micro exam 2

What methods of antimicrobial control can destroy all microorganisms, including endospores and viruses?

sterilization methods like autoclaving with high pressure steam, dry heat, incineration, ethylene oxide gas, and ionizing radiation like gamma rays. important in medical settings because even a few surviving microorganisms could cause contamination.

is microwaving food an effective way to kill potentially harmful microorganisms?

no because althought it can reduce the number of microorganisms by damaging proteins/membranes/enzymes with the heat, it isn’t always reliable because food can heat unevenly and create cold spots where bacteria can survive. The temperature also might not be high enough to kill some organisms like endospores. stirring and proper cooking can help make microwaving more effective.

Difference between low, intermediate, and high-level disinfectant.

Low-level:kill more vegetative bacteria, some fungi, and some viruses but don’t destroy endospores or resistant microbes.

Intermediate-level:stronger, can also destroy mycobacteria, most viruses, and fungi.

High-level:kill nearly all microorganisms and are often used for medical equipment that can’t be sterilized with heat.

Higher level=broader, more effective disinfectant

Describe physical and chemical methods of growth control.

Physical: heat, radiation, filtration, refrigeration, freezing, drying. Heat destroys proteins and membranes, radiation damages DNA and cell structures, filtration physically removes microorganisms.

Chemical: disinfectants, antiseptics, preservatives. Damage cell walls, proteins, membranes, or nucleic acids.

Both are important in food safety, medicine, lab work.

How does ultraviolet light destroy microorganisms?

UV light damages microbial DNA by causing thymine bases to form thymine dimers, which are abnormal covalent bond links that cause a kink in the DNA, which interferes with DNA replication and transcription and prevents the microorganism from reproducing. If enough damage occurs the cell dies. UV light is often used to disinfect surfaces, air, and water, but it doesn’t penetrate deeply into solids or liquids.

What is ozone and what is it used for?

a highly reactive form of oxygen made of 3 oxygen atoms (O3). It is unstable and reacts easily with cellular comonents like proteins, lipids, and nucleic acids which damages microorganisms. It is commonly used in water treatment plants, air purification systems and food processing, because it kills many bacteria, fungi, viruses, protozoa, and breaks down into oxygen so it doesn’t leave toxic residue.

Chemical disinfectants are widely used to destroy microorganisms and viruses. How effective are they and do the benefits outweight any side effects there might be?

Very effective when used at the right concentrations and contact times. they disrupt membranes, denature proteins, or damage genetic material. side effects can include skin irritation, toxicity if misued, environmental pollution, and respiratory issues. overuse may contribute to microbial resistance. benefits usually outweigh risks because chemicals are important for infection control.

how do chemical preservatives or adding salt/sugar preserve perishable products?

chemicals directly inhibit microbial growth or disrupt cellular processes like enzyme activity, membranes, and DNA replication to slow spoilage.

salt and sugar preserve food through osmotic pressure. when it is added, environment becomes hypertonic and causes water to leave microbial cells through osmosis. this process (plasmolysis) dehydrates cells and slows/stops metabolic activity to prevent growth and reproduction since they require water. ex: jams, salted meats, pickled products, dried fruits.

Preservation vs pasteurization

preservation: any method used to slow or stop microbial growth over a long period of time, such as drying, freezing, salting, chemical additives, refrigeration.

pasteurization: a specific heat treatment to reduce the number of microorganisms in liquids like milk or juice. does not sterilize the product but uses controlled heating to significantly lower microbial load while mantaining taste and nutritional value.

Give three examples of why hydrogen peroxide is a useful disinfectant.

it is an oxidizing agent that produces free radicals, which are reactive oxygen species that damage cell membranes, proteins, lipids, and DNA of microorganisms.

Wound cleaning to kill bacteria around the injury, and the enzyme catalase breaks it down into water and oxygen gas (bubbling).

Surface disinfection on countertops, medical equipment, and bathrooms by killing bacteria and viruses.

Sterilization in healthcare settings with vaporized hydrogen peroxide, only leaves behind water and oxygen.

Explain the process of autoclaving.

it uses heat and high pressure steam to kill all microorganisms. standard conditioins are 121 degrees C and 15 psi pressure for 15-20 minutes. the moist heat and high pressure destroys cell membranes, denatures proteins, and kills endospores. used on lab equipment, surgical tools, culture media, biohazard waste.

