides RNA Primase- lays/adds RNA primer/precursor to the new daughter strand is the 5prime to 3 prime direction (temporary) **DNA Polymerase- removes RNA primer and adds complementary DNA nucleotide to daughter strand (AT-GC) DNA Ligase- links the Olcazaki fragments on lagging strand by dehydration DNA Gyrase- rewinds /supercoilds the DNA strands back together

Enviornmental Factors That Influence Microbial Growth

Temperature: - Cardinal ranges (minimum, maximum, and optimal) - Psychrophile: cold living; can grow at 0 degrees Celsius optimum growth at 15 and do not survive above 20 - Meophile: middle; most human pathogens reside**; 20-40 degrees celcius optimal temp is 35-37 C - Thermophiles: warm or hot living; 45-65 degrees celcius - Hyperthermophiles: ABOVE 65 ****80-110 - AUTOCLAVE IS AT 120 C Gaseous Requirements: Aerobe(obligate, facultative anaerobe, microaerophile) - Usually dealing with oxygen (O2) - Obligate has to have normal oxygen in order to thrive - Facultative: can grow both with or without oxygen - Microaerophile: require small concentration Anaerobe(obligate, aerotolerant) - Obligate: has to be oxygen free to trhive - Faculative: I can let a little oxygen but too much is deadly - Aerotolerant: can tolerate O2; is an anerobe can tolerate small amount but does not utilize it pH(acidophiles, alkalinophiles) - Acids vs Bases - Acidophiles (*Preference 3 and below) are below 6 and are acidic, and 8-14 is alkalinophiles (*Perfered 10 or higher) or basic Osmophiles: prefer hypertonic conditions Osmotic Pressure(Halophiles) - Halophiles: prefer salt; salt lovers Miscellaneous (radiation, barophiles) - Radiophiles: radiation, lower wavelengths of light do not harm them; they like the sun coming at them - Barophiles: pressure; organisms that prefer increased hydrostatic pressure (HP is pressure exerted by liquid in a confined space)

WRITTEN QUESTION 3. Describe the Central Dogma of Molecular Biology: How a protein is made from genetic parts; include the step processes.

The central dogma of molecular biology states that DNA contains instructions for making a protein, which are copied by RNA. RNA then uses the instructions to make a protein. Protiens determine the structure and functions of our cells and we know that those proteins are made up of amino acids. Instructions for making proteins with the correct sequence of amino acids are encoded within our DNA. DNA is first transcriped into RNA by taking the DNA strand unwound by helicase to match it up with the RNA complementary nucleotide which will create our RNA strand. RNA polymerase creates this strand until termination which will result in one of three RNA types: mRNA, tRNA, or rRNA. The processed RNA will travel to the ER to be translated into amino acids which as we stated earlier, is what we need to create proteins.

Electron Transport Chain (ETC)

The electron transport system (ETS) is the last component involved in the process of cellular respiration; it comprises a series of membrane-associated protein complexes and associated mobile accessory electron carriers. Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons from NADH and FADH2 are passed rapidly from one ETS electron carrier to the next. These carriers can pass electrons along in the ETS because of their redox potential. For a protein or chemical to accept electrons, it must have a more positive redox potential than the electron donor. Therefore, electrons move from electron carriers with more negative redox potential to those with more positive redox potential. The four major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems are the cytochromes, flavoproteins, iron-sulfur proteins, and the quinones. In each transfer of an electron through the ETS, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions (H+) across a membrane. In prokaryotic cells, H+ is pumped to the outside of the cytoplasmic membrane (called the periplasmic space in gram-negative and gram-positive bacteria), and in eukaryotic cells, they are pumped from the mitochondrial matrix across the inner mitochondrial membrane into the intermembrane space. There is an uneven distribution of H+ across the membrane that establishes an electrochemical gradient because H+ ions are positively charged (electrical) and there is a higher concentration (chemical) on one side of the membrane. (Chemiosmosis- flow of hydrogen ions across the membrane; the electron carriers (NADH and FADH2) take their electrons and protons to the ETC to cash in for ATP Molecules) The bacterial electron transport chain is a series of protein complexes, electron carriers, and ion pumps that is used to pump H+ out of the bacterial cytoplasm into the extracellular space. H+ flows back down the electrochemical gradient into the bacterial cytoplasm through ATP synthase, providing the energy for ATP production by oxidative phosphorylation.

