Lecture 1-3 (Quiz 1) Intro, Bacteria, Archaea, Molec Bio,

Define micron

Micron is actually short for micrometer, which is the official unit of measurement. Put simply, a micron is one millionth of a meter, 10^-6, or .000001 meters.

Define LUCA

Otherwise known as the Last Universal Common Ancestor, which hypothesized to be the single ancestral cell or population of cells from which all life on Earth—including bacteria, archaea, and eukaryotes—descended from. They had their important characteristics: 1.) DNA as genetic material. 2.) Proteins and RNA to catalyze essential processes/reactions needed to grow and reproduce. 3.) A lipid cell membrane

Define Bioremediation

The use of microbes, or other organisms, to remove or detoxify anthropogenic environmental contaminants.

Define human microbiome

the collection of microbes that live in and on a human.

Define Metagenomics

DNA sequencing to identify which microbes are present in an environmental sample. (The direct study of all genetic material recovered from an environmental or clinical sample).

Essentially, the defining feature of a microbe is ____.

Their size. Microbes are small organisms* that cannot be seen with the naked eye. typically < 100 µm long (remember: 1 µm = 1 x 10^-6 m)

Consider a typical E. coli cell about 1.5 µm long. Consider a typical E. coli cell about 1.5 µm long. How does its length compare with the length of a virus?

E.coli = µm = 10^-6 m
Virus (e.g. Ebola) = nm = 10^-7 m = E.Coli is 10^1 times longer than a virus

Consider a typical E. coli cell about 1.5 µm long. How does its length compare with the diameter of the head of a pin?

E.coli = µm = 10^-6 m
Diameter of the head of a pin = mm = 10^-3 m = pin head is 10^3 times longer than E.Coli

Consider a typical E. coli cell about 1.5 µm long. How does its length compare with the width of your thumbnail?

E.coli = µm = 10^-6 m
thumbnail: 1 cm = 10^-2 m = thumbnail is 10^4 times longer than E.coli.

Consider a typical E. coli cell about 1.5 µm long. How does its length compare with the length of your hand? The diameter of an American football?

E.coli = µm = 10^-6 m
Length of hand = 15 cm = 0.15 m = length of hand is 10^5 longer than E.coli
Diameter of an American football= 20 cm = 0.20 m = football is 10^5 longer than E.coli

Consider a typical E. coli cell about 1.5 µm long. How does its length compare with the height of a person?

E.coli = µm = 10^-6 m
Height of a person = 2 m = height of person is 10^6 longer than E.coli

Consider a typical E. coli cell about 1.5 µm long. How does its length compare with the height of a building?

Height of a building = 10-30 m = height of building is 10^7 longer than E.coli.

What is one key benefit of being small?

Being smaller gives a higher surface area-to-volume ratio which allows better chemical exchange with the environment, and thus faster growth

Who are the microbes?

Prokaryotic microbes: Bacteria and Archaea.
Eukaryotic microbes: Fungi and the following protists: Slime molds, microscopic algae, and Protozoa.

What is LUCA and what are its characteristics?

Otherwise known as the Last Universal Common Ancestor, which hypothesized to be the single ancestral cell or population of cells from which all life on Earth—including bacteria, archaea, and eukaryotes—descended from. They had their important characteristics: 1.) DNA as genetic material. 2.) Proteins and RNA to catalyze essential processes/reactions needed to grow and reproduce. 3.) A lipid cell membrane

Why are microbes well-suited to perform bioremediation?

Microbes are uniquely well-suited to perform bioremediation because of their diverse metabolic versatility, rapid reproduction rates, microscopic size that maximizes surface contact with pollutants, and extraordinary capacity to survive in extreme or toxic environments.

What type of microbe is Cyclospora?

It is a protozoan parasite. (Protozoa are eukaryotic organisms).

Measles was declared eradicated in the US in 2000. What is the best way to protect against Measles? Which populations are most vulnerable to complications and hospitalization from Measles? Describe “Immune Amnesia”

The best way to protect against Measles is taking the two dose MMR vaccine. Young children (under 5 years old) and immunocompromised individuals are most vulnerable to Measles. Immune Amnesia refers to a unique phenomenon where a natural measles infection causes a severe, long-term reset of an individual's pre-existing immunological memory.

