DNA Bases

Polymer of Nucleotides

A- adenine

G-guanine

T- thymine

C- cytosine

RNA polymerase

enzyme that produces primary transcript RNA. In cells, RNAP is necessary for constructing RNA chains using DNA genes as templates, a process called transcription.

RNA

Ribonucleic acid o

DNA

deoxyribose nucleic acid

three major classes of cellular RNAs

(i) ribosomal RNA (rRNA),

(ii) messenger RNA (mRNA)

(iii) transfer RNA (tRNA).

transcription

these three types of molecules originate as complementary copies of one of the two strands of a DNA segment that constitutes a gene

Ribosomal RNA (rRNA)

structural component of ribosomes, the sites where translation occurs during protein synthesis (machinery of protein synthesis)

Messenger RNA (mRNA)

responsible to carry the genetic message from DNA to the ribosome. Their length and sequence vary depending upon the gene which is being transcribed into m RNA

Transfer RNA (tRNA)

the smallest of the three types. It carries amino acids to the ribosomes (protein) during translation.

RNA Bases

A-

G -

C-

U - uracil

Pair DNA with RNA

A

G

T

C

RNA

U

C

A

G

Where does replication occur in DNA

at the replication fork

how many replication forks are in bacteria

two replication forks in bacteria

in which directions do the replication forks move in bacteria

opposite directions

what are the two replication forks called in bacteria

bi-directional

what direction does synthesis occur in DNA

5'- 3'

What is the 5'- 3' strand called

leading strand

what is the non synthesizing strand called

lagging strand 3'- 5'

what are the short pieces on the lagging strand called

okazaki fragments

what does RNA require to begin each fragment

primers

what closes the gaps in the strands

DNA ligase

genetics

study of genes

gene

segment of DNA that encodes a functional product usuall a protein

The three essential macromolecules of life are

DNA

RNA

Protein

Phenotype

expression of gene (protein that can be seen)

Semiconservative replication

describes the mechanism by which DNA is replicated

1 strand of old and one strand of new DNA

DNA to RNA is called what....

RNA to Protein is called

transcription

translation

all RNA is transcribed from DNA by

RNA polymerase

DNA is

double helix (double strand)

RNA is

mono strand

codon

a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule

what forms codons

triplets of bases in mRNA

what does each triplet correspond to

a specific amino acid

what determines which amino acid goes with which codon

genetic code

how many codons for amino acid

61

how many stop codons

3

what is the sequence based on the genetic code chart

from left, top, to right side (top to bottom)

UCAG left (top to bottom), UCAG top (left to right), UCAG, UCAG, UCAG (right top to bottom 4x's) 4 columns

how many bases are genetic in genetic code

3 bases

is there a concern if there is a mutation in the 3rd base

no, only time there is a concern is if there is mutation in base 1 or 2

what is RNA start codon

A U G

what are the most common stop codons

UAA, UAG, UGA

what marcomolecule do disenfectants normally effect in bacteria

disenfectants normally effect PROTEINS in bacteria which prevents metabolism

how many stages are there in translation

there are 3 stages in translation

1. initation
2. elongation
3. termination

what do these three translation stages require to be functional

enzymes and proteins

what are the 3 steps in elongation translation

1. codon recognition
2. peptide bond formation
3. translocation

where does mutation occur

mutation occurs in DNA

what is mutation

a change in genetic material (beneficial, netural, harmful)

ex. beneficial mutation- evolution

harmful mutation- cancer

netural mutation- no effect

what causes mutation

mutagen

what is a mutagen

a gene that causes a mutation

nonsense mutation

a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA

frameshift mutation

insertion or deletion of one or more nucleotide pairs

*shorten or extend frame of DNA, RNA

ionizing radiation

x-rays and gamma rays that cause the formation of ions that can react with nucleotides and DNA phosphate backbone

what does UV radiation cause

thymine dimers

thymine dimers (t-dimers)

A pair of abnormally chemically bonded adjacent thymine bases in DNA, resulting from damage by ultra-violet irradiation. The cellular processes that repair this lesion often make errors that create mutations. (cancer)

transformation

naked dna from environment transfers to another bacteria

conjugation

transfer of genetic material (plasmid) between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells...... through pilli (gram negative)

