DNA synthesis

Dna polymerase - enzymes which catalyze the synthesis of DNA

Helicases - are responsible for unwinding dna

Topoisomerase (such as DNA Gyrase) -

relieve tension caused by helicases by removing supertwists

Replicon - the unit of the genome which is to be replicated.

Nucleosome - histones + DNA

Histones - proteins used for coiling the DNA

SSBs - single-stranded DNA binding protein which keeps the

chromosomes unbound

Polymerase - DNA or RNA synthesizing protein

RNA &DNA primers attach to the lagging strand in order to give it a place to start synthesizing the new DNA.Polymerase or Rnase then remove the primers one at a time & they are replaced by their complementary base pairs.

DNA Ligase will create a phosphodiester bond after the primers are removed, joining together all the Okazaki fragments.

Replisome - The collection of proteins & enzymes which carry out genetic replication. Organisms that replicate faster, may have more than one.

DNA Polymerase I & III can proofread strands of copied DNA & fix incorrectly matched base pairs.

RNA polymerase binding site or Pribnow box site where the RNA polymerase begins to unwind the DNA.

Template strand & non-template strand dna is double-stranded, and only one is used to transcribe mRNA, that is the template. One gene on the template strand includes four portions that aren't used in the translation process, two at each ends. They include the Promoter/Terminator, which act as start & stop signs for the polymerase synthesizing the mRNA. Then on the mRNA we have the leader & trailer sections which also act as start & stop signs but for the ribosome (AUG codon for start). These two are called anti-promoter/trailer when looking at them on the template strand. In-between these is the coding region, the codons which are used in translation.

Regulatory sites are sites where regulatory DNA-recognizing regulatory proteins bind at either stimulate or prevent gene expression

Auxotrophs - a mutant because a certain biochemical pathway isn't producing an endproduct, which must be added to its diet for it to survive

Prototroph the opposite of an auxotroph

Spontaneous mutations occur without any type of exposure and result from errors or sometimes transposons.

Tauterism when one of the base pairs is in an interchangeable structural isomeric form (enol or imino instead of keto). This steric change will cause the hydrogen bonds to occur elsewhere than normal, and A binds to C - G binds to T

Transition mutations occur when a purine is changed for another purine, or a pyrimidine is changed for another pyrimidine. They're common and easily fixed by proofreading.

Transverse mutations occur when a purine is changed for a pyrimidine or vice-versa. They're rare because of the steric issues with pairing purines w/ purines or pyrimidines w/ pyrimidines. May have to do with the size of the molecules…

Depurination is the loss of the base portion of a nucleotide resulting in changes in the way it pairs. Apurinic site or apyrimidinic site is what they are called. Deamination is the change of a uracil to cytosine.

Induced mutations caused by mutagens.

Base analogs structurally similar to bases yet bind differently (5-BU) which can get incorporating into growing polynucleotide

Specific mispairing mutagen changes a base's structure altering its pairing. methyl-nitrosoguanidine adds a methyl group to a guanine, making it pair with thymine. Proof-reading functions have a 1 in 2 chance of fixing this problem, since it doesn't know which base pair was originally there.

intercalating agents insert themselves between base pairs by distorting DNA.

A mutation to the wild type is called a forward mutation, when it's reversed back to the wild type this is called a reversion mutation. And when the forward mutation truly becomes the wild type again this is a back mutation.

Suppressor mutation when the wild type is regained by a second mutation in a different gene. Thus the phenotype is regained, but the genotype remains different.

Most mutations are point mutations, and only affect a single basepair.

silent mutation is the change in a basepair that doesn't affect the product. In this case the old & new codon make the same amino acid, and isn't detectable unless the genome is sequenced.

missense is the change in a base pair which although makes a different amino acid can range from either no change or vast changes in the phenotype.

 
 

The complex which includes the polymerase + accessory proteins is called

• a primosome. It is believed that both the leading & lagging strands are synthesized simultaneously on the same complex. The lagging strand is done in the 5' 3' direction & is discontinuous. The product of the lagging strand is called Okazaki Fragments.
  
