UAB BY 123L Exam 3

karyotyping

number and type of chromosome present

Barr body

-condensed inactive X chromosome near nucleus of cell

nondisjunction

failure of chromosomes to separate during meiosis

autosomal nondisjunction

-failure of chromosomes (other than sex chromosomes) to separate during meiosis

-exs: trisomy 21, trisomy 18

translocation

portion of one chromosome is transferred to another (usually nonhomologous)

isolation of DNA

1. homogenization

2. deproteinization

3. precipitation

homogenization

-solubilizing membranes and denaturing proteins

-exposes DNA

-mechanical disruption: blender

-added salt: pulls water away

-added detergent: breaks down cell wall

deproteinization

-stripping chromosomal proteins from DNA

-add meat tenderizer to help pull away histone proteins

precipitation

-DNA comes out of solution

-slowly and gently add ethanol

-put on ice for process to take place

-DNA floats into ethanol layer

-looks like snot

replication, transcription, translation

DNA -> RNA -> proteins

nucleic acids

-DNA (deoxyribonucleic acid)

-RNA (ribonucleic acid)
what are they?

subunit of nucleic acids

nucleotides

nucleotides

sugar (deoxyribose or ribose) + phosphate group + nitrogenous base

purines

(2 rings)

-adenine

-guanine

pyrimidines

(1 ring)

-thymine (uracil)

-cytosine

DNA

-2 strands held together by hydrogen bonds

-antiparallel polynucleotide chains (if you know one strand, you know the other)

-5' end (phosphate) vs. 3' end

-negatively charged

-can be denatured (disruption of H bonds)

-has an edit function

Chargaff's rule

-amount of A = amount of T

-amount of C = amount of G

2

A-T: how many hydrogen bonds?

3

C-G: how many hydrogen bonds?

DNA replication

-during S phase of interphase

-semiconservative (one old strand and one new strand)

steps of DNA replication

1. helicases unwind parental double helix

2. single strand binding proteins stabilize unwound DNA

3. DNA polymerase makes leading strand (5' -> 3') continuously

4. lagging strand (3' -> 5') made discontinuously in Okazaki fragments (DNA primase makes short RNA primer & extended by DNA polymerase (5' -> 3'), makes short fragments)

5. RNA primer replaced with DNA and DNA ligase joins Okazaki fragments

RNA (vs. DNA)

-uracil instead of thymine

-usually single-stranded

-sugar is ribose (one more OH)

transcription

1. initiation

2. elongation

3. termination

initiation

RNA polymerase binds to promoter region and unwinds DNA

elongation

-template strand vs. non-template strand: to synthesize 5' to 3' only (only 1 strand is copied)

-RNA polymerase moves along DNA to assemble complementary RNA (mRNA)

termination

-RNA reaches STOP sequence

-RNA polymerase and new mRNA are released

-DNA winds back up

translation

protein synthesis

codon

-3 consecutive nucleotides

-codes for 1 amino acid on mRNA (degenerate)

initiation codon

AUG (protein synthesis starts here)

must find it first; excess at beginning and end

stop codons

UAA, UAG, UGA (terminates protein synthesis)

20

how many different amino acids?

what's needed for translation?

-ribosome

-mRNA

-tRNA with anticodon and AA

steps of translation

1. codon recognition

-tRNA binds to codon in the A site

2. peptide bond formation

-catalyzed by ribosome

-between new amino acid and carboxyl end of growing peptide chain

3. translocation

-tRNA in A site moves to the P site, takes mRNA with it

-tRNA from P site moves to E site, released by ribosome

gene

coding for a particular trait

allele

different variations of a gene

gene pool

set of genes within a population

genotype

genetic makeup, alleles present on your chromosome

homozygous

(AA or aa) having the same allele for a gene

heterozygous

(Aa) having different alleles for a gene (dominant allele will be expressed)

homozygous dominant

(AA) having the dominant alleles

homozygous recessive

(aa) having the recessive alleles, only expressed when they're homozygous

phenotype

the visual characteristics that are being expressed

assumptions of Hardy-Weinberg

1. no selection

2. no mutation

3. no migration

4. large population

5. random mating

Hardy-Weinberg equations

p + q = 1

p^2 + 2pq + q^2 = 1

-p is frequency of dominant allele

-q is frequency of recessive allele

-p^2 is frequency of homozygous dominant

-2pq is frequency of heterozygous

-q^2 frequency of homozygous recessive

3 characteristics distinguishing prokaryotes from eukaryotes

1. circular DNA (rather than linear)