What are some important roles of microbes on earth? Describe many ways (both trivial and profound) in which microbes impact our lives.

Atmospheric Oxygen Production
Biogeochemical Cycling
Primary Production without Sunlight
Organic Decomposition
Human Digestion & Physiology
Culinary & Fermentation
Medicine & Biotechnology
Environmental Cleanup
Body Odor

How can the human gut microbiome be considered a metabolic “organ”? Give an example.

The human gut microbiome acts like a metabolic "organ" because it performs complex chemical tasks and processes that our own human cells and genes cannot do on their own.

Why It Is a Metabolic Organ

Extra Genes: The microbiome contains millions of genes, far outnumbering human genes, which provide a vast array of metabolic enzymes

Nutrient Processing: It breaks down substances from food that bypass human digestion, turning them into bioactive molecules that affect the whole body

Shared Control: Like an internal organ, it regulates energy balance, synthesizes vital nutrients, and communicates with other organs via chemical signals.

Example: Breakdown of Dietary Fiber into Short-Chain Fatty Acids

Humans lack the enzymes required to digest complex plant fibers like pectin and cellulose, but gut bacteria use anaerobic metabolism to ferment these non-digestible carbohydrates into short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate. These SCFAs then nourish gut lining cells, reduce inflammation, and enter the bloodstream to regulate energy metabolism in the liver and adipose tissue, functioning just like a hormonal or metabolic secretion from a traditional organ.

Describe how the gut microbiome can influence obesity. What are several ways in which the microbiome of obese mice differs from the microbiome of lean mice?

Gut microbiome affects degradation of otherwise indigestible components of our diet, and therefore may have an impact on our energy balance. In addition, it can affect leptin production, which can cause increased food consumption. The gut microbiome of obese mice differs from lean mice in that microbial fermentation of dietary polysaccharides that cannot be digested by the host; subsequent intestinal absorption of monosaccharides and short-chain fatty acids; their conversion to more complex lipids in the liver; and microbial regulation of host genes that promote deposition of the lipids in adipocytes. These findings have led us to propose that the microbiota of obese individuals may be more efficient at extracting energy from a given diet than the microbiota of lean individuals.

Describe the key experiments and the conclusions of these experiments from the Turnbaugh et al., 2006 paper.

Key experiments: Biochemical analysis and microbiota transplantation.

Conclusion: Obesity can be transmitted through microbiota transplantation. Obesity is affected by gut microbiota, which changes energy digestion and absorption.

Describe why Koch's postulates are no longer adequate to describe the relationship between microbes and all diseases

Unculturable Microorganisms (Violates Postulate 2): Many pathogens cannot be isolated and grown in pure culture on standard lab media.
Asymptomatic Carriers and Commensals (Violates Postulate 1): Pathogens are frequently found in healthy individuals without causing illness.
Host-Specific Pathogens and Ethical Limits (Violates Postulate 3): Many severe pathogens infect only humans (e.g., HIV, measles, Salmonella Typhi). Infecting human test subjects to satisfy Postulate 3 is unethical, and non-human animal models often fail to mimic human clinical pathology.
Polymicrobial Infections (Violates Postulates 1, 2, and 3): Diseases such as bacterial vaginosis, periodontal disease, and chronic lung infections in cystic fibrosis are caused by complex microbial communities or shifts in the microbiome (dysbiosis), rather than a single isolation-ready organism.

Consider a typical bacterial cell about 1 µm long. How many of these bacteria, end to end lengthwise, would span the width of the nail of your little finger? Estimate and answer within a factor of 10 (do not use a calculator).

nail = 1 cm = 0.01 m = 1*10-2 m
Bacteria = 1 µm = 0.000001 m = 1*10-6 m
(1*10-2 m) / (1*10-6) = 1*104 m = 10,000 bacterial cells.

It is often said that less than 1% of microbes cause disease. So, what are examples of “good” things that microbes do?