Induced Fit vs Lock & Key

The key difference between Induced Fit and Lock and Key is that in induced fit theory, the binding of the substrate with the active site of the enzyme induces the modification of the shape of the active site into the complementary shape of the substrate. Whereas, in the lock and key theory, the substrate and the active site of the enzyme are complementary in shape at the beginning. Enzymes are catalysts of metabolic reactions. Therefore, they are specific for their substrates. The substrate binds with the active site of the enzyme and then converts into the product. Two hypothesis namely, Induced Fit hypothesis and Lock and Key hypothesis explains this binding of the substrate into the enzyme.

Respiration (cellular)

The process by which cells break down simple food molecules to release the energy they contain; the process by which organisms combine oxygen with foodstuff molecules, diverting the chemical energy in these substances into life-sustaining activities and discarding, as waste products, carbon dioxide and water.

Protein Synthesis (transcription & translation)

Transcription: Synthesis of RNA strand/molecule from a DNA template strand; strand that is transcribed is the template and the non transcribed DNA strand is the coding strand; Starts/begins at the promoter region/site; theres a beginning, middle, and end - initiation, elongation, and termination; 3 Enzymes: Helicase- opens up/unwinds the two DNA strands to expose the nucleotides (in sections). RNA Polymerase- add or lay many RNA nucleotides to the building RNA/transcribing strand (mRNA) - It will keep building until termination Gyrase- rewinds the two DNA strands that have been transcribed *RNA polymerase continues to build the RNA strand until it reaches a termination sequence; the mRNA transcript will detach/pull away, capped for protection so it is not destroyed before translation, the RNA polymerase gets removed, and once it is removed the two DNA strands rewind together by gyrase* There are primarily THREE IMPORTANT TYPES OF RNA THAT GET TRANSCRIBED FROM DNA - mRNA (determins which amino acids build the protein) (code is written in triplets -codons= amino acid) *20 naturally occuring amino acids* - tRNA (transfer) carries the anticodon and specific amino acid to the ribosomes/mRNA during translation (AUG> UAC) - rRNA (ribosomal) two ribosomal pieces made of rRNA and specialized proteins to make ribosomal subunits; Pro- 50s + 30s is 70s/ Eu- 40s and 60s is 80s ; when their not translating they are two pieces and when they are translating they come together and read mRNA *Methionine (MAIN START CODON- AUG) Translation: The process through which information encoded in messenger RNA (mRNA) directs the addition of amino acids during protein synthesis. Translation takes place on ribosomes in the cell cytoplasm, where mRNA is read and translated into the string of amino acid chains that make up the synthesized protein.

Medical Importance of Viruses

Viruses are most common cause of acute infections that do not result in hospitalization; there are exceptions

Genetic Recombination

When prokaryotes and eukaryotes reproduce asexually, they transfer a nearly identical copy of their genetic material to their offspring through vertical gene transfer. Although asexual reproduction produces more offspring more quickly, any benefits of diversity among those offspring are lost. How then do organisms whose dominant reproductive mode is asexual create genetic diversity? In prokaryotes, horizontal gene transfer (HGT), the introduction of genetic material from one organism to another organism within the same generation, is an important way to introduce genetic diversity. HGT allows even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes but that only a small fraction of the prokaryotic genome may be transferred by this type of transfer at any one time. As the phenomenon is investigated more thoroughly, it may be revealed to be even more common. Many scientists believe that HGT and mutation are significant sources of genetic variation, the raw material for the process of natural selection, in prokaryotes. Although HGT is more common among evolutionarily related organisms, it may occur between any two species that live together in a natural community. HGT in prokaryotes is known to occur by the three primary mechanisms: Transformation: naked DNA is taken up from the environment Transduction: genes are transferred between cells in a virus Conjugation: use of a hollow tube called a conjugation pilus to transfer genes between cells

Polymerase Chain Reaction (PCR)

a laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA, which can then be studied in greater detail. PCR involves using short synthetic DNA fragments called primers to select a segment of the genome to be amplified, and then multiple rounds of DNA synthesis to amplify that segment.