What is plasmolysis and what is its importance in bacterial growth control?

plasmolysis occurs when a cell loses water in a hypertonic environment by osmosis, which causes membrane shrinkage and dehydration, inhibiting growth. it is effective in food preservation because high salt or sugar environments remove water from microorganisms so they can’t grow well. ex: salted meat, jam, pickled foods.

Defenitions of microbial agents.

sterilization: destruction of all microbes and viruses.

disinfection: destruction of most pathogens on surfaces.

antisepsis: chemical treatment to reduce microbes on living tissue.

sanitation: reduces microbes to safe levels.

pasteurization: mild heat to reduce pathogens in food.

-cidal: kills microbes.

-static: inhibits microbial growth.

What are the classes of germicides and how do they kill?

Alcohols (ethanol, isopropanol) dissolve lipid membranes, denature proteins and enzymes so they lose their function.

Aldehydes (formaldehyde, glutaraldehyde) cross-link alkyl groups with proteins and DNA in all microbese including endospores.

Halogens (iodine, chlorine) are oxidizing agents that oxidize cellular components, break disulfide bonds in proteins, and destroy macromolecules in bacteria, fungi, viruses, and some spores.

Heavy metals (silver, mercury, copper) bind to sulfhydryl groups of proteins to permanently denature them and disable enzymes in vegetative bacteria and fungi.

What is the mode of action of antimicrobial agents against cell walls?

they damage the cell wall by blocking its synthesis, digesting it, or breaking down its surface. this makes the cell fragile and more prone to lysis. example is penicillin.

What is the mode of action of antimicrobial agents against cell membranes?

they disrupt the lipid bilayer, causing cytoplasmic contents to leak out. examples are alcohol and quaternary ammonium compounds.

What is the mode of action of antimicrobial agents against cellular synthetic processes?

they interfere with microbial replication, transcription, and translation, preventing the cell from multiplying or producing essential enzymes. examples are UV radiation and alkylating agents.

What is the mode of action of antimicrobial agents against proteins?

they break the bonds of proteins or alter their folded state to denature them and cause them to lose their normal function. examples are heat, alcohol, acids.

what kind of techniques are used in food preservation?

chemical preservation: nitrites and preservatives are added to inhibit microbial growth.

low-temp storage: food is refrigerated or frozen because the cold temperature slows metabolism and reproduction

reducing water inhibits microbial growth because microbes need water to grow. includes air drying, freeze-drying, adding salt and sugar

plasmolysis: when foods like cured meats, jams, and pickled food is when foods have a high salt/sugar content and it causes water loss from microbes.

Explain the role of potential and kinetic energy.

Potential energy is stored energy such as glucose and ATP which are stored in chemical bonds in cells. kinetic energy is energy of motion in moving molecules.

What is the difference between catabolic and anabolic reactions and what are their roles in metabolism?

Catabolism: exergonic, breaks down molecules to release energy. produces ATP, precursor metabolites, and NADH/FADH2. ex: cellular respiration, digestion, glycolysis.

Anabolism: endergonic, uses energy produced by catabolic reactions to build molecules. ex: protein synthesis, DNA synthesis, glycogen formation.

Describe the structure of ATP including the location of highest energy bonds.

adenosine triphosphate is composed of adenine, a ribose sugar, and three phosphate groups. there are phosphoanhydride bonds between phosphate groups where energy is stored, with the highest energy bonds between the second and third phosphates.

when atp is hydrolyzed it breaks down into adenosine diphosphate and Pi, so the products are more stable and electrostatic repulsion is reduced and energy can be released and used for active transport, biosynthesis, movement, metabolism.

Explain the first and second laws of thermodynamics

1. energy can’t be created or destroyed, it can only change forms. cells convert energy from one form to another (glucose to ATP and heat)

2. energy transformations increase entropy (disorder). natural, spontaneous processes always result in an increase of overall disorder. cells are highly organized, so they must continuously use energy to mantain order. some energy is always lost as heat.

Explain the function of a coenzyme.

coenzymes are organic, non-protein helper molecules, usually vitamin-derived, that assist enzymes. they bind to enzymes to activate them and allow them to catalyze reactions, and they transfer electrons, atoms, or functional groups between molecules to keep metabolism running.

ex: NAD+ acts as an electron shuttle during cellular respiration, CoA acts as a molecular carrier to help enzymes break down food into usable energy and build new molecules, FAD drives energy production and metabolism by accepting and storing electrons during cellular respiration.