Bioremediation
Gut Digestion
Immune Support
Oxygen Production
Fermentation/Food Production

Define 16S rRNA

encodes the ribosomal RNA (~1500 nt long) in the small subunit of prokaryotic ribosomes (remember, ribosomes are made of ribosomal proteins and rRNA)

Define Operational Taxonomic Unit (OTU)

a category used to classify prokaryotic organisms based on solely DNA sequence similarity.

Why is it difficult to categorize prokaryotes using methods traditionally used to categorize higher organisms? Why are OTUs useful for categorizing newly-discovered prokaryotes?

It is difficult to categorize prokaryotes using methods traditionally used to categorize higher organisms because most microbes can’t be cultured in the lab, thus studying phenotypes is difficult. Why useful? For microbes discovered in a metagenomic study, it’s easier experimentally to obtain DNA sequences than phenotypic information.

How were archaea discovered? What is the one most important difference between bacteria and archaea? What are other differences between bacteria and archaea?

Archaea were discovered in 1977/1990 by microbiologist Carl Woese and his colleague George Fox via 16S rRNA (ribosomal RNA) sequencing, this led to the creation of the Three-Domain System: Bacteria, Archaea, and Eukarya. The one most important difference between bacteria and archaea is the difference in the genetic makeup of their ribosomal RNA (rRNA) via 16S rRNA (ribosomal RNA) sequencing. Other differences between bacteria and archaea are the following:  

• The two differ in chemical properties of cell wall and membranes. 

• Bacteria are sensitive to antibiotics; archaea are not sensitive to many of them

• The archaeal protein- and nucleic acid- synthesizing enzymes resemble those of eukaryotes; not so the bacterial ones. 

• Bacteria include animal and plant pathogens; archaea do not. 

• Typical bacteria are Escherichia coli, staph (Staphylococcus), and step (Streptococcus). 

• Typical archaea are extreme thermophiles and methane producers. 

Suppose you have discovered a new prokaryotic organism that lives in a boiling hot spring and is not sensitive to any antibiotics. Would you hypothesize that the organism is a bacterium or an archaea? What additional characteristics would you look for to test your hypothesis?

Based on the organism being a thermophile and not sensitive to any antibiotics, I would hypothesize the organism is an archaea. Some additional characteristics. I would look for to test my hypothesis through cell membrane chemistry, cell wall composition, and 16S rRNA Sequence Analysis. 

• Cell membrane chemistry 

  • Archaea: Membrane lipids feature ether linkages connecting glycerol to branched isoprenoid chains (often forming a stable lipid monolayer resistant to heat denaturation). 

  • Bacteria: Membrane lipids feature ester linkages connecting glycerol to unbranched fatty acid chains. 

• Cell Wall composition 

  • Archaea: Lacks true peptidoglycan (may contain pseudopeptidoglycan, S-layer proteins, or complex polysaccharides). Treatment with lysozyme or beta-lactams will have no structural effect. 

  • Bacteria: Almost universally contains a peptidoglycan meshwork with N-acetylmuramic acid.

What are important features of cyanobacteria?

Prokaryotic design: They lack a membrane-bound nucleus and organelles like mitochondria or chloroplasts.

Their oxygenic photosynthetic machinery is embedded in extensive internal membrane folds called thylakoids located within the cytoplasm.

Cyanobacteria contain proteinaceous microcompartments called carboxysomes that pack RuBisCO (the primary carbon-fixing enzyme) alongside carbonic anhydrase. This localizes high concentrations of carbon dioxide (CO2) directly around RuBisCO to maximize carbon fixation efficiency.

What are the classes of Proteobacteria? Which class includes famous enterobacteria pathogens, vibrios, and pseudomonads? Which class includes many bacteria that live with plants?

The classes of Proteobacteria are Alpha, beta, gamma, delta, epsilon, and zeta. Alphaproteobacteria – include bacteria that live with plants (Agrobacterium tumefaciens, Rhizobia).

Betaproteobacteria – include pathogens Bordatella pertussis, Neisseria gonorrhoeae, and Neisseria meningitidis.