-phage

virus

Transposons

jumping gene

transduction

the process by which DNA is transferred from one bacterium to another by a virus

sterilization

completely destroys all forms of microbial life

disinfection

• destroys VEGETATIVE cells on SURFACE
• reduces # of viable organisms in material

antisepsis

the chemical disinfection of living tissue, such as skin or

mucous membrane

• removal of pathogens from living tissue

degerming

physical removal(mechanical cleansing) of microbes via alcohol, swab, soap

ex. cleaning the skin with alcohol prior to injection

asepsis

the absence of significant contamination

bactericidal (-cidal, to kill)

kill ALL bacterial

bacteriostatic (-static, to stop)

halt (inhibit) the growth of bacteria for as long as the inhibitory substance is present, NO DUPLICATION

ex. freezing food method

once inhibitor is removed, growth begins

ex. removing food from freezer

Thermal Death Time (TDT)

the TIME at a given temperature in which all the micoorganisms in a liquid culture will be killed

• time is the variable (it changes)
• temp is the constant (remains the same)
• ex. temp is 50 degrees celcius but bacteria may not die at 5, 10 or 15 mins but may die at 30 mins

Thermal Death Point (TDP)

the lowest temperature at which all microorganisms in a liquid suspension are killed in 10 mins

• temperature is the varaiable (it changes)
• time is the constant (it remains the same)

Pasteuriztion

heat (below boiling) for short period of time to kill pathogens and reduce bacteria count, does not kill all bacteria- some useless ones survive

flash pasteurization

high heat at a short period of time

tyndallization

method used to destroy spores

consists of heating the substance to boiling point and holding it there for 15 minutes, three days in succession. After each heating, the resting period will allow spores that have survived to germinate into bacterial cells; these cells will be killed by the next day's heating. During the resting periods the substance being sterilized is kept in a moist environment at a warm room temperature, conducive to germination of the spores (favorable environment for bacteria). When the environment is favourable for bacteria, it is conducive to the germination of cells from spores, and spores do not form from cells in this environment

autoclave

a pressure chamber used to sterilize equipment and supplies by subjecting them to high pressure saturated steam at 121 °C (249°F) for around 15–20 minutes

KILLS SPORES

non ionizing radiation

NO PENETRATION (ex. sound waves, visiable light)

ionizing radiation

PENETRATION (ex. gamma rays, Xrays, electron beams)

filtration

the passage of a liquid or gas (air) through a filter with pores small enough to remain microbes

pore size .45 or .2 micron

used with heat liable samples

photophosphorylation

light reactions

2 kinds of photophosphorylation

cyclic (mostly found in bacteria, used by cyanobacteria)

non-cycllic (found in green plants and cyanobacteria)

dark reaction

the cycle of reactions (the Calvin cycle) that occurs in the second phase of photosynthesis and does not require the presence of light

It involves the fixation of carbon dioxide

oxygenic photosynthesis

produces oxygen

carbon dioxide + water + light energy → carbohydrate + oxygen.

Anoxygenic photosynthesis

process where light energy is captured and converted to ATP, without the production of oxygen

water is not the electorn donor

photosynthesis

light energy transformed into chemical energy

2 parts.....

• light reactions (require light)
• dark reactions (no light required)

minimum temperature

lowest temperature where growth can occur

optimum temperature

temperature where species grows the best

maximum temperature

highest temperature where growth can occur

what are the PHYSICAL growth requirements for microbacterial growth

ph, osmotic pressure, food

psychrophiles

cold-loving, grow at 0 to 20 degrees celsius,

• (optimum cold-loving temp 15 degrees Celsius)

mesophiles

middle temperature loving, human body temp, 20 degrees to 45 degrees celsius,

• (optimum middle-loving temp 20 - 37 degrees celsius) PATHOGEN

thermophiles

heat loving, grow at 37 to 65 degrees celsius

psychrotrophs

A psychrotroph can survive at a similar, but larger range than a psychrophile. It can survive from 0 - 35 degrees celsius but (optimally at 20 - 30 degrees celsius) These organisms can be found in refrigerated spoiled food.

