double helix, antiparallel, runs 5' → 3' and 3' → 5' (new always made 5' → 3
which nucleotides complementary base pair with each other?
A and T
C and G
genetic makeup, represents only potential charecteristics
expression of genotype, the actual observable characteristic
what is the leading strand? how is it formed?
continuous strand that is made in 5' → 3' direction
what is the lagging strand? how is it formed?
synthesized in pieces because there is no free 3' end
components of DNA replication: helicase
enzyme that unwinds the double helix
components of DNA replication: template
original DNA strand
components of DNA replication: replication fork
where 2 strands are separated and new nucleotides are added
components of DNA replication: DNA polymerase
enzyme that adds new nucleotides and proofreads
components of DNA replication:RNA primer
small pieces of RNA where DNA polymerase can attach (only on lagging strand)
components of DNA replication: DNA ligase
enzyme that joins fragments of DNA (glue) on the lagging strand
DNA vs. RNA
DNA: deoxyribose, thymine, double stranded
RNA: ribose, uracil, single-stranded
process of making mRNA from a DNA template
what does RNA polymerase do in transcription?
enzyme that makes a new strand of mRNA
what does the promoter do in transcription?
site on DNA template where RNA polymerase binds (start)
what does the terminator do in transcription?
site on DNA template that ends transcription (stop)
steps of transcription
1. RNA polymerase binds to promoter site on DNA template
2. RNA polymerase synthesizes a complementary base strand of the DNA template working in a 5' → 3' direction.
3. transcription continues until a terminator is reached
4. RNA polymerase and a new mRNA are release from DNA template
process of protein synthesis
components in translation: mRNA
messenger RNA, carries info transcribed from DNA, specifies the amino acid sequence of the protein products
components in translation: tRNA
carries amino acids, contains anticodons which pair with the codons on mRNA
components in translation: ribosomes (structure)
site of translation, attaches to mRNA, small and large subunits
3 tRNA BINDING SITES:
A site (acceptor), holds tRNA carrying next amino acid
P site (peptide), holds tRNA with growing peptide chain
E site (exit), where tRNA leaves ribosome
components in translation: rRNA
ribosomal RNA, part of the ribosome
steps in translation: initiation
1. start codon, AUG signals mRNA to bind to small subunit of ribosome
2. initiator tRNA (with the amino acid methionine) attaches its anticodon (UAC) to mRNA in P SITE!!!!!!
3. large and small subunits join
steps in translation: elongation
1. mRNA is threaded through ribosome
2. 2nd tRNA (with amino acid) binds its anticodon with mRNA's codon in the A SITE! of the ribosome
3. peptide bond forms between amino acids
4. polypeptide chain is transferred to tRNA in A site and 1st moves to E site and is released
5. tRNA with growing polypeptide chain moves from A to P site.
steps in translation: termination
1. elongation continues until a stop codon reaches the A site
2. ribosome splits apart and polypeptide chain is released
PROTEIN FOLDS AND BECOMES FUNCTIONAL! (active)
set of three nucleotides bases on mRNA that encode for a specific amino acid
64 codons, 20 amino acids
61 sense, 3 nonsense
how do codons code for amino acids to form proteins?
the nucleotides (3) on the mRNA code for a specific amino acid that together build up to create proteins.
code for amino acids
UAA, UAG, UGA
how is bacterial gene expression regulated and why?
using feedback inhibition (inhibit enzyme reactions when unnecessary) regulated if only needed at certain times
making enzymes is controlled by genetics, transcription and translation
how are genes repressed?
by a process that turns off transcription, repressor block RNA polymerase at the promoter
caused by overproduction of end products
turned on (induced) by substrate of enzyme
system of gene regulation
includes genes promoter and operator
starts/ stops transcription of (lac) gene
where RNA polymerase initiates transcription
E. coli and the lac operon
lac operon ON: lactose → allolactose → binds to tell ribosomes get rid of repressor and to make beta-galactosidase
lac operon OFF: repressor bound to operator, nothing happens
a change in a base sequence of DNA, permanent and passed on
ex. antibiotic resistance
a single base is replaced with another base
base substitution results in amino acid substitution
base substitution codes for a stop/nonsense codon
one or more bases are deleted or inserted
a substance that causes mutations
what are the different types of mutagens?
chemicals (nitrates/nitrites, household cleaners)
radiation (UV light, xrays. causes thymine dimers to form)
exchange of genes between 2 DNA molecules to form new combinations of genes
what is crossing over?