Gammaproteobacteria – include enterobacteria (including E. coli and Salmonella), vibrios (including Vibrio cholerae), and pseudomonads (including Pseudomonas aeruginosa)

Contrast main characteristics of Firmicutes and Bacteroidetes. Give examples of bacteria in each of those phyla.

Firmicutes
• Low GC content in genomes
• Gram positive phylum, but includes the mycoplasmas
• Include endospore-forming bacteria, in the Bacilli and Clostridia classes
• Includes pathogens such as Staphylococcus aureus, Streptococcus pyogenes, and Listeria monocytogenes
• Includes yogurt and cheese bacteria, Lactobacillus species

Bacteroidetes
• Gram negative rods that may be obligate aerobes, facultative aerobes, obligate anaerobes
• Includes the genus Bacteroides, a major component of the human gut microbiota
• Bacteroides thetaiotamicron lives in the large intestine and specializes in breaking down polysaccharides

What are important features of Streptomyces? In which phylum is Streptomyces found?

Important features of Streptomyces is that it has Filamentous( Fungal-like Growth), and can produce antibiotics. High GC content in genomes. Streptomyces is found in the phylum Actinomycetota (traditionally and commonly also referred to as Actinobacteria - Gram Positive Bacteria)

Contrast the Crenarchaeota with the Euryarchaeota.

Crenarchaeota

• Includes thermoacidophiles that live in hot springs (grow at >70∘C and prefer pH as low as 2.0)

• Many metabolize sulfur

• Many live in the ocean in non-extreme environments

Euryarchaeota

• Includes methanogens (methane producers) and extreme halophiles (grow in high salt conditions)

How is the traditional prokaryotic “species” definition different from an OTU species?

Traditional prokaryotic species definitions rely on whole-genome coherence and phenotypic traits from isolated strains, whereas Operational Taxonomic Unit (OTU) species are pragmatic, culture-free sequence clusters based (solely) on marker gene similarity.

Which of these is not a polymer (a covalently-linked chain of repeating subunits): proteins, DNA, RNA, polysaccharides, and phospholipids?

Phospholipids are not polymers.

Describe the main purpose(s) of the following molecules in a cell: protein

Catalyze biochemical reactions (enzymes), provide structural support (cytoskeleton), transport molecules across membranes, mediate cellular signaling, and drive motility.

Describe the main purpose(s) of the following molecules in a cell: DNA

Serves as the permanent genetic material storing the master instructions required for organismal growth, development, and cellular reproduction

Describe the main purpose(s) of the following molecules in a cell: RNA

Converts genetic information encoded in DNA into functional proteins (mRNA, tRNA, rRNA), regulates gene expression (miRNA, siRNA), and performs catalytic functions (ribozymes)

Describe the main purpose(s) of the following molecules in a cell: Polysaccharides

Provide long-term chemical energy storage (glycogen in animals, starch in plants) and rigid structural integrity (cellulose in plant cell walls, chitin in fungi/arthropods).

Describe the main purpose(s) of the following molecules in a cell: Phospholipids

Forms the semi-permeable lipid bilayer of cellular membranes, providing structural compartmentalization and regulating selective transport into and out of the cell.

Define the primary structure levels of protein structure

the linear amino acid sequence

Define the secondary structure level of protein structure

a repeating structure due to hydrogen bonds between amino acid side chains; alpha helix or beta sheet

Define the tertiary structure level of protein structure

the 3-dimensional structure or “fold” of the protein; depends on hydrogen bonds, electrical charges, and hydrophobic interactions between amino acid side chains; critical for protein function

Define the quaternary structure level of protein structure

2 or more independently-folded polypeptides together in a complex; often held together with disulfide bonds

What happens to protein structure and function if a protein is denatured?

Non-covalent bonds (hydrogen bonds, ionic interactions, hydrophobic packing) break, causing the tightly folded, native protein to unfold into a random, disordered chain.

Biological function is completely lost. Protein function depends entirely on its precise 3D shape (e.g., an enzyme's active site must perfectly fit its substrate). Once denatured, the active site is disrupted, rendering the protein biologically inactive.

What does it mean for a gene to be “expressed”?