• Frameshift mutations changes in the reading frame of the codons. Must be the addition of less than three codons. At three codons, it simply adds the extra amino acid, and may have minimal affect on the functionality and reading frame.
  
• nonsense mutations are early terminations caused by a point mutation. The sooner in the coding portion they are, the more damaging they usually are.
  
  • If the reading frame is restored by another point mutation, then we call that an intragenic suppressor mutation.
    

  DNA methylation is the addition of a methyl group to DNA bases ,done by dna methyltransferases. newer strands lack methyl groups, which helps corrective enzymes differentiate between the old and new strands
  

 
 

Read John Cairns

Direction/adaptive & hypermutations.

Tauterism. Imino enol keto forms.

 
 

 
 

 
 

chapter 2. microscopy

chapter 2. microscopy

 
 

refraction ray of light is bent at the interface

 
 

heat fixation keeps morphology intact but not internal structures

chemical fixation is used for larger organisms, and to preserve substructures. Reacts with proteins and lipids by rendering them insoluble, inactive and immobile. ethanol, acetic acid, mercuric chloride, formaldehyde, and glutaraldehyde.

 
 

dyes have two common features. chromophore groups (gives its color - conjugated double bonds) and bind ionically, covalently, or hydrophobically.

ionizable

basic dyes methylene blue, crystal violet, etc. are + charged (chloride salts) bind to nucleic acids, most proteins and bacterial cell surface.

acid dyes eosin, rose bengal, acid fuchsin have negatively charged groups (carboxyl) and phenolic hydroxyls (-OH), bind to positively charged cell structures

since pH affects the degree of electrical charges

higher pH - use basic dyes

Lower pH - use acidic dyes

simple staining is the use of only one kind of dye on fixed smears

differential staining divides the bacteria based on different staining procedures, such as gram's stain (g+ & g-)

mordant increases the level of interaction between the stain and the smear.

acid-fast staining, bacteria with high lipid content in their cell wall, using basic fuchsin and phenol turns red. methylene blue in this case is the counter-stain. This is used to detect Mycobacterium tuberculosis and Mycobacterium leprae

Structure staining - Negative staining - India ink (pink) or Nigrosin dye - the bacteria itself appears lighter than the dark blue background stain, since the color fills the entire slide except where the bacteria itself is (thus why it's lighter)

spore staining for genera Bacillus and Clostridium

Schaeffer-Fulton procedure heat with malachite green, wash dye off, counter-stain with safranin

 
 

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Prokaryotic structure

inclusion bodies - includes ribosomes - granules of in/organic material lying in the cytoplasmic matrix

amphipathic - lipid bilayer - polar & non-polar ends - hydrophobic/phyllic regions

hopanoids - sterol-like substance (pentacyclic - 5 carbon chain) helps stabilize the plasma membrane

fluid mosaic model - includes integral proteins (2/3rd of membrane proteins & usually insoluble - amphipathic) and peripheral proteins, which are easily removed. Oligosaccharides (carbs) are attached to the ends of most integral proteins, possible for cell-cell recognition, chemotaxis, & active transport in and out of the cell

mesosomes - invagination of the plasma membrane, usually found near the septa in dividing bacteria, mostly in G+ bacteria. Could be involved in cell wall formation

protoplast = cytoplasm + plasma membrane

inclusion bodies
inorganic

polyphosphate/volutin granules store phosphate as orthophosphates (PO4 -3 if it loses all 3 Hydrogens) w/ ester groups

organic inclusion body

gas vacuole found in many cyanobacteria, stores gases to make the organism float so that it can get light

ESTER LINKAGE - When a Carboxyl Acid (group) reacts with a Hydroxyl group (Alcohol) the H in the hydroxyl group combines with HO from the carboxyl group to make water. This is a dehydration(or condensation) reaction. The opposite occurs when an ester bond reacts with an acid or base in an aqueous solution. This is called hydrolysis.