2 chromosomes break apart and rejoin, resulting in 2 original chromosomes having a combination of eachother
why is it important for genes to transfer?
contributes to genetic diversity, genes for resistance to drugs develop, new nutritional and metabolic capacities develop, increases virulence
circular pieces of DNA, replicate separately from chromosomal DNA
3 types of genetic transfer
what is transformation and how does it work?
process of genetic transfer when a cell lyses and naked DNA is transferred to another bacteria, donor combines with recipient DNA to form a new recombinant
what is the significance of plasmids?
can enhance pathogenicity (disease causability)
fertility, used in conjugation, carries genes for a sex pilus
resistance, transfers antibiotic resistance, can transfer resistance to heavy metals, synthesize factors such as toxins, enzymes and adhesion
what is conjugation and what components are involved?
sex pilus: connection between 2 cells
donor has F+ plasmid
recipient has no plasmid, F-
what are the steps in conjugation?
1. sex pilus grows out of F+ call and attaches to F- cell
2. copy of F+ is transferred to F--results in two F+
process of genetic transfer in which DNA is passed from one bacterium to another by a bacteriophage (virus)
transposons (also advantages and disadvantages)
segments of DNA tht move from 1 region to another, "jumping genes"
advantages: genetic diversity, change in morphology and pigmentation traits, replaces damaged DNA
disadavantages: mutations, cell dysfunction
genetic engineering/ recombinant DNA technology
techniques in microbiology that manipulate DNA
benefits of biotechnology
use of microbes to produce food antibiotics, vitamins, and enzymes
basics of restriction enzymes/ endonucleases
enzymes from bacteria, recognize foreign DNA and can break bonds when adjacent nucleotides, used in recombinant DNA technology
technique that produces readable patterns of DNA fragments, uses a soft agar gel and electrical current to separate fragments based on SIZE
purpose of DNA sequenceing
used to determine the exact genetic code (order of bases), Sanger method
why is polymerase chain reaction used?
makes multiple copies of a piece of DNA enzymatically (Taq polymerase from T. aquaticus)
basics of DNA profiling/ fingerprinting and uses-
DNA profiling, forensic tool, uses restriction enzymes to cut DNA at specific parts and separate with gel electrophoresis
idea of classifying organisms
3 domain system
2 are prokaryotic cells- archea and bacteria
Eukarya is other domain
What is the only domain that has kingdoms?
What is the endosimbiom theory?
Chroloplasts in past were prokaryotic cell. Then they were endocitosed and evolved into organelle. Same is true with mitochondria.
Is archea more closely related to eukara or bacteria?
What are three major groups of archea domain?
1. hypothermophiles (like to grow in hot environment)
2. extreme halophiles- like to grow in salty enviroment
3. methanogens- like to produce methanin
What does bacteria contain in cell walls?
What is found in arches walls?
What is found in plant cell walls?
What is found in fungi cell walls?
each species retains some characteristic from ancestor(idea behind taxonomy)
look at: anatomy, fossils, and rRNA
What do we use to name species?
Binomial Nomenclature (genus + specific epithet)
Why are viruses excluded from the 3 domains?
They are not made of cells. This system divides organisms into eukaryotic and prokaryotic cells.... Can't put them in either.
Which phylum does staph lacoccus belong to? Micrococcus?
Fermacutes, Atino bacteria
Kingdom, Phylum, Class, Order, Family, Genus, Species
Grown in laboratory media
population of cells derived from a single cell
Ex: streak out plate and get a colony... all came from one cell.
genetically different cells within a clone
Ex: streak out plate and get a mutation... it starts to reproduce within colony
What do orders end in?
What do families end in?
What order and family does pseudomonas aeruginosa belong to?
pseudomonales and psedomonaceae.
Main characteristic used in putting organisms in phylum
how much G + C they had (high G + C) (low G + C)
4 basic classifications in eukara domain
multi-cellular, no cell wall, chemoheterotrophic (organic carbon, energy source)
multicellular, cellulose cell wall, usually photoautotrophic
Chemoheterotrophic (just like you and i), unicellular or multicellular, cell walls of chitin, have sexual and asexual reproduction
Most people don't consider this a kingdom anymoreA catchall kingdom of eukaryotic organisms that so not fit in any other kingdoms(Grouped into clades based on rRNA)
What do we call unicellular fungi?
yeast and molds.
How do all herpes viruses end?
Virus Genus endings
Common, everyday name.
Virus Sub Species
end in number.
ex: HIV 1 or HIV 2
Classification vs identification
Classification- looking at how they are related to one another
Identification- looking more at what we do in the lab and see how we can identify them
What 3 things to you need to know to identify your unknown
1. Morphological characteristics- cocci, balicilli, presence and endospores, capsules, flagella
2. Differential staining (gram stain, acid fast)
3. Biochemical tests- determines presence of bacterial enzymes (catalase)
Whats the first thing we do in identification?
What do all differential stains have in common?
Give you information about cell wall.