When a gene is expressed, its stored DNA instructions are actively used to make a functional product, usually a protein or a functional RNA molecule. This is through a combination of transcription and translation.

Who are the main players in [prokaryotic] transcription? Of the players you mentioned, indicate which ones are enzymes and which ones are regions on DNA or RNA.

RNA Polymerase (Core) / Enzyme: Catalyzes the addition of ribonucleotides to build the RNA strand.

Sigma Factor (sigma) / Protein Subunit: Directs the core enzyme to the correct starting location.

Rho Factor (rho) / Enzyme (Helicase): Unwinds the RNA-DNA hybrid to terminate transcription.

Promoter (-10 and -35 boxes) / DNA Region: The binding and unwinding site located upstream of the gene.

Transcription Start Site (+1) / DNA Region: The exact DNA base pair where RNA synthesis begins.

Terminator Sequence / DNA Region: The DNA sequence that signals the polymerase to stop.

Rut Site / RNA Region: A sequence on the newly made mRNA where the Rho factor binds.

Who are the main players [prokaryotic] in translation? Of the players you mentioned, indicate which ones are enzymes and which ones are regions on DNA or RNA.

Ribosome (70S) / Enzyme / Complex: The factory that reads the mRNA and synthesizes the protein. (Specifically, its 23S rRNA acts as a ribozyme to catalyze peptide bonds).

Aminoacyl-tRNA Synthetases / Enzyme: "Charges" empty tRNAs by attaching the correct amino acid to them.

Translation Factors (IFs, EFs, RFs) / Proteins: Helper proteins that initiate the process, elongate the chain, and trigger release at the end.

Shine-Dalgarno Sequence / Region on RNA: The landing pad on the mRNA that aligns the ribosome correctly before the start codon.

Start Codon (AUG) / Region on RNA: The 3-base sequence on mRNA that signals exactly where to begin reading the protein code.

Stop Codon (UAA, UAG, UGA) / Region on RNA: The 3-base sequence on mRNA that signals the end of the protein sequence.

Anticodon / Region on RNA: A 3-base sequence on the bottom of a tRNA that perfectly matches and binds to the mRNA codon.

When does prokaryotic replication needs to occur?

Prokaryotic DNA replication needs to occur before a cell divides so that each new daughter cell receives an identical copy of the genetic material.

Who are the main players in prokaryotic replication? Of the players you mentioned, specify which ones are enzymes and which ones are regions on DNA or RNA.

Helicase (DnaB)	Enzyme	Unzips the double helix by breaking hydrogen bonds between base pairs.
DNA Gyrase (Topoisomerase II)	Enzyme	Relieves the physical tension (supercoiling) ahead of the replication fork as DNA is unwound.
Primase (DnaG)	Enzyme	Synthesizes a short RNA primer to provide a starting point for DNA synthesis.
DNA Polymerase III	Enzyme	The primary builder; adds DNA nucleotides to the growing leading and lagging strands.
DNA Polymerase I	Enzyme	Removes the RNA primers and replaces them with DNA nucleotides.
DNA Ligase	Enzyme	Seals the structural nicks in the sugar-phosphate backbone, joining DNA fragments together.
oriC (Origin of Replication)	Region on DNA	The specific sequence where replication initiates.
Ter Sites	Region on DNA	Terminator sequences opposite oriC where the two replication forks meet and stop.
RNA Primer	Region on RNA	A short, temporary sequence laid down by primase to provide a free 3'-OH group.
Okazaki Fragments	Region on DNA	Short segments of newly synthesized DNA on the lagging strand.

define Genome

The complete set of genetic material (DNA) present in an organism or cell. It contains all the instructions needed to build and maintain that organism.

Define gene

A specific, physical segment of DNA that codes for a functional product—usually a protein, but sometimes a functional RNA molecule (like rRNA or tRNA).

Define Recombination

The process where genetic material is rearranged or exchanged between two different DNA molecules, creating a new, unique combination of alleles.

Define Replication

The biological process of copying the entire cellular genome before a cell divides, ensuring both daughter cells receive an identical copy of DNA.