2. no membrane-bound nucleus

3. no membrane-bound organelles

domain

kingdom

phylum

class

order

family

genus

species

taxonmanic hiearchy

(prokaryotes)

1. bacteria

2. archaea

(eukaryotes)

3. eukarya

3 Domains

domain archaea

-found in extreme environments: extremophiles

-no peptidoglycan (unique to bacteria)

-some scientists believe that archaea are more closely related to the domain eukarya than to organisms in the domain bacteria

-have unique lipid construction in their plasma membranes

-some have introns (non-coding, intervening sequence within a gene)

methanogens

-"methane makers"

-obligate anaerobes (have to live without oxygen)

-reduce CO2 to methanogen (swamp gas)

-found in swamps and cow stomachs

halophiles

-"salt lovers"

-live in hypersaline environments

-use light (but with carotenoids so not called photosynthesis, simplest form of photophosphorylation

-bacteriorhodopsin causes color

thermoacidophiles

-"low PH, high temperature lovers"

-hot springs or deep sea vents

domain bacteria

-most have peptidoglycan in cell wall (either little or a lot)

-use gram-staining techniques to distinguish between gram+ or gram- bacteria

-1 to 10 um

-use plasma membrane for many functions of those seen in eukaryotic organelles

-have ribosomes, but they have different subunits than eukaryotes

-1 double-strained ring of DNA within a nucleoid region

-can have extra-chromosomal DNA in plasmids

-some have a capsule (protective layer outside the cell wall); can protect against dehydration or host's immune system

-soma have pilli (projections attached to outer layer of cell); pilli can be used for attachment of bacterium to substrate or during conjugation

-3 basic shapes: bacillus, cocci, and spirilli

-3 arrangement shapes: staphylo, strepto, and diplo

-flagella for movement (made of flagellin, no microtubules or tubulin as in eukaryotes)

-no sexual reproduction= no meiosis, no mitosis= only binary fission

-major source of variations: mutations

-3 (minor) ways of recombination

-can form endospores (to withstand harsh conditions): dormant

bacillus

rod shaped

cocci

round, spherical shaped

spirilli

corkscrew/helical shaped

always gram negative

gram-negative

(like E. coli)

-outer membrane makes it resistant to antibiotics such as penicillin

-very little peptidoglycan in cell wall

-stains pink/red

gram-positive

-lot of peptidoglycan in cell wall

-stains violet

gram staining

-crystal violet (+ charged): primary stain= + is purple

-iodine binds to crystal violet and fixes it

-alcohol= shrinks peptidoglycan OR dissolves outer membrane

-safranin (- charged): counterstain= - is pink/red

staphylo

clusters

strepto

chains

diplo

pairs

positive chemotaxis

movement towards chemicals

negative chemotaxis

movement away from chemicals

positive phototaxis

movement towards light

negative phototaxis

movement away from light

bacterial transformation

process of taking in DNA from the external environment

bacterial transduction

transfer of DNA between prokaryotes by viruses (bacteriophages)

bacterial conjugation

transfer of DNA between two bacterial cells which are temporarily joined (transfer of plasmid)

nutrition of domain bacteria

-most are heterotrophic and saprobes (feeds on dead stuff)

-heterotroph vs. autotroph: carbon source (can they fix their own or need organic compounds)

-photo vs. chemo: where do they get their energy from

-majority are chemoheterotrophs

photoautotroph

-energy source: light

-carbon source: CO2

chemoautotroph

-energy source: oxidation of inorganic compounds

-carbon source: CO2

photoheterotroph

-energy source: light

-carbon source: organic compounds

chemoheterotroph

-energy source: organic compounds

-carbon source: organic compounds

obligate anaerobe

cannot survive with oxygen

faculative anaerobe

can survive with or without oxygen

obligate aerobe

cannot survive without oxygen

symbiosis

ecological relationship between different species in direct contact with each other (4 categories)

mutualism

(++) both benefit

exs: sharks and cleaning fish, gut microbiota and humans, clownfish and anemone, and bees and flowers

commensalism

(+O) one benefits and one is unaffected

ex: spider and tree

parasitism

(+-) one benefits and one is harmed

exs: tapeworms and mosquitos

ammensalism

(-O) one is harmed and one is unaffected

ex: algal blooms lead to death of fish

Kingdom Proteobacteria

Subgroup Alpha Proteobacteria

-many species are symbiotic with eukaryotic hosts

-Rhizobium lives within root nodules of legume plants where they fix atmospheric nitrogen into forms the plant can use