What are dichotomous key
always used for identification of bacteria, series of yes or no question... "Is it gram positive" Y or N... not "gram positive"
you don't have to inoculate anything, scoring with 5 digit number... look up number in book. (no critical thinking)
3 tests based on same principle: antibody (proteins)- antigen binding
**bc the bonding of antibodies and antigens is so specific... great for IDing
3 types of serology tests
1. Slide agglutination test: bacteria clumps together if positive test
2. ELIZA test- attach an enzyme to antibody... if antibody binds to antigen we can tell by adding a substrate and see if it attaches to the enzyme or not
3. Western blot- put proteins on gel and they'll be separated by size using gelophoreeses... transfer it to filter paper. antibodies will stick.
Always uses lytic phage.
Primarily used for tracing outbreaks, see where original source was... look at patternsPlate bacteria out, Put it on grid, if phage infect bacteria... it is gonna replicate cause cell too lyse and create clearing called a plaque
What is a phage?
Virus that invades bacteria
Part of Transduction
use glass slide and spot DNA on slides. one slide can have 10,000 different sequences of DNADNA on slide is SINGLE stranded! (its hybridization)take DNA sample from patient, put florescent label on it.. which dot lights up
Nucleic Acid Hybridization
drug to knock out expression of specific gene
used for identification
used to try and see what organisms are related.. classification
how do we define a node?
similarity in rRNA
Eukaryotic, unicellular, classified by motility, some parasitic, heterotrophic (get food from outside of body by vacuoles/cell membrane absorbtion)
Moisture, water and soil, some can live in extreme environments
Protozoa Trophozoite Life Cycle
Motile feedingstage, requires water and food
Protozoa Cyst Life Cycle
Dormant stage, conditions unfavorable
Protozoa Asexual Reproduction: Binary Fission
Division of 1 cell into 2 identical cells
Protozoa Asexual Reproduction: Budding
Protrusion off of parent cell
Protozoa Asexual Reproduction: Schizogony
Nucleus undergoes multiple divisions before the cell divides (plasmodium)
Protozoa Sexual Reproduction: Conjugation
Genetic exchange between 2 mating pairs that requires cell to cell contact
nonmotile, most parasitic, example plasmodium causes malaria or toxoplasma can harm babies transmitted by cat poop
Eukaryotic, uni or multi cellular, classified by color/pigment, contain chloroplasts, photoautotrophic (make food from the sun)
Body, performs photosynthesis
Aquatic, soil, rocks, cool water often near surface
Asexually by binary fission, sexual not very frequent
Phyla of Algae: Phaeophyta
Brown algae, kelp, big, can get to 50 meters, found in coastal waters, used in ice cream/ toothpaste/ soap/ lotion
Phyla of Algae: Rhodophyta
Red algae, deeper in ocean, used to make agar
Phyla of Algae: Chlorophyta
Green algae, contain chlorophyll, most microscopic, example volvox or spirogyra
Most numerous unicellular algae, important in food chain, have shells
Plankton, cause red tide, photosynthetic, have shells
Blue-green, domain bacteria, prokaryotic, example oscillatoria and anabaena
Study of fungi
Eukaryotic, multicellular (except yeast), classified by spores, some parasitic, macrofungi (mushrooms), microfungi (molds & yeast), cell walls made of chitin
Heterotrophs, absorb or decompose animal and plant debris
Low moisture, pH 5, can grow in high salt and sugar concentations
Filaments of cells, develop from spores, grow by elongating at tips, each part can form a new mold
Group of hyphae
Cross-walls in hyphae
Fungi Asexual Reproduction: Conidiospore
Fragmentation of hyphae, produced in chains
Fungi Asexual Reproduction: Sporangiospore
Fragmentation of hyphae, produced in sacs
Fungi Sexual Reproduction: Zygospore
Union of 2 nuclei of 2 morphologically similar cells, (+) and (-) come together
Fungi Sexual Reproduction: Ascospore
Union of 2 nuclei of 2 morohologically similar or not similar cells, produced in ascus (sac-like structure)
Fungi Sexual Reproduction: Basidiospore
Union of 2 mating strains that bud off of parent cells, produced in club shaped structure
Phyla of Fungi: Zygomycota
Nonseptate hyphae, asexual sporangiospores, sexual zygospores, example rhizopus or phycomyces
Phyla of Fungi: Ascomycota
Septate hyphae, asexual conidiospores, sexual ascospores, example aspergillus or penicillium or yeast
Phyla of Fungi: Basidiomycota
Septate hyphae, sexual basidospores, asexual conidiospores, example club fungi or mushrooms or puff balls
unicellular, nonfilimentous, spherical or oval, can grow with or without oxygen, can ferment carbs to create carbon dioxide and alcohol, make bread/ beer/ wine (cereviseae), yeast infections (candida albicans)
Budding example cereviseae and fission (2 new cells) example longname octosporous