micro review

resolution definition

the smallest distance by which two objects can be separated and still be distinguished as separate objects

magnification definition

will increase the apparent distance between objects and lead to their resolution

sterilization def

killing all living organisms

antisepsis

killing or removal of pathogens from the surface of living tissue

disinfection

killing or removal of pathogens from inanimate objects. Might not kill non pathogenic microorganisms and so is not considered sterilization

generation time definition

the time it takes for a population to double

for an object to be resolved, the wavelength of the radiation must be _____________ to or _____________ than the size of the object

equal to , smaller

if the wavelength is larger that obejct the wave's energy will simply ________________________ the object

pass through the object

know parts of the microscope

what type of microscope produces this image

transmission electron microscope (TEM)

• specimen are cut

what microscope creates this image?

Scanning electron microscope

• does not cut in half

• absorbs electrons

what microscope creates this image?

bright field microscopy

• type of light microscopty

what microscope creates this image?

phase contrast micrscopy

• type of light microscopy

what microscope creates this image?

florescent microscopy

bacterial cell wall is made of

peptidoglycan

cell wall vs cell membrane

• structure,

• order

• composition

• function

gram positive vs gram negative cell walls

know the unique components of each

• gram positive has thick peptidoglycan

• gram negative has thin peptidoglycan

• teichoic acids thread through peptidoglycan to create layer

• s layer

micronutrients definition

trace elements necessary for enzyme function, essential to cell, needed in small amounts

• Co, Cu, Mn, Zn

Macronutrients

are major elements in cell macromolecules (Carbohydrates, proteins, lipids, and nucleic acid) necessary for protein function. Ions, needed in larger quantities

• Mg+2, Ca2+, Fe2+, K+

types of transport

facilitated diffusion and active transport

types of active transport

• ABC transporters

  • breaking ATP

• group translocation

  • against concentration gradient

• active coupled transport

  • those which energy released by moving a driving ion down its gradient is used to move a solute up its gradient

  • symport

  • antiport

  • energy comes from gradient separation

complex media

are nutrient rich but poorly defined, composition are not well defined

synthetic media (defined media)

are precisely defined and all the chemicals used are known

phase of growth curve in order. know of cell number is increasing, decreasing, or staying constant. know what happens in each phase

biofilm life cycle

1. initiation

2. maturation

3. dissolution/ dispersal

know what each stage of biofilm life cycle

what constitutes an extreme condition

anything outside of normal conditions

• normal cond: sea level, temp 20 to 40*C, neutral pH, 0.9% salt, and ample nutrients

halophiles

requires high salt concentrations

halotolerant

bacteria can grow at elevated salt concentrations but do not require high salt to grow

Organisms of pH range

Neutrophiles

• grow at pH 5-8

• most human pathogens

Acidophiles

• pH 0-5

Alkaliphiles

• pH 9-11

organisms in temp

psychrophiles

• 0-20*C

Mesophiles

• 15-45*C (most human pathogens)

Thermophiles

• 40-80*C

Hyperthermophiles

• 65-121*C

Organisms in pressure

Basophiles

• adapted to grow at very high pressures

Barotolerant

• grow well over the range of 1-50MPa, growth falls off after

Barophilic hyperthermophiles

• form the basis of thermal vent communities on the ocean floor

organisms in oxygen

strict aerobes

• can only grow in oxygen

Microaerophiles

• grow only at lower O2 levels

Strict anaerobes

• Die in the least bit of oxygen

Facultative anaerobes (aerotolerant)

• can live with or without oxygen

ultraviolet light does what

sterilize

high temp is a

phsycial agent

• bioling

pasteurization is a

psychical agent

• autoclave

filtration

physicals agent

chemical means of controlling microbial count

ethanol

iodine

cholrine

(disinfectants and Antiseptics)

irridation

light, physicals agent

• UV, gamma, electron,x rays

transcription

reads a DNA Template to make an RNA copy

Translation

After a gene has been transcribed into mRNA, we decode the RNA message by the ribosome to synthesis protein.

• RNA to protein

conjugation

form of unidirectional gene transfer from a donor to a recipient cell that requires cell to cell contact

• plasmid is usually transferred

transcription vs translation. go

transduction

process in which bacteriophages carry host DNA from one cell to another

• two types of transduction

  • generalized and specialized

transformation

Process of importing free (naked) DNA into bacterial cells. Living cells uptake free floating DNA from dead lysed cells

three types of gene transfer

transformation

conjugation

transduction

types of mutations

point

insertion

deletion

genotype vs phenotype

quorum sensing

the process where bacterial cells work together at high density

• look at how many of the same cell are in the environment and determines if it can multiply or not by the amount food in the environment (which they can tell by the amount of cells of the same species there is)

chemotaxis

the ability of the cell to move towards environments favorable for growth and away from harsh environments

phage

viruses that infect bacteria

prophage

A bacteriophage that integrates its genome into its bacterial host’s
genome

phage vs prophage

temperate

This means it exhibits two different types of replication cycles

• has a lytic cycle

• has a lysogenic cycle

virulent

phage that can only do lysis

virulent vs temperate

genome vs chromosome vs plasmid

genome: genetic information that defines an organism, total of all genes in an organism

chromosome: a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

Plasmid : a small circular DNA molecule found in bacteria and some other microscopic organisms.

viruses vs microbes in prokaryotic and eukaryotic domains

viruses are acellular organisms (noncellular) microbes and microbes in prokaryotic and eukaryotic domains are cellular

what makes DNA ideal to encode the genome?