What is competive vs non-competitive inhibition?

competitive: inhibitor resembles the substrate and binds an active site, competing with the substrate for the active site because it blocks access. includes sulfa drugs that compete with PABA in bacterial folic acid synthesis.

noncompetitive: inhibitor binds to a different spot on the enzyme (allosteric site), not competing for the active site but changing the enzyme’s shape so the substrate can still bind the enzyme won’t function properly. includes heavy metals such as mercury binding to the sulfhydryl group on enzymes.

How do enzymes denature?

enzymes denature when their shape changes so much that they can’t bind to substrates properly.

How do temperature, pH, and inhibitors affect enzyme activity?

high heat can break hydrogen bonds and other interactions that mantain enzyme structure, causing it to unfold. low temperatures cause molecules to move more slowly which slows enzyme activity.

changes in pH alter the charges of amino acids within the enzyme, changing its shape and active site.

enzyme inhibitors reduce enzyme activity by blocking the active site or changing the enzyme’s shape.

What are the functions of enzymes and how does structure determine specificity?

enzymes are catalysts that speed up chemical reactions by lowering activation energy, involved in digestion, metabolism, DNA replication, protein synthesis, and energy production.

they’re highly specific because the shape of their active site only fits certain substrates. the amino acid sequence determines its structure, which determines the shape of the active site, allowign enzymes to recognize and bind to specific molecules.

What are precursor metabolites?

intermediate molecules formed during metabolic pathways that can be used to build larger cellular molecules. they connect catabolic and anabolic pathways and are essential for mantaining cellular metabolism. cells use them to synthesize amino acids, lipids, nucelotides, and carbohydrates needed for growth and repair. without precursor metabolites, cells wouldn’t be able to produce important biomolecules.

in cellular respiration, glucose is converted to pyruvate. why?

conversion of glucose to pyruvate during glycolysis allows the cell to begin extracting energy stored in glucose. it releases energy that is captured in the form of ATP in NADH. pyruvate can enter later stages of cellular respiration where even more ATP is produced. breaking glucose into smaller molecules also creates precursor metabolites for other pathways. glycolysis is the first major step in energy production.

How/why is Acetyl CoA cformed from a pyruvic acid inside a mitochondrion?

in the mitochondrial matrix, pyruvate is oxidized by the pyruvate dehydrogenase complex to form acetyl CoA.

one carbon is removed as CO2 and electrons are transferred to NAD+, forming NADH. the remaining 2-carbon acetyl group attaches to CoA, forming acetyl CoA which is important because it enteres the krebs cycle for further breakdown and ATP production, linking glycolysis to the krebs cycle.

what is the summary equation of cellular respiration?

C6H12O6 + 6O2 = 6CO2 + 6H2O + ATP.

shows that glucose and oxygen are used to produce carbon dioxide, water, and ATP, releasing stored chemical energy from glucose. Most of the ATP is produced during oxidative phosphorylation. Cellular respiration is one of the main ways cells obtain usable energy.

What are the three stages of cellular respiration and where do they occur in eukaryotes vs prokaryotes?

1. Glycolysis: occurs in the cytoplasm of eukaryotes and prokaryotes.

2. Krebs cycle/citric acid cycle occurs in the mitochondrial matrix in eukaryotes, and in teh cytoplasm of prokaryotes.

3. Electron transport chain occurs in the inner mitochondrial membrane of eukaryotes, and in the plasma membrane of prokaryotes.

Why is ATP required for the preparatory steps of glycolysis, and how many?

ATP is required to phosphorylate glucose and make it more reactive. adding phosphate groups destabilizes glucose so it can be split later in the pathway. 2 ATP molecules are invested during this phase, and more ATP is produced later in glycolysis.

How many ATP and NADH are produced during glycolysis (net and total)?

total of 4 ATP produced, byt 2 ATP are used earlier resulting in net gain of 2.

2 NADH are produced through oxidation reactions, which carry high energy electrons to the ETC.

glycolysis also produces 2 pyruvate molecules from one glucose molecule

this pathway can occur with or without oxygen.

Where is pyruvate oxidized to Acetyl CoA, and what/how many molecules are produced?

occurs in the mitochondrial matrix of eukaryotic cells, and in the cytoplasm of prokaryotic cells.

each pyruvate molecule produced from glycolysis is converted to acetyl CoA by the pyruvate dehydrogenase complex. as pyruvate is oxidized, one C atom is removed and released as Co2. electrons are transferred to NAD+, forming NADH. since once glucose produces 2 pyruvate molecules ,the intermediate step produces 2 acetyl CoA, 2 NADH, and 2 Co2 total.