ETHER BONDS - are when two hydrocarbon chains are bonded to one oxygen. This happens when

nucleoid region where the dna is in prokaryotes. most have single circle of double stranded dna, some have a linear dna chromosome, while very few have more than 1 chromosome (use feulgen stain for nucleoid). nucleoid isn't compact and may project in the cytoplasm during active growth

plasmids circular double stranded dna independent of the nucleoid

Gram+ are stronger, more often pathogenic. cell membrane>periplasmic space(periplasm)>PG

peptidase - enzyme which catalyzes peptides into amino acids

teichoic acid polymers of glycerol or ribitol (carbs) joined by phosphate grp. If attached to membrane lipids (through periplasmic space) they're called lipotechoic acids

Growth

Growth phases – lag,

exponential phase(log) – growth at maximal rate un/balanced growth – depends on nutrient levels and environmental factors

stationary – can occur because of lack of nutrients, sometimes o2 is only available for those on the surface, because it's not very soluble. Or waste accumulation, such as lactic acid [high pH] from streptococci(anaerobic)

starvation – protoplast shrinkage, nucleoid condensation, and starvation proteins make the bacteria more virulent. Stronger cell wall, chaperones prevent denaturation, Dps [dna-binding protein from starved cells, protect the dna]

death phase

coenocytic – multinucleate organism (such as fungi)

batch cultures – closed system (usually liquid) in which waste products can accumulate

Petroff-Hausser Counting machine

extremophiles (bacillus infernus) live in extreme environments

inclusion bodies? 49-52

Hypotonic environment can cause the cell the lyse, or the reverse is plasmolysis

Compatible solutes are compatible with metabolism, and used to modify the osmotic concentration to keep the cell turgid

water activity is tested by sealing a sample and waiting for equilibrium. Then the air humidity is compared to what pure water, which is humidity(air saturation) calculated over humidity of pure water (100%). This result describes the relationship between the solutions vapor pressure divided by pure waters vapor pressured, and gives us osmotic pressure/water activity.

Halophiles require high sodium environment because they have adapted to hypertonic environments by storing lots of K[potassium], which is now required for them to live.

Chapter 5, 6

Chapter 5, 6

Microbio – growth and nutrition

 
 

Classified by nutrition modes. Gather food by endocytosis (eukaryotes) and membrane carrier proteins.

 
 

Macronutrients 10

 
 

makes lipids, nucleic acid, amino acids, and carbohydrates (macromolecules)

CARBON, HYDROGEN, OXYGEN, NITROGEN, PHOSPHORUS, SULFUR

exist mainly as cations

POTASSIUM (K), CALCIUM for heat resistance, MAGNESIUM ribosome stability, cofactor, and ATP complexes, IRON cofactorand part of electron carrying enzymes (think mitochondria)

 
 

Micronutrients trace amounts

manganese, zinc, cobalt, molybdenum, nickel, and copper SODIUM if found in seawater usually

 
 

The more reduced a molecule is, the more energy it contains, thus lipids > carbs. Thus carbon sources usually also provide energy, Oxygen and Hydrogen and is required as the backbone of all organic molecules

CO2 is oxidized? As opposed to reduced like ch2o

 
 

Actinomycetes can degrade amyl alcohol, paraffin, and rubber

 
 

electron sources

lithotrophs get their electrons from reduced non-organic compounds

organotrophs get theirs from organic compounds

 
 

algae get their e- from water, and release o2, green/purple sulfur bact. Get e- from H, H2S, and Sulfur

ALL PATHOGENS ARE CHEMOORGANOHETEROTROPHIC HETEROTROPH

Chemolithotrophs are responsible for NH3 → NO3 or S → SO3

PIT SYSTEM, PST [ PHOSPHATE SPECIFIC TRANSPORT ] ABC Transporter

growth factors – any essential organic compound which cannot be synthesized by the organism

amino acids, vitamins (part or whole cofactors), pyramidines/purines

assay- quantitative analysis of a substance...

NUTRIENT UPTAKE

Passive diffusion – h2o, o2, co2, glycerol

Facilitated diffusion by permeases (carrier integral proteins)

MIP major intrinsic protein, transmembrane proteins grouped based on their amino?sequence.