what is the optimum ph for bacteria to grow

6.5- 7.5

what pH is favorable for molds and yeasts

5 & 6

acidophiles

• grow in acidic enviroments such as: digestive tracts, dairy foods (yogurt), vagina
• considered probiotic Lactobacillus acidophilus (L. acidophilus) lactic acid bacteria

basophiles

basic loving grown in intestines

optimum pH 8.5

hoe can organisms change the culture media

due to their own waste products may be toxic due to pH change

pH change is due to

bacterial metabolism

what percentage of cells are water

80-90%

hypotonic

water will move INTO cell (can cause cell to BURST)

hypertonic

water will move OUT of the cell (can cause cell to SHRINK)

halophiles

salt loving

facultative halophiles

organism that can grow at high salt concentrations but DO NOT require high salt concentrartons

obligate halophile

REQUIRES high salt concentration for growth

macro-nutrients

carbon, hydrogen, oxygen, nitrogen, phosphorus

trace elements

inorganic elements required in small amounts (usually enzyme co-factors)

oxygen effects

organisms produce more energy when growing in oxygen but toxic byproducts can be fatal to cells

example of oxygen byproducts

superoxide radical (superoxide dismutase)

hydrogen peroxide (catalase, peroxidase)

what do AEROBES require for growth

oxygen

facultative ANArobes

grow with or without oxygen

ANArobes

can NOT survive in oxygen environments

microAEROphiles

require SMALL (micro) or low amounts of oxygen

what enzyme do AERObes require

• superoxide dismutase
• catalase
• peroxidase

obligate AERobes

REQUIRE oxygen

facultative ANAerobes

can grow with or without oxygen

obligate ANAerobes

can NOT live with oxygen

AEROtolerant

tolerate oxygen

synthetic or defined medium

medium made of KNOWN amounts of chemicals

complex medium

some ingredients are of unknown composition or amounts (extracts of plants, yeast, or meat) ex. nutrient broth tryptic soy broth

selective medium

encourages the growth of certain organisms while discouraging the growth of others

• (ex. crystal violet, or basic dyes selective for Gram- against Gram+ (2 groups)
• MacConkey

differential medium

distinguishes between different groups of bacteria. medium contains constituents which cause an OBSERVABLE change (color or pH change)

• ex: MacConkey contains lactose and netural red, lactose fermenters appear pink

generation time

the time required for cells to divide (and double the population) can be a short as 20 mins or longer than a day

2 bacteria to one culture equals how many generations at 64

5 generations

what phase does bacterial begin to adjust to environment

lag phase

based on the chart, what phase should antibiotics be added

log phase

what phase of microbial growth is the gram stain performed

log phase

direct methods of measuring bacterial growth

1. plate counts
2. filtration
3. most probable number (statistical method)
4. direct microscopic count

turbidity (indirect method)

cloudy (turbid) broth indicates greater bacterial population; estimate number of bacteria by analyzing turbidity with spectrophotometer (measures the amount of light passing through a culture); transmission of light is inversely proportional to population size of bacteria

does not distinguish between living and dead cells

Metabolic Activity (indirect method)

estimates number of cells in a culture by measuring changes in metabolic processes (e.g., nutrient utilization, waste production, pH) ......ADD GLUCOSE

Dry Weight (Biomass)

involves filtering mo's from culture medium, drying and then weighing; suitable for broth cultures, useful when there is an abundance of mo's; growth cannot be followed over time b/c mo's are killed in the process

What are the sources of antibiotics

more than half from Streptomyces and Bacillus and molds (fungi)

What does the term broad-spectrum antibiotic refer to

an antibiotic that acts against a wide range of disease-causing bacteria. A broad-spectrum antibiotic acts against both Gram-positive and Gram-negative bacteria.

• binds 50s subunit, inhibits peptide bond formation

What does the term narrow-spectrum antibiotic refer to

an antibiotic effective against specific families of bacteria.

(small range of pathogens they are effective against)

Give an example of a narrow-spectrum antibiotic

penicillin (affects Gram positive bacteria)

Is there any danger in using broad-spectrum antibiotics

Yes, broad-spectrum antibiotics can destroy the normal microbial flora.

Define selectively toxic

highly effective against the microbe but have minimal or no toxicity to humans (host).

Discoverer of penicillin

Alexander Fleming 1928

Who performed the first clinical trial of penicillin

(when was penicillin first used)

Howard Florey and Ernst Chain 1940

What fungus does penicillin originate from

Penicillum

What is spectrum of activity in antibiotics

mode of action and which pathogen it is effective against

What can happen as a result of the normal microbial flora being destroyed

destruction of normal microbial flora can lead to a superinfection in which a survivng organism overgrows

What is a superinfection

A superinfection is generally defined as a second infection superimposed on an earlier one, especially by a different microbial agent of exogenous or endogenous origin, that is resistant to the treatment used against the first infection. An example of this in bacteriology is the overgrowth of endogenous Clostridium difficile which occurs following treatment with a broad-spectrum antibiotic.