List the products of Krebs cycle. Explain why it is called a cycle. How many ATP, FADH2, and NADH are produced.

produces CO2, ATP, NADH, and FADH2. For every glucose molecule, the cycle runs twice because two acetyl CoA molecules are formed from glucose. total products are 2 ATP, 6 NADH, 2 FADH2, and 4 CO2 molecules. the NADH and FADH2 carry high energy electrons to the ETC.

it’s called a cycle becuase the starting molecule, oxalacetate, is regenerated at the end of the pathway so the process can repeat continuously.

Explain where and how the respiratory electron transport chain creates proton gradient.

electrons from NADH and FADH2 move through a series of membrane proteins and electron carriers. as electrons move down the chain, energy is released and used to pump hydrogen ions across the membrane which creates a proton gradient with a higher concentration of protons on one side. the stored energy in this gradient is then used by ATP synthase to produce ATP through chemiosmosis.

Distinguish between fermentation and anaerobic cellular respiration.

they both produce ATP without oxygen, but fermentation doesn’t use an ETC and relies on glycolysis to make ATP. produces much less ATP because only generates 2 from glycolysis. anaerobic respiration uses ETC but uses final electron acceptor (nitrate, sulfate) instead of oxygen, prdouces more ATP because ETC creates proton gradient for additional ATP.

What is the net yield of ATP for eukaryotes at the end of glycolysis?

net yield: 2 ATP (4 produced, 2 used)

theoretical total including oxidative phosphorylation: 5-7 ATP (2 NADH)

What is the net yield of ATP for eukaryotes at the end of glycolysis and intermediate step?

net yield: 2 ATP (no additional ATP from intermediate step)

theoretical total: 10-12 ATP

What is the net yield of ATP for eukaryotes at the end of glycolysis, intermediate step, and citric acid cycle??

net yield: 4 ATP (2 from citric acid cycle)

theoretical total: 20-22 ATP (before final ETC stage)

What is the net yield of ATP for eukaryotes at the end of complete cellular respiration?

net yield: 4 ATP

theoretical total: 30-32 ATP

what is the basic function of fermentation and how many ATP and NADH are produced?

to regenerate NAD+ from NADH under anaerobic conditions, allowing glycolysis pathway to continue operating and generate ATP without oxygen.

net ATP: 2 ATP (generated during glycolysis before fermentation)

net NADH: 0 (NADH from glycolysis is consumed and oxidized back to NAD+ during fermentation)

Compare the fate of pyruvate in lactic acid and alcohol fermentation.

lactic acid: pyruvate is directly reduced by NADH to form lactate (lactic acid)

alcohol fermentation: pyruvate is first broken down into acetaldehyde, a 2 carbon molecule, and CO2. acetaldehyde is then reduced by NADH to ethanol.

What is the summary equation of photosynthesis?

6CO2 + H2O + light = C6H12O6 (glucose) + 6O2

converts light energy into chemical energy

What are some photosynthetic pigments?

chlorphyll a: blue-green, primary pigment in photosynthesis, directly involved in light reactions, found in reaction centers of plants, algae, cyanobacteria.

chlorophyll b: yellow-green accessory pigment that broadens the light absorption range and transfers energy to chlorophyll a in plants and green algae.

carotenoids (beta-carotene, xanthophylls: yellow/orange/red pigments, absorb excess light energy, prevent oxidative damage through photoprotection, transfer energy to chlorophyll in plants, algae, photosynthetic bacteria.

phycobilins (phycoerythrin and phycocyanin): extra pigment to absorb wavelengths that chlorophyll can’t in cyanobacteria and red algae.

What is the Calvin cycle?

a process that occurs in the stroma of chloroplast to convert CO2 into carbohydrates using ATP and NADPH from light reactions.

What are the three stages of the Calvin cycle?

1. carbon fixation: convers inorganic carbon into organic molecules. CO2 combines with RuBP (ribulose biphosphate), catalzyed by RuBisCo enzyme, to form an unstable 6-carbon intermediate which splits into 3-PGA molecules.

2. reduction: ATP and NADPH from light reactions are used to reduce 3-PGA and form G3P (glyceraldehyde-3-phosphate), a high-energy sugar molecule. some leaves the cycle to build glucose.

