MBI Exam 1 Structure and Function

Model of a bacteria cell

outer membrane, peptidoglycan, inner membrane, ribosome, nucleoid; no organelles

Properties of all cells

metabolism, growth evolution

Metabolism

cells take up nutrients, transform them, and expel waste

1. genetic (replication, transcription, translation)

2. catalytic (energy biosyntheses)

growth

nutrients from the environment are converted into new cell materials to form new cells

evolution

cells evolve in response to environmental factors; tracked by phylogenetic trees

Properties of SOME cells

differentiation, communication, genetic exchange, motility

differentiation

some cells can form new cell structures such as spores. Spores can survive extreme conditions

Communication

some cells can interact with each other by chemical messengers

Genetic Exchange

some cells can exchange genes by several mechanisms. Ex: donor cell gives DNA to recipient cell

motility

some cells are capable of self-propulsion (flagellum)

simple biochemical composition of microorganisms

water, essential ions and inorganic molecules, organic molecules (sugars, amino acids, nucleic acidbases)

macromolecule biochemical composition of microorganisms

proteins, lipids, carbs, nucleic acids. Macromolecules are formed by polymerization of smaller subunits

Macromolecule Class: DNA

nucleic acid subunits. Functions to hold genetic info. Found in the nucleoid

Macromolecule class phospholipid

lipid subunits. Functions to protect/shape/and maintain selective permeability. Found in the cell membrane

Macromolecule class: protein

amino acid subunits. functions to carry out genetic code. found in the membrane and all throughout the cell.

Macromolecule Class: polysaccharide

sugar subunits. found in LPS unit, starch

biochemical composition of bacteria

70% water, 20% RNAs, 1% DNA (only 1 chromosome)

Main components of cell wall

-membranes (gram+ many peptidoglycan, gram- 1 peptidoglycan): semi-permeable barriers to keep pH and contain everything in the cell

-Cell Wall: Stability

-Periplasm (only in gram-): Space between inner membrane and cell wall

-LPS layer (only in gram-): Lipopolysaccharides

Membranes

Contains hopanoids (like sterols to keep rigidity), transporter proteins, phospholipids, proton-driven ATP synthase

Permeability Barrier Function

prevents leakage and functions as a gateway for transport of nutrients in and out of the cell

Protein Anchor Function

Site of many proteins involved in transport, all components of the ETC

Energy Conservation Function

Site of generation and use of the proton motive force. Conserving energy to run ATPase and all transport

ester linkage

links fatty acids and glycerol in the phospholipid bilayer (C-O bond)

Membrane Lipids - Hopaniods

-similar to steroids in eukaryotes

-make the membrane stiffer and reinforce the structure of membranes

-can be used for ID in bacteria

Membranes: Ester vs. Ether bonds

Ether bonds are found in Archaea. More stable bond to allow archaea to be extremophiles. used to differentiate archaea from bacteria and eukaryotes.

Archaeal Membranes

Ether bonds + terpenoids + monolayer = very stable membrane

-terpenoids are the archaean version of fatty acids

membrane protein functions

structure, detection of environmental signals, secretion of virulence factors and signals, transport of ions, energy generation (metabolism)

Cell Wall Gram+

HUGE peptidoglycan layer (40+ layers), membrane

Cell Wall Gram-

much more complicated

outer membrane (lipopolysaccharide and protein) -> periplasm (containing just 1 peptidoglycan layer) -> membrane

cell wall (peptidoglycan)

string of two sugars: N-Acetylglucosamine and N-Acetylmuramic Acid

strings connected by amino acids to make sheets of peptidoglycan

Penicillin

Prevents binding between sugars and proteins. Strings of sugars are still made, but proteins cannot connect the strings to form sheets. Humans are unaffected by penicillin because we don't have a peptidoglycan cell wall.

Gram+ Cell Wall

sheets of sugar + amino acid layered and held together by teichoic acid (40+ layers)

- S-layer at the outside of the membrane (connects glycosyl chains to the outer cell wall)

- Inner membrane with membrane proteins for transporters and energy generation

Gram - cell wall

One layer of peptidoglycan connected to outer membrane for stability

-two membranes and periplasmatic space in-between

-outer membrane with LPS layer

-Inner membrane with membrane proteins for transport and energy generation

Transcription and Translation

Occur at the same time. Can be blocked by antibiotics

- Rifampin blocks RNA polymerase

- Tetracycline blocks tRNA

Erythromycin blocks peptide elongation

DNA Replication

1 chromosome at the origin of replication is replicated to form two replisomes. FtsZ is activated once the chromosome is replicated. FtsZ forms Z ring where the cell divides and DNA starts next round.

Cell Division

Septum forms from the Z-ring and the cell divides into two (while this is happening, the chromosome is replicating agains and the process is continuing).

Flagella

Driven by proton motor force. Can move the cell in all directions.

How does membrane lipid composition influence membrane fluidity?

Saturated fatty acids create a more rigid membrane, while unsaturated fatty acids create a more fluid membrane.

How do differences in the membrane composition and structure help to distinguish bacteria, archaea and eukaryotes?

Ester bonds are found in bacteria and eukaryotes (carbon double bonded to an oxygen). Ether bonds and terpenoids are found in Archaea.