Define Origin (oriC)

The specific sequence on a chromosome where the replication machinery binds and DNA unwinding first begins.

Define DNA Polymerase

The primary enzyme responsible for synthesizing new DNA strands by adding complementary deoxyribonucleotides to a growing chain during replication.

Define Transcription

The process of reading a gene's DNA sequence and synthesizing a complementary single-stranded messenger RNA (mRNA) copy.

Define Promoter

A specific region of DNA located just upstream of a gene. It acts as the binding site for RNA polymerase and determines exactly where transcription will initiate.

Define RNA Polymerase

The enzyme that unwinds the DNA double helix and links ribonucleotides together to build the RNA transcript.

Define Transcription Start Site (+1)

The exact, single base pair on the DNA template where RNA polymerase adds the very first RNA nucleotide of the transcript.

Define mRNA (Messenger RNA)

The temporary RNA copy of a gene that carries the genetic instructions from the DNA to the ribosome for protein synthesis.

Define Translation

The process where the genetic code carried by mRNA is decoded by a ribosome to synthesize a specific chain of amino acids (a polypeptide/protein).

Define ribosome

The complex molecular machine (made of proteins and rRNA) that reads mRNA and catalyzes the formation of peptide bonds between amino acids.

Define rRNA (Ribosomal RNA)

The RNA molecules that make up the structural and catalytic core of the ribosome. (rRNA acts as a ribozyme to form the actual bonds between amino acids).

Define tRNA (Transfer RNA)

Small, folded RNA molecules that act as adapters. They carry specific amino acids to the ribosome and match their anticodon to the corresponding codon on the mRNA.

Define Start Codon

A three-letter sequence (almost always AUG) on the mRNA that signals the ribosome to begin translation and sets the reading frame.

Define Stop Codons

Three-letter sequences (UAA, UAG, UGA) that signal the ribosome to terminate translation and release the finished protein.

Define Amino Acids

The fundamental monomer building blocks of proteins. There are 20 standard amino acids, each with a unique side chain (R-group) that determines the protein's folding and function.

Define N-terminus

The start of the protein, characterized by a free amine group (-NH2). It corresponds to the 5' end of the mRNA.

Define C-terminus

The end of the protein, characterized by a free carboxyl group (-COOH). It corresponds to the 3' end of the mRNA.

Which types of microscopy will you be using in Bio302 lab? What are the smallest microbes that can be seen with those types of microscopy?

We will be using mainly Bright-field light microscopy, though we will have the opportunity to use Fluorescence microscopy at some point. The smallest microbes visible to a brightfield microscope are typical bacteria like Escherichia coli or Staphylococcus aureus (roughly 0.1 to 0.2 µ wide). The smallest microbes visible with a standard fluorescence microscope are ultra-small bacteria and large viruses, limited by the light diffraction limit to objects around 200 nanometers (0.2 micrometers) in size.

How does electron microscopy differ from light microscopy? Which type of electron microscopy yields a 3-D image?

Electron microscopy differs fundamentally from light microscopy by substituting light (photons) with a beam of electrons and using electromagnetic lenses instead of glass lenses.

SEM - scanning EM coat sample with a thin layer of heavy metal; see 3-D structure of the outside.
TEM - transmission EM make thin slices of sample so electrons can pass through - see internal structure of cells.

During which process(es) is/are new phosphodiester bonds formed?

DNA replication, transcription (RNA synthesis), DNA repair, and DNA recombination

During which process(es) is/are new peptide bonds formed?

New peptide bonds are formed during translation (protein synthesis).

In living cells, how often do the processes of transcription and translation occur? (all of the time, some of the time, or never?)

The processes of transcription and translation occur all of the time in living cells

In living cells, how often does the process of replication occur? (all of the time, some of the time, or never?)

Some of the time

Would you expect a fast-growing bacterial cell to have more, fewer, or the same number of ribosomes as a slowly growing bacterial cell? Justify your answer.

A fast-growing bacterial cell would have significantly more ribosomes than a slowly growing bacterial cell. Because ribosomes are the molecular factories that synthesize proteins, a higher concentration of ribosomes is required to meet this production demand within a shorter cell cycle.