3. regeneration of RuBP: most G3P molecules (that haven’t left the cycle) are rearranged using ATP to regenerate RuBP, allowing the cycle to continue

For every 3 CO2 = 1 G3P

For every 6 CO2 = 1 glucose

Where is the photosystem located in purple bacteria?

their photosystems are located in the plasma membrane instead of chloroplasts, embedded in the infolded membrane systems containing vesicles called chromatophores that act as pseudo-organelles to harvest light for photosynthesis

Describe the structure of chloroplasts.

double-membrane organelles in plants and algae.

outer membrane: permeable protective layer

inner membrane: selectively permeabel, controls transport into stroma

intermembrane space: area between membranes

stroma: fluid-filled interior with calvin cycle enzymes, DNA, ribosomes. site of calvin cycle

thylakoids: flattened membrane sacs with chlorophyll, photosystem, and ETC proteins. site of light reactions

thylakoid lumen: space inside thylakoid, important for proton accumulation

grana: stacks of thylakoids to increase surface area for light absorption

Describe the first main stage of photosynthesis.

light-dependent reactions, located in the thylakoid membrane, converts light energy into chemical energy. chlorophyll absorbs solar energy and uses it to split water molecules into oxygen, protons, and electrons. sunlight + water = oxygen (byproduct), ATP, NADPH.

Describe the second stage of photosynthesis.

light-independent reactions/calvin cycle, in the stroma of the chloroplast. uses energy and electrons produced by the first stage to convert CO2 into organic sugar molecules. CO2 + ATP + NADPH = glucose, recycled forms of ATP and NADPH

What photosynthetic reaction produces O2 as a byproduct, and is it produced from H2O or CO2?

O2 is a byproduct of the light dependent reaction stage, produced entirely from H2O. water undergoes photolysis (water splitting) inside the thylakoid membrane, and splits into protons and electrons to create cellular energy, and oxygen as a byproduct. 2H2O = 4H+ + 4e- + O2.

List the components of photosystems (protein-pigment complexes in thylakoid membranes) and explain the functions of each component.

Antenna complex: light harvesting, contains proteins and pigments (chlorophyll a, b, carotenoids). acts as a solar funnel, absorbs solar energy and transfers it from pigment to pigment via resonance energy transfer, channeling it towards the center.

reaction center complex: protein complex at the core of the photosystem containing a special chlorophyll a pair (P680 in photosystem II, P700 in photosystem I) that receives incoming energy. the energy excites the electrons and causes the chlorophyll pair to lose one which starts the conversion of light into chemical energy. a molecule next to the pair acts as the electron acceptor and captures the high-energy electrons and passes them into the ETC.

Why is water a crucial electron donor during photosystem II?

when electrons in P680 become excited in photosystem II, the p680 ejects the electrons to the primary electron acceptor and becomes P680+ (an oxidizing agent) that needs electrons to function again.

during the water splitting process, an oxygen-evolving complex binds and splits water molecules into 4 hydrogen ions that are released into the thylakoid space to create a concentration gradient to manufacture ATP, 4 electrons that are fed to P680+ to neutralize it so photosynthesis can occur again, and oxygen as a byproduct.

Where are ATP and NADPH made in photosynthesis?

they’re both produced during light reactions in the thylakoid membrane. ATP is produced by ATP synthase using a proton gradient (chemiosmosis), and NADPH is produced by electrons that reduce NADP+ into NADPH, near photosystem I.

Define light.

electromagnetic radiation that travels in waves. it is the primary energy source that drives photosynthetic reactions.

Define color spectrum.

the visible portion of the electromagnetic spectrum, spanning wavelengths from about 380-750 nanometers. shorter wavelengths (purple and blue) carry higher energy, while longer wavelengths like red carry lower energy. prisms separate the spectrum into distinct colors.

Define photons.

discrete packets of light energy with no mass, each one carrying a fixed amount of energy that inversely corresponds to its wavelenth. they act as the physical units that plant pigments absorb.

Define photosynthetic pigments.

chemical molecules embedded in thylakoid membranes that absorb specific wavelengths of visible light while reflecting others. primary pigment is chlorophyll a (absorbs blue-violet and red light, initiating photosynthesis). acessorry pigments like chlorophyll b and carotenoids capture other wavelengths and pass them to chlorophyll a.

Explain the functions of chloroplasts.

specialized intracellular organelles that serve as the site of photosynthesis, capturing light energy and converting into chemical energy, manufacturing food for the plant cell.