How does peptidoglycan contribute to the cell wall strength?

The larger the layer of peptidoglycan, the stronger the cell wall. This is why gram+ bacteria stain purple; the thick wall keeps the stain inside.

Semi-permeable barriers keep pH stable

How does chemotaxis and flagella help the bacteria to respond to environmental signals?

They help move the cell away from danger and towards food

How can understanding the cell wall structure help to design effective antibiotics?

By identifying specific enzymes involved in synthesis (like penicillin-binding proteins), drugs can be created to disrupt cell wall integrity.

What is inside a bacterial cell?

Water, inorganic ions, small organic molecules, macromolecules

How does water get into the cell?

Passive transport

how do inorganic ions get into the cell?

active transport

how do small organic molecules get into the cell

active transport, synthesis by bacteria

how do macromolecules get into the cell

synthesis by bacteria

Macronutrients (need lots)

C, N, P, H, O, S, Na, Fe, Ca. Needed for Carbs, Lipids, Nucleic acids, proteins

Micronutrients (small amounts)

Zinc, Molybdenum, Nickel, Copper. Function as enzyme cofactors.

Ex. Molybdenum is needed for nitrogenase to to make nitrogen biologically available.

Carbon

50%. Needed for carbon cycle. Organic and inorganic (CO2) molecules. Assimilated and build into new cell materials

Nitrogen

12%. Needed for the nitrogen cycle. Organic and inorganic (ammonia, nitrate, N2) sources protein and nucleic acids

Growth factors

Needed for growth. Obtain from animal or human host cells.

Chemically defined culture media

inorganic nutrients plus carbon source. All substances are known

Chemically complex culture media

contains many organic compounds, undefined.

Culture media

solutions of all essential nutrients required by a bacterium to grow. Different for different bacteria

Energy generation

generated by the oxidation (take electrons) of chemical compounds. Stored in forms of rich compounds and ATP. Energy comes from sunlight and glucose (fermentation or oxidation)

Chemoorganotrophs

Organisms that harvest energy by oxidizing organic compounds like glucose and protein. (glucose + O2 = CO2 +H2O)

Chemolithotrophs

Organisms that use inorganic chemicals as their energy source (H2+O2=H2O)

Microbial carbon cycle

Organotrophs breakdown polysaccharides and glucose into inorganic compounds. Autotrophs fix inorganic compounds into sugars.

Chemolithautotrophs

use inorganic chemicals for source of electrons (ATP). Examples :H2, NH4+. Carbon source is CO2

Chemoorganoautotrophs

use organic chemicals for source of electrons (ATP). Examples: glucose, acetate. Carbon sources are organic compounds.

Photoautotrophs

use light for energy. Carbon source is CO2.

Photoheterotrophs

An organism that uses light to generate ATP but that must obtain carbon in organic form.

Chemolithoheterotrophs

get energy by oxidizing inorganic compounds (like sulfur, iron, or hydrogen) but require organic carbon sources for growth

Chemoorganoheterotrophs

use organic compounds for both energy and carbon

Rate of solute entry

Transporters increase the rate of solute entry into a cell. Transporters get saturated because there is a limited amount of them, and they can only transport 1 substrate at a time.

Permeability of different molecules

the more permeability a molecule is, the less charged it is. Increasing the charge of a molecule decreases the permeability and increases the need of a transporter.

Facilitated diffusion of glycerol

Glycerol enters the GlpF channel from the extracellular fluid. GlpF changes shape and opens the channel to the cytoplasm. Glycerol enters the cell.

symporter

Coupled transporter that moves two molecules (often one proton) into the cell at the same side. Gets energy from the proton motor force.

Antiporter

Coupled transporter that moves two molecules (often one proton) at the same time. One molecules moves in, the other moves out.

ABC transporter (ATP-binding Cassette)

Solute binding protein with a very high affinity for substrate. Solute binds to periplasmic protein. The complex binds to the membrane transporter. Conformational changes activate ATPase. ATP hydrolysis opens the dimer and releases solute to the cytoplasm.

Group translocation - PTS system

Phosphate from PEP is passed along PTS to the Enzyme 2 proteins. Substrates are transformed by phosphorylation during transport across the membrane.

simple transport

Driven by PMF. The substrate is not changed. Transported substances along with protons move into the cell.

group translocation

Chemical modification of the transported substance to prevent driven by phosphoenolpyruvate.

PTS

phosphotransferase system. Group translocation system that uses energy from PEP to attach a phosphate to surgars during transport into the cell.

PEP

phosphoenolpyruvate. An intermediate in glycolysis.

Microaerophilic

requires only a small amount of oxygen

facultative or aerotolerant anaerobes

can grow throughout the medium but will primarily grow in the middle of the tube, between the oxygen-rich and oxygen-free zones.

Catalase

Enzyme that breaks down hydrogen peroxide into water and oxygen.

Peroxidase

enzyme that breaks down hydrogen peroxide into water and NAD+

superoxide dismutase

catalyzes conversion of superoxide radicals to hydrogen peroxide

toxic and antitoxin system

neutralizes toxins

starvation

antitoxins degraded and the toxins kill the cell or impacts growth