• (1) it is stable and not readily degraded within the lifetime of the cell

• (2) it is a mutable, so it can allow the organism to evolve through heritable genetic change

• (3) easily and readily replicated by using the original strands as template

DNA Structure

is made of deoxyribose sugar, phosphate, and a nitrogenous base

• connected by phosphide bonds

• base interactions are bonded by hydrogen bonds

  • AT has 2 H bonds

  • CG has 3 hydrogen bonds

• the two strands are antiparallel to each other, run in opposite directions, complementary

  • 5’ to 3’ and 3’ to 5’

• Purine: A and G

• Pyrimidine: C and T

  • U is a pyrimidine replaces T in RNA

RNA structure

• composed of nitrogenous base

  • A pairs with T

  • C-G

  • G-C

  • U-A

• ribose sugar (deoxyribose in DNA nucleotides)

• phosphate group

DNA structure vs. RNA structure

how do enzymes pack their DNA

by packing their DNA into a series or loops called nucleoids by supercoiling

steps in DNA replication

1. initiation

2. elongation

3. termination

transcription: initiation

melting or unwinding of the helix and the loading of the DNA polymerase enzyme complex. starts at ori - Origin of replication

• Sigma factor recognizes the promotor and guides
  RNA polymerase to bind to the promoter. RNA polymerase
  then melts open the DNA helix, and catalyzes placement of the first RNA nucleotide

Transcription: elongation

the RNA chain is extended by the sequential
addition of ribonucleotides using the information in the
template strand of DNA. The added ribonucleotides
temporarily base pair to the template DNA strand

Transcription: Termination

at defined termination sites located opposite to the origin

-- RNA pol detaches from the DNA, after the transcript is made.

describe the importance of tRNA, ribosome and, mRNA in translation

Ribosomes catalyze the linkage of amino acids during translation, using mRNA as the code and charged tRNAs as the source of amino acids.
• A ribosome is a massive complex of protein and ribosomal RNA (rRNA).
• Ribosomes are composed of two subunits, each of which includes rRNA and proteins.

tRNA

• dDuring translation, amino acids are attached to small adapter RNAs, called tRNAs, which have RNA sequences called anticodons that match and bind to specific
  codons on the mRNA being translated.

• A tRNA molecule has two functional regions:
  – Anticodon: Hydrogen bonds with
  the mRNA codon specifying an
  amino acid
  – 3 ́ (acceptor) end: Binds the
  amino acid

  
  

transcription process: i recommend a video

Generalized transduction

bacteriophages capable of generalized transduction have trouble distinguishing their own DNA from host when packaging DNA into capsids

• pieces of host DNA accidentally become packaged in the phage capsid instead of phage DNA

• no new phages are made if that is the case but it can change the genetic makeup of the cell

specialized transduction

phage mediated gene transfer mechanism that requires alternating lysogenic and lytic events to move genes from a donor cell to a recipient cell

• during activation of lysogeny, packaging less viral genes is possible but will included host genes lying adjacent to the phage attachment cite

• creates hybrid DNA that can be introduced to new host

silent mutation

doesnt change amino acid sequence

• due to the fact that the genetic code is degenerate

missense mutation

changes the amino acid to another

• changes codon and codes for another amino acid

nonsense mutation

changes the mutation to a stop codon

frame shift mutation

changes the open reading frame of the gene, usually caused by an insertion or deletion that will shift the codons

what type of mutation does a point mutation result in

missense, silent, nonsense

do all mutations affect protein function? what is the relationships between genotype, phenotype and mutation?

Methyl mismatch repair

depends on recognizing the methylation pattern in DNA to repair the mismatch

• Newly replicated DNA are not methylated right away. Mean that the newly synthesized strand of DNA will be unmethylated for a while, while the old strand is methylated

• methylated repair enzymes recognize the mismatch, cut it out and correct the error

• nucleotide cannot be damaged, only incorrect

base excision repair

removes damaged bases

• nitrogenous base is removed without breaking phosphodiester bond.

  • enzymes specific to the damaged base carry out this step

• The site without the base is recognized and cleaved by another enzyme

• base is then replaced by the undamaged one by DNA polymerase

nucleotide excision repair

excises a patch of 12-13 nucleotides, including the damaged one

• DNA polymerase fills the gap with correct nucleotides

• DNA ligase seals he nicks

different types of repairs

methyl mismatch repair

base excision repair

nucleotide excision repair

which repair does not involve damaged bases?

methyl

controlling gene expression

how cells monitor outside and inside environment

• they sense the environment and change depending on it

intracellular control of gene expression

DNA level

Transcription level

transcription level using sigma factors

post transcription level

translation level

post translation level

sensing the external environment: two component transduction system

1st component: chemotaxis

2nd component: Quorum sensing

what are the two components of signal transduction?

What are the levels of gene expression?

1. DNA level

2. Transcription

3. post transcription

4. translation

5. post translation

how is the signal in 2 comp. signal trans. relayed?

What is involved in Quorum sensing? and in relationship to biofilm?