Explain the function of thylakoids.

flattened membranous sacs inside the chloroplast that contain chlorophyll and photosystems, serving as the site for light-dependent reactions and ATP generation.

Explain the function of grana.

columns formed by stacks of thylakoids that organize the thylakoids to maximize the surface area available for absorbing light photons.

Explain the function of stroma.

dense, alkaline fluid filling the inner space of the chloroplast surrounding the grana, containing enzymes necessary to run the calvin cycle and synthesize sugars.

what is RuBisCo?

ribulose-1,5-biphosphate carboxylase-oxygenase, the primary enzymes used in the calvin cycle and the most abundant protein on earth. it catalyzes carbon fixation, binding atmospheric CO2 to RuBP (a 5-C sugar), converting inorganic carbon to organic matter.

How much of CO2 is required to make one glucose?

6 molecules of CO2 are required to synthesize one molecule of glucose.

glucose has 6 C atoms, each CO2 molecule provides one. the calvin cycle fixes one CO2 molecule at a time, requiring 6 turns of the cycle to yield one glucose molecule.

What is it called when organisms can “sense” the density of cells within their own population?

quorum sensing, when cells secrete signaling molecules called autoinducers into their environment and the concentration of these molecules builds up as the cell population density increases. once the threshold concentration is reached, the molecules bind to receptors and trigger a coordinated change in gene expression across the entire population.

When does transcription begin in eukaryotes vs prokaryotes?

In prokaryotes, transcription begins immediately when the RNA polymerase binds directly to a promoter sequence on the DNA strand. In eukaryotes, transcription begins only after a complex cluster of proteins (transcription factors) first binds to the promoter to recruit and position RNA polymerase II.

Describe the major differences between prokaryotic transcription and translation.

Prokaryotes:

• transcription and translation occur in the cytoplasm

• simultaneous: translation beings while mRNA is still being transcribed

• no RNA processing, mRNA immediately ready for translation

• single type of RNA polymerase for all genes

• smaller 70S ribosomes (30S and 50S subunits)

• initial signal: ribosomes find Shine-Delgarno sequence on mRNA

• mRNA structure can be polycistronic, one mRNA molecule codes for multiple proteins

Eukaryotes

• transcription in nucleus, translation in cytoplasm

• temporal separation: transcription must finish before translation starts

• extensive RNA processing: requires 5’ cap, 3’ poly-A tail, intron splicing

• three types of RNA polymerase (I, II, III)

• larger 80S ribosomes (40S and 60S subunits)

• initial signal: ribosomes find 5’ methylguanosine cap on mRNA

• only monocistronic, one mRNA molecule per protein

Describe the structure of DNA

double-stranded molecule in a double helix shape. backbones are two outside strands made of alternating sugar (deoxyribose) and phosphate groups, running antiparallel to each other. nitrogenous bases are attached to each backbone and meet in the center, held together by weak hydrogen bonds.

What are the nitrogenous bases of DNA and what is the base-pairing rule?

adenine, thymine, cytosine, and guanine. A and G are purines (two-ringed structures), T and C are pyrimidines (one-ringed).

base pairing rule is that nitrogenous bases bond with one specific partner, and a purine must bond with a pyrimidine to keep the uniform width. A pairs with T via two H bonds, C pairs with G via three H bonds.

Why is the base pairing rule significant?

it is fundamental to how genetic information is preserved and read. allows high-fidelity replication since each strand contains a perfect complementary template of the other and allows DNA to replicate flawlessly. when cells divide, each old strand acts as a blueprint to build new partner strand. allows DNA repair, if one cell becomes damaged cellular repair enzymes can read the intact opposite strand.

What is a repressor and what does it do?

a specialized regulatory protein that shuts down gene expression by binding to a specific DNA sequence called the operator, usually near promoter site, which prevents RNA polymerase from binding to the promoter or moving forward along the template strand. repressors contain secondary binding sites for small effector molecules (inducers, co-repressors) that shift the protein’s shape and alter its affinity for the operator DNA.

What is the explanation of the elongation process in DNA?

RNA polymerase can only synthesize nucleic acid in the 5’ to 3’ direction and must read the template in the 3’ to 5’ direction.

what is a codon?

a sequential triplet of mRNA nucleotides that establishes the fundamental reading frame for protein synthesis. codons are formed in triplets, creating 64 possible combinations.

61 code for specific amino acids, and the other 3 are stop codons. AUG codes for the first amino acid, methionine, but also serves as the start codon to establish the initial reading frame.