What are some examples of a superinfection from antibiotic use

• Clostridium difficle (c-diff)
• Candida albicans (yeast)

What is the criteria for ideal antibiotics

1. selectively toxic
2. soluble
3. resists excretion (breakdown)
4. shelf life
5. does NOT lead to resistance
6. cost

Describe: Inhibition of cell wall synthesis

Peptidoglycan is found only in bacterial cell walls (animals do not have PGC/cell walls).
-Penicillin prevents the synthesis of PGC, weakening the walls and the cell undergoes lysis.

penicillins common core is called

b-lactum ring

penicillinases

enzymes produced by some bacteria that provide resistance to β-lactam antibiotics like penicillins

what interferes with cross-linking

penicillin and cephalosporin

what prevents stand synthesis

vancomyicin

is penicilinase resistant to penicillin

yes penicilinase is resistant to penicillin

What is synergism

occurs when the effect of two drugs together is greater than the effect of either alone

What is antagonism

occurs when the effect of two drugs together is less than the effect of either alone

ex. penicillin does not worl well with tetracycline because cells are not growing

Misuse of antibiotics include

1. using outdated (weakened) antibiotics
2. using antibiotics for common cold and other inappropiate conditions
3. using antibiotics in animal feed
4. faliure to complete subscribed regimen of antibiotics
5. using someone else's leftover prescription

Antibiotic resistance

occurs when bacteria change in some way that reduces or eliminates the effectiveness of drugs, chemicals, or other agents designed to cure or prevent infections. The bacteria survive and continue to multiply causing more harm

Compare the terms bacteriocidal and bacteriostatic

Bactericidal: kills the bacteria.
-Bacteriostatic: inhibits the growth of the bacteria.

what percentage of Americans get a viral disease each year

90%

are anti-virals limited in the groups they are effective against

yes

nucleoside analogs

synthetic nucleosides which interfere with DNA and RNA synthesis

Enzyme inhibitors

inactivate reverse transcriptase

what is transcriptase needed for

to make DNA from RNA viral genome

what are the tests used to guide chemotherapy

Kirby-Bauer

Broth dillution

Vancomycin (last resort)

is an antibiotic useful for the treatment of a number of bacterial infections.

effective mostly against gram-positive (cell wall) bacteria

Kirby-Bauer antibiotic testing

test which uses antibiotic-impregnated wafers to test whether bacteria are affected by antibiotics. In this test, wafers containing antibiotics are placed on an agar plate where bacteria have been placed, and the plate is left to incubate. If an antibiotic stops the bacteria from growing or kills the bacteria, there will be an area around the wafer where the bacteria have not grown enough to be visible. This is called a zone of inhibition.

minimal inhibitory concentration (MIC)

the lowest concentration of an antimicrobial that will inhibit the visible g rowth of a microorganism after overnight incubation.

minimal bactericidal concentration

the lowest concentration of an antibacterial agent required to kill a particular bacterium.

how can minimal bactericidal concentration be determined

from both dilution

the major modes of antimicrobial drugs

1. inhibition of cell wall synthesis
2. inhibition of protein synthesis
3. inhibition of nucleic acid synthesis
4. injury to plasma membrane
5. inhibit the synthesis of essential metabolites

chloramphenicol

• simple structure
• easily manufactured
• broad spectrum
• SERIOUS SIDE EFFECTS (used only as last resort)

macrolides

contain macrocyclic lactone ring

ex. erythromycin (not able to penetrate most Gram negative cell walls

what is alternative to penicillin

erythromycin (macrolides)

side effects of streptomycin (bactericidal)

• auditory nerve damage
• kidney damage

tetracyclines (broad spectrum) is produced by (protein synthesis)

streptomyces

disadvantages and side effects of tetracyclines (protein synthesis)

supress normal flora (causing superinfection)

not advised to:

children-brownish teeth

pregnant women-liver damage

sulfonamides

stop folic acid synthesis (broad spectrum)

ciprofloxacin

stops DNA gyrase (urinary tract infections)

polymyxin B

topical

combined with bacitracin and neomycin in O-T-C preparation

why are quinolones and fluoroquinolones not given to children

they stop cartilage development

Describe: Injury to plasma membrane

Antibacterial & anti-fungal drugs.
Polymyxin B and bacitracin cause damage to plasma membranes.