Kingdom Proteobacteria

Subgroup Beta Proteobacteria

-nutritionally diverse group, some are important nitrogen recyclers

-Neiserria gonnorrhoeae (causes gonorrhea) goes here

Kingdom Proteobacteria

Subgroup Gamma Proteobacteria

-includes "sulfur" bacteria which oxidizes H2S, producing sulfur as a by-product

-Legionella (causative agent of Legionnaire's disease), Escherichia coli, Vibrio chlolerae, and Salmonella belong here

Kingdom Proteobacteria

Subgroup Delta Proteobacteria

-includes slime-producing Myxobacteria

-includes Bdellvibrios which attack other bacteria

Kingdom Proteobacteria

Subgroup Epsilon Proteobacteria

-most members are pathogenic to humans or other animals

-Camphylobacter (a causative agent of blood poisoning and intestinal inflammation) goes here

-Helicobacter pylori (a causative agent for stomach ulcers) goes here

Kingdom Chlamydia

-survives only in animal cells; depends on host cell for resources such as ATP

-has odd cell wall which stains gram negative; cell wall has no peptidoglycan

-Chlamydia trachmatis (the most common cause of blindness in the world) and also causes non-gonococchal urethritis (the most common sexually transmitted disease) belongs here

Kingdom Spirochetes

-uses flagella to spiral themselves through their environment

-Treponema pallidum (the causative agent for syphilis) belongs here

-Borrelia burgdorferi (the causative agent for Lyme disease) goes here

Kingdom Cyanobacteria

-photosynthetic

-uses photosystems I and II

-has chlorophyll A

-chlorophyll is not in chloroplasts but rather found in the thylakoid membranes, which are scattered

-these organisms are often arranged in filaments

-some are heterocysts, specialized cells which "fix" atmospheric nitrogen into ammonia

Kingdom Gram Positive Bacteria

-the subgroup actinomycetes belongs here

-2 species of actinomycetes cause tuberculosis and leprosy

-actinomycetes are also responsible for the "earthy" odor of rich soil

-members of genus, Streptomyces, have been the sources for several antibiotics

-Bacillus anthracis (the causative agent for anthrax) belongs here

-Clostridium botulinum (the causative agent for botulism) goes here

-Streptococcus and Staphylococcus sp. belong here

-includes Mycoplasmas, the only bacteria known to lack a cell wall; they are also the tiniest known cells

-one species of Mycoplasma causes walking pneumonia

disinfectant

-lyses most cells

-used on non-living surfaces

antiseptic

-lyses some cells, prohibits growth

-used on living tissue

disinfectant vs. antiseptic

-cepacol (mouthwash)? antiseptic

-listerine (mouthwash)? antiseptic

-rubbing alcohol? disinfectant

-clorox? disinfectant

-iodine? antiseptic

-amphyl? disinfectant

spread plate

looking for growth

streak plate

looking for different colonies; separate mix of bacteria

observation of antibiotic susceptibility

-one bacterium per plate

-each dot is a different antibiotic

-look at zone of inhibition

what domain are protists in?

Domain Eukarya

protists

-all are eukaryotic

-most are unicellular

-some exist as colonies

-some are multicellular

-most have aerobic respiration

-can be free-living, parasitic, or symbiotic

-some are heterotrophic

-some are autotrophic

-some can be mixotrophic (heterotrophic and autotrophic)

-all protists require some source of moisture or moist environment

-once classified into their own kingdom: protista are far too diverse

-now various lineages of protists are recognized as their own kingdoms

-more structural and functional diversity than any other group of eukaryotes

-single cells must carry out basic functions performed by all specialized cells of a multicellular organism

-most nutritionally diverse of all eukaryotes

-life cycles vary: some exclusively asexual and some syngamy (fertilization) = sexual reproduction: meiosis happens

pseudopodia

("false feet") temporary cytoplasm-filled projections of the cell wall used for motion or for ingesting nutrients

most cells are amoeboids

photoautotrophs

contain chloroplasts, differ in their chlorophylls