What are introns and exons?

introns are non-coding, intervening sequences of RNA that don’t contain information for building proteins and are cut out of the pre-RNA strand during splicing.

exons are the coding, expressed sequences that carry the blueprint for the final polypeptide chain, and are chemically pasted together after the introns are removed to form a continuous, mature mRNA sequence.

Describe the structure of ribosomes.

macromolecular assembly plants composed of 60% rRNA and 40% protein. The small subunit (30S or 60S) forms the base of the machine, with a specialized groove that locks onto the mRNA strand to ensure the codons are positioned flatly for reading. The large subunit (50S or 60S) sits on top, contains the peptidyl transferase center (an RNA catalyst or ribozyme) which forms peptide bonds between amino acids

What are the three internal binding sites of ribosomes?

aminoacyl site: the entry port where an incoming tRNA with an amino acid docks and tests its anticodon against the mRNA codon

peptidyl site: holding slot that carries the tRNA attached to the growing polypeptide chain

exit site: final slot where depleted, uncharged tRNAs are shifted before being ejected

what is the difference between a genotype and a phenotype?

genotype: complete, inherited inventory of DNA sequences, contained within an organisms’s genome (AA, Aa, or aa), representing potential biochemical instructions.

phenotype: physical manifestation of those genetic instructions, encompassing structural, physiological, and behavioral traits

genotype dictates the exact primary amino acid sequence of a cell’s proteins, which fold into structural components and enzymes that drive the metabolic pathways that ultimately construct the visible phenotype. environmental factors often interact

What is the function of DNA gyrase?

it is a specialized bacterial type II topoisomerase that loops around the DNA ahead of the fork that becomes overwound during replication (positive supercoiling). the gyrase loops around the overwound DNA, cuts both strands of the backbone, passes an intact section of the loop through the break to undo the twist, and chemically pastes the cut backbone ends back together. this relaxes the stress and prevents the fork from stalling or the backbone from tearing.

What is an anticodon?

a specific triplet of nucleotides at the base of a transfer RNA molecule. during translation, it forms temporary H bonds with its matching complementary codon on the mRNA strand inside the ribosome’s A site. because a specific enzyme attaches only one amino acid to the opposite end of that tRNA molecule, the anticodon acts as the translator to ensure that the sequence of nucleotides in the mRNA is translated into the exact sequence of amino acids intended by the genetic code.

What did Frederick Griffith do?

he injected mice with different combination of heat-killed pathogenic bacteria (S strain), live S-strain, and harmless live bacteria (R-strain). the mice with only the heat-killed S strain and only the R strain lived, but the mice with the live S-strain or a mixture of heat killed S-strain and live R-strain died, proving that something from dead S cells transformed R cells into virulent S cells. this is called a transforming principle, when hereditary information transfers between bacteria.

What did Oswald Avery, Colin MacLeod, and Maclyn McCarty do?

isolated Griffith’s mixture and destroyed specific components using enzymes. the transformation still occured unless DNA was destroyed, proving that DNA is the transforming principle that carries genetic information.

What did Alfred Hershey and Martha Chase do?

They labeled the protein coats of bacteriophages with radioactive sulfur and their DNA with radioactive phosphorus, then let them infect bacteria. after blending and centrifuging, they found that DNA entered cells and proteins stayed outside, providing final confirmation that DNA is genetic material.

What did Erwin Chargaff do?

he analyzed the base compositions of DNA across various species, finding that the base composition always followed the rule of A=T and G=C, helping explain complementary base pairing and DNA structure. became known as Chargaff’s rules.

What did Matthew Meselson and Franklin Stahl do?

determined how DNA replicates by growing bacteria in heavy nitrogen then shifting them to light nitrogen, and tracking DNA density after replication and saw that the DNA had one old pparental strand and one newly synthesized strand, showing that DNA replication is semiconservative.

What did James Watson and Francis Crick do?

they synthesized Franklin’s structural data and Chargaff’s base ratios to build the first physical, mathematically accurate 3D cardboard and metal model of the DNA double helix, detailing the complementary base-pairing mechanism.

What did Rosalind Franklin do?

used advanced x-ray crystallography techniques to capture photo 51, revealing the double helix structure, dimensions, and spacing between bases of DNA.

Explain the role of DNA polymerase in replication.

primary enzyme that assembles new DNA strands during cell division. it attaches a primed template strand and adds complementary nucleotides sequentially to extend the chain. also proofreads as it goes and removes any incorrectly paired nucleotides and replaces it to prevent mutations. can’t start building a new chain from scratch. requires a primer, a pre-existing short sequence of RNA to initiate synthesis.

