Microbiology - Exam #1 Material

What molecule determines placement on the phylogenetic tree?

SSUrRNA

It is hypothesized that RNA is most likely found in
early life. Why?

Because RNA can both store genetic information and catalyze chemical reactions, suggesting it played a key role in the origins of life.

Describe the origin of mitochondria.

Bacterial endosymbiont - used to be bacteria before being taken up by eukaryotes.

Evidence for the Endosymbiont theory.

• Mitochondria and chloroplasts used to be bacteria

  • They have their own circular DNA (found in prokaryotes/bacteria)

  • They have double membranes (seen in gram-negative bacteria)

  • Have ribosomes (bacterial-like)

• Chloroplasts and mitochondria were taken in by early eukaryotic cells, and that relationship became permanent

Refractive index

how greatly a substance slows the velocity of light

• When light travels from a low refractive index to a high refractive index, light bends toward “normal”

• If light travels from a high refractive index to a lower refractive index, it bends away from the normal

Normal

The “normal” line is 90 degrees perpendicular to the surface of the glass

Resolution

the ability of a lens to separate or distinguish small objects that are close together

• Shorter wavelength = greater resolution

  • 450nm = blue light

• Numerical aperture = ability of a lens to gather light

What bacterial structural component determines
the Gram stain results?

the composition of the cell wall, specifically the amount of peptidoglycan present in the bacterial cell wall.

Gram-positive bacteria have a thick layer of peptidoglycan, while Gram-negative bacteria have a thinner layer and an outer membrane.

Differential staining

process that uses multiple dyes to differentiate between different types of microorganisms or cellular components of a single organism

• Gram-positive = purple

  • Lots of peptidoglycan

• Gram-negative = red

  • Thin peptidoglycan

• Crystal violet (primary stain) for 1 minute, water rinse

• Iodine for 1 minute, water rinse

• Alcohol (decolorizer) for 10-30 seconds, water rinse

• Safranin (counterstain) for 30-60 seconds. Water rinse. Blot dry

Electron microscopy vs light microscopy –
differences in use and function

Electron microscopes have higher resolution to see smaller organisms like small bacteria and viruses. Light microscopes use visible light and are suitable for larger specimens, while electron microscopes utilize electron beams for much higher magnification and resolution.

What proteins can make up the bacterial
cytoskeleton? What are these proteins
homologous to?

Proteins such as FtsZ, FtsA, and MreB, and CreS which are homologous to eukaryotic tubulin and actin

What are the three types of inclusion bodies?

They are granules, lipid bodies, and gas vesicles, which serve as storage for nutrients, energy.

Describe bacterial ribosomes. What are they
made of and what are their sizes?

Bacterial ribosomes are made of ribosomal RNA and proteins, typically consisting of a 70S size, which is composed of a 50S large subunit and a 30S small subunit

Describe bacterial chromosomes and plasmids.
How are they similar and how are they
different?

Bacterial chromosomes are typically circular, double-stranded DNA molecules containing essential genetic information, aid in folding, and are looped and coiled extensively. Plasmids are smaller, circular, double-stranded DNA that can carry additional genes, and they can exist and replicate independently of chromosome, have relatively few genes present, and genes on plasmids are not essential to host but may confer selective advantage (drug resistance). Both are involved in genetic replication and can be found in the cytoplasm of bacterial cells.

When light travels from a medium with a high refractive index to a media of a lower refractive index the light bends _______ the normal.

away from

The sequence of the rRNA in mitochondria is most similar to Rickettsia. This is evidence for

Endosymbiont theory

You've discovered a new bacterium and want to determine it's evolutionary relationship to other organisms by sequencing it's 16s ribosomal RNA (rRNA). What ribosomal subunit contains the bacterial 16s rRNA?

30S

To clearly see a sample of microorganisms isolated from a lake you need a magnification of 60,000x. This magnification can be achieved with 

an electron microscope

On the graph below, click on the line  that best represents passive diffusion.

x= concentration gradient, y = rate of transport

line should be linear

How does passive diffusion differ from
facilitated diffusion? How are they similar?

Similar: The movement of molecules is not energy-dependent, The direction of movement is from high concentration to low concentration

different: (facilitated) It uses carrier molecules (permeases) that transport closely related solutes, Smaller concentration gradient is required for significant uptake of molecules, Effectively transports glycerol, sugars, and amino acids

What mechanisms of transport require
energy? What are the possible sources of
energy?

active transport. used ATP or ion motive force (PMF)

Explain group translocation, including the
proteins involved, and the movement of the
phosphoryl group. Why is the incoming
sugar phosphorylated?

• Chemically modifies molecule as it is brought into the cell

• The best-known system is the phosphoenolpyruvate: sugar phosphotransferase system (PTS)

  • Transported sugar is phosphorylated during transport using phosphoenolpyruvate (PEP) as the phosphate donor

    • More energy than ATP

• Energy-dependent process

• 1. PEP releases high-energy phosphate

  • Comes into contact with enzyme 1 (EI)

• 2. Phosphate goes to heat-stable protein (HPr)

  • Ends up at enzyme 2 (EII)

True or False: The outer membrane is a semi-permeable barrier.