Enzyme

a substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction - Simple vs. conjugated: *STRUCTURE Conjugated = Usually two pieces; have a nonprotein (Co- helper or assistant can be inorganic (cofactor) or organic(coenzyme) portion and an Apoenzyme (basic protein) (if carb is attached = glycoprotein);** apoenzyme and cofactor/coenzymes= HOLOENZYME**; while simple enzymes contain protein (organic-apoenzyme) and are regular peptide chains with no other nonprotein attachments.(organic contains multiple units of C and H) - Exoenzyme vs. Endoenzyme: *LOCATION; just like what they sound like; exoenzyme (enzyme secreted by cell and carries out function outside the cell) and endoenzymes ( enzyme produces and contained by cell that carries out functions inside of that cell). - Constituted and Regulatory: *AVALIBILITY; Constituted are those that are almost always present and in ample amount for the cell; Regulatory enzymes are those which are produced/ present when the substrate is present- as needed - Induced fit: for induced fit, enzymes have to bind to a substrate in order to carry out functions; fit like puzzle pieces; induced fit involves the enzyme actively binding, closing, and taking action.

Catalyst

a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change.; speed up the rate of chemical reactions (by reducing the amount of activation energy needed); Most are composed with specialized proteins (-ase)

Reverse Transcriptases

cDNA; converts RNA to DNA (mRNA to cDNA); required to eukaryotic gene expression

Heterotrophs

depends on others for food; other feeders; feeding off of organic substances; typically they are chemoorganic organisms (feeding off organic chemicals); they are parasites (bc they feed off of living tissue); decomposer (saprobe- feed on dead and decaying matter)

Transponsons

jumping genes; exist in plasminds and chromosomes, and contain genes that encode for enzymes that remove and reintegrate the transposon; small transposons are called indertion elements

Autotrophs

makes their own food; self feeder; gain energy chemically or physically to make food; most common physical energy is radiant energy (sun) these are photo synthesizers (cyanobacteria); major producers of molecular oxygen; another type is chemotrophs= use chemicals for energy source; if they use organic chemicals for energy = chemoorganic organisms; lithoautotrophs= only rely on inorganic elements for carbon energy and food source.

Nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

Fermentation (anaerobic)

the breakdown of sugars without the use of oxygen, regenerate NAD+ so glycolysis can continue; Fermentation is the breaking down of sugar molecules into simpler compounds to produce substances that can be used in making chemical energy. Chemical energy, typically in the form of ATP, is important as it drives various biological processes. Fermentation does not use oxygen; thus, it is "anaerobic". The cells cannot make more than 2 ATP in fermentation because oxidative phosphorylation does not happen due to a lack of oxygen. There are two types of fermentation alcoholic fermentation and lactic acid fermentation. Our cells can only perform lactic acid fermentation; however, we make use of both types of fermentation using other organisms. Alcoholic Fermentation:The two pyruvate molecules are shown in this diagram come from the splitting of glucose through glycolysis. This process also produces 2 molecules of ATP. Continued breakdown of pyruvate produces acetaldehyde, carbon dioxide, and eventually ethanol. Alcoholic fermentation requires the electrons from NADH and results in the generation of NAD+. Yeast in bread dough also uses alcoholic fermentation for energy and produces carbon dioxide gas as a waste product. The carbon dioxide that is released causes bubbles in the dough and explains why the dough rises. Lactic Acid fermentation: Again, two pyruvate and two ATP molecules result from glycolysis. Reduction of pyruvate using the electrons carried by NADH produces lactate (i.e. lactic acid). While this is similar to alcoholic fermentation, there is no carbon dioxide produced in this process. Did you ever run a race, lift heavy weights, or participate in some other intense activity and notice that your muscles start to feel a burning sensation? This may occur when your muscle cells use lactic acid fermentation to provide ATP for energy. The buildup of lactic acid in the muscles causes the feeling of burning. The painful sensation is useful if it gets you to stop overworking your muscles and allow them a recovery period during which cells can eliminate the lactic acid.

Activation Energy

the minimum amount of energy required to start a chemical reaction; Activation energy is the energy needed to form or break chemical bonds and convert reactants to products.