Define antiparallel and explain why continuous synthesis of both DNA strands is not possible.

antiparallel means DNA’s two complementary strands are parallel to each other but run in opposite directions, one goes 5’ to 3’ but the other runs 3’ to 5’. continuous synthesis isn’t possible because DNA polymerase can only build new strands in the 5’ to 3’ direction.

What are the leading and lagging strands of DNA?

leading strand is the 5’ to 3’ strand, synthesized continuously in the same direction as the advancing replication fork. Requires only a single RNA primer to initiate synthesis, allowing the enzyme to smoothly build the strand in one motion.

lagging strand is the 3’ to 5’ strand, synthesized discontinuously in Okazaki fragments because it grows in the opposite direction of the fork, causing it to continually backtrack as more DNA is unraveled so it requires a new RNA primer for every individual fragment which are later stitched together by ligase to form a continuous strand

How is the lagging strand is synthesized even though DNA polymerase can build only at the 5’ to 3’ direction?

enzyme helicase unzips DNA to create the fork, then an RNA primase attaches a short RNA primer to the lagging strand. the polymerase attaches to the primer and builds a short DNA fragment moving away from the opening fork. as the fork unzips further, the primase lays down a new primer closer to the fork and polymerase synthesizes another fragment. polymerase replaces the RNA primers with DNA, and DNA ligase stitches the separated fragments into a single continuous strand.

Explain the roles of DNA ligase, primer, primase, helicase, and binding proteins.

ligase: enzyme that joins DNA fragments together by forming phophodiester bonds, connecting the okazaki fragments and sealing gaps where primers were replaced

primer: short, temporary strand of RNA that serves as a starting point for DNA synthesis

primase: enzyme that synthesizes the primer and attaches it to the single-stranded DNA so the polymerase can begin building the new strand

binding proteins: coat the separated DNA strands to keep them apart and prevent them from re-annealing or degrading during replication

Differences beween RNA and DNA.

DNA: deoxyribose sugar, uses A, T, C, and G, double-stranded and forms helix, strands held together by H bonds, stores and protects genetic information long-term, acts as the hereditary material passed from parent to offspring, found in nucleus or nucleoid region, more stable

RNA: ribose sugar with one more oxygen (less stable), uses uracil instead of thymine, single-stranded and can fold into different shapes, transfers and transcribes genetic information to carry out protein synthesis, often temporary. includes messenger RNA that carries instructions from DNA, transfer RNA that brings amino acids to ribosomes, and ribosomal RNA that forms part of ribosomes.

How does central dogma information flow from gene to protein?

1. transcription: a section of DNA containing a gene is copied into mRNA. RNA polymerase binds to DNA and builds an RNA strand. mRNA carries the genetic instructions out of the nucleus in eukaryotes

2. translation: ribosomes read the mRNA three bases at a time (in codons). tRNA molecules bring amino acids to each codon and they form a polypeptide chain that folds into a functional protein.

central dogma explains how genes control cellular activities.

Define codon and anticodon.

a codon is a sequence of three nucleotides on mRNA, each one specifying an amino acid or a stop signal. an anticodon is a three-base sequence on tRNA that pairs with the complementary codon on mRNA during translation

What is the relationship between the sequence of codons on mRNA and sequence of amino acids on a polypeptide?

the order of codons on mRNA determines the order of amino acids in a protein. each codon corresponds to an amino acid, and changing one codon can change the amino acid sequence and protein function

How does RNA polymerase recognize where transcription should begin?

it recognizes specific DNA sequences called promoters, which are located before the gene. special proteins called transcription factors help the polymerase bidn to the promoter. once attached, RNA polymerase separates DNA strands and begins synthesis

Describe the promoter, TATA box, transcription factor, termination sequence.

promoter: DNA sequence before a gene that signals where transcription should begin, that RNA polymerase binds to. strength varies depending on the gene

TATA box: specific DNA sequence with A and T, common in eukaryotic promoters, usually about 25 bases before the start site. helps position RNA polymerase

transcription factors: proteins that help regulate transcription by helping RNA polymerase recognize and bind promoters. some activate transcription, some repress it.

termination sequence: DNA sequence that signals the end of transcription, causing RNA polymerase to stop synthesis and the newly made RNA molecule is released.