True

True or False: The cell membrane is a rigid structure that provides bacteria with their characteristic shapes

False

Bacterial capsules are made up of 

sugars

What is the cell wall? Is it the same in Gram positive
and Gram negative bacteria? Explain

The cell wall is a protective layer that provides structural support and shape to bacteria. It is not the same in Gram positive and Gram negative bacteria. Gram positive bacteria have a thick peptidoglycan layer, while Gram negative bacteria have a thinner peptidoglycan layer accompanied by an outer membrane.

Describe the structure of peptidoglycan

Peptidoglycan is a polymer composed of sugars and amino acids. Its structure consists of long chains of repeating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), which are cross-linked by peptide bridges. This mesh-like structure provides rigidity and strength to the bacterial cell wall.

What are teichoic acids?

Polymers of glycerol or ribitol phosphate found in the cell wall of Gram-positive bacteria. They are connected to the peptidoglycan layer and play a role in maintaining cell wall structure, regulating cell division, and acting as a receptor for certain bacteriophages.

What is LPS?

Stands for lipopolysaccharide, a large molecule found in the outer membrane of Gram-negative bacteria. It consists of a lipid portion (lipid A), a core oligosaccharide, and an O-antigen. LPS is an important component of the bacterial cell wall and plays a key role in the immune response as it can act as an endotoxin.

Why is peptidoglycan beneficial to bacteria?

Peptidoglycan provides structural support and rigidity to the bacterial cell wall, protecting the cell from osmotic pressure and physical stress. It helps maintain the shape of the bacterium and is crucial for its survival, especially in hypotonic environments.

What is a bacterial capsule? What are the benefits
to the bacteria when they have a capsule?

dense, protective layer that surrounds the cell wall of some bacteria. It is typically composed of polysaccharides or proteins. Capsules provide several advantages to bacteria, including protection against phagocytosis by immune cells, prevention of desiccation (drying out), aiding in adherence to surfaces and other cells, and providing an additional layer of defense against environmental stresses.

How does a bacterial flagellum move? What is the
energy source? Where are flagella located?
Describe the assembly of the bacterial flagellum.

A bacterial flagellum moves by rotating like a propeller, allowing the bacterium to swim through its environment. The energy source for the movement of bacterial flagella is typically proton motive force (PMF) generated across the membrane. Flagella are usually located at one or both ends of the bacterial cell (polar flagella), or they can be distributed all over the cell surface (peritrichous flagella).

The assembly of the bacterial flagellum involves the formation of a basal body, hook, and filament. The basal body anchors the flagellum in the cell membrane and cell wall, the hook connects the basal body to the filament, and the filament is made up of flagellin proteins that extend outside the cell, forming the long tail-like structure.

Describe chemotaxis

movement of an organism or cell toward or away from a chemical stimulus. In bacteria, this involves sensing chemical gradients in the environment and moving in a directed manner toward attractants (e.g., nutrients) or away from repellents (e.g., toxins). This process relies on specialized receptor proteins that detect chemical changes in the environment and initiate a signaling cascade to coordinate movement.

What is the linkage in archaeal lipids?

ether linkages between glycerol and fatty acids, as opposed to the ester linkages found in bacterial and eukaryotic lipids.

Describe the features of archaeal plasma membranes that
allow survival at 85C or higher temps.

Archaeal plasma membranes have several features that enable survival at high temperatures, including: 1) The presence of monolayer structures formed by long-chain ether lipids, which provide greater stability than typical lipid bilayers; 2) the presence of saturated fatty acids that reduce fluidity, helping to maintain membrane integrity; 3) the structural composition of the membranes, which can withstand heat-induced stress; 4) proteins with a high thermal stability and special adaptations that allow them to function effectively in extreme temperatures.

How does pseudomurien differ from peptidoglycan?

Pseudomurein is a component of the cell wall in some Archaea and differs from peptidoglycan in several ways: 1) It contains N-acetylglucosamine (NAG) and N-acetyltalosaminuronic acid (NAT) instead of N-acetylmuramic acid (NAM), which is found in peptidoglycan; 2) Pseudomurein has a different linkage structure, using β-1,3-glycosidic bonds, as opposed to the β-1,4-glycosidic bonds in peptidoglycan; 3) Pseudomurein is not sensitive to lysozyme, which can break down peptidoglycan.

Is pseudomurien affected by lysozyme?

No it’s not affected

How do archaeal flagella move? What is the energy source?

Archaeal flagella move by rotating in the same manner as bacterial flagella, allowing the archaeon to swim through its environment. The energy source for movement of archaeal flagella is typically ATP, which is used to drive the rotation of the flagellum.

Describe assembly of archaeal flagella

The assembly of archaeal flagella involves the formation of filamentous structures composed of flagellin proteins, which are then attached to a basal body. The process is similar in function to bacterial flagella assembly but may utilize different protein components and energy sources, such as ATP, for the rotation and maintenance of the flagellum.