Aquaporins & glycerol facilitators (more prominent in euk)

Active Transport

abc transporter ATP-binding cassette transporter – Nucleotides domains across the membrane (periplasm or membrane lipid for -/+ bacteria) – Solute binding transporters

symport linked transport of two substances at once.

Proton & Sodium gradient Protons are pumped outside of the cell (uses atp), Na+ is expulsed which comes back to the carrier protein complex and changes its conformation. This new conformation binds the solute, which again changes the conformation and both are released into the cell. Group Translocation – molecule is chemically altered while being taken in [active transport] PTS - phosphoenolpyruvate: sugar phosphotransferase system

siderophores form complexes with iron molecules for transport inside of cell [abc trans]

Synthetic/Defined Media When all the mediums' components are known

Differential Media used to differentiate between groups of bacteria

Complex Media Some ingredients chemical composition is unknown

Peptones protein hydrolysates prepared by partial proteolic digestion of meat casein

colony – macroscopically visible growth cluster of microorganism

spread plate technique – each colony represents a pure culture

streat & pour plate techniques

antiport transfer used to correct small changes in internal pH

phosphate group transfer potential – ATP's suitability comes from the fact that the moelecule breaks down to ADP very readily, and nothing to do with the bonds energy itself.

Catalysts are substances which speed up chemical reactions without being consumed or permanently altered, such as enzymes which are protein catalysts. Some are pure proteins while others have protein and non-protein components (apoenzyme & cofactor respectively)

Chapter 1 Reading

Chapter 1 Reading

 
 

Discontinuous Variations

Variations which are very distinct in a population (such as albinism - total lack of melanin, made by defective tyrsinase) - either or

Polymorphism

Many common distinct variations in phenotypes

Continuous Variations

Unbroken range of varieties in a population's phenotype (such as height and weight)

Haplosufficient

When only a single allele is required for normal function (such as sickle-cell)

Null Allele

Alleles which fail to code for a functional protein (recessive?)

types of genetic mutations

nucleotide-pair substitution leads to amino acid substitution or premature stops

deletion and duplication

frameshift mutations is an alteration in the codon reading frame usually caused by a nucleotide deletion at sites where there is a short stretch of the same nucleotide sequence.

probing is a technique for detecting the presence of certain molecules. The probe will only bind with the specific macromolecule, and it is usually dyed fluorescent or made radioactive so the location can be recorded.

DNA probing relies on base complementation. DNA needs to be extracted and cut by restriction enzymes. Afterwards it is mixed with the probe in solution, this technique relies on the random motion of the genetic particles in the solution.

Southern Blot DNA is placed on a gel, and an electrical field (electrophoresis) is activated which makes the strands move at speeds inversely proportional to their size. The fragments are then placed on a porous membrane and heated to keep them in place, then in a solution filled with the probe.

Northern Blot probe technique for RNA. Western Blot probe technique for proteins using antibodies (probes - usually extracted from some animal, such as a rabbit) to bind to antigens (proteins being tested for).

Law of Segragation alternative traits (factors) that come together for one offspring, may be separated in the gametes

Independent Assortment differences for one trait are inherited independently of differences in another trait

Height in the pea plant is continuous

Norm of Reaction – The wide range of phenotype which can occur for each genotype by environmental influences.

Developmental Noise – Random environmental factors that might affect phenotype despite a fixed phenotype, and environment. This can be

Negative feedback processes limit the range of variations from environmental influences

Three levels of development - First is embryonic stages that are common to a wide variety of species in which genes alone account for the morphology (without environment)

Second level accounts for similarites shared between different species which may come from genes alone.

Third level is between the same species, and accounts for morphological, behavioral, and physiological differences affected by genes alone.

 
 

CHAPTER 2

 
 

autosomal inheritance variation based on a single gene on regular chromosomes

sex linked variation on single gene on the sex determining chromosomes

cytoplasmic variations are from differences in the genes of a cytoplasmic organelle

 
 

pure line were setup to make sure that any observed variations were a result of his deliberate manipulations, which is in effect a control experiement. In addition, he made reciprocal crosses, meaning each cross was done with both combinations of male/female and female/male, which produced the same result. This tells us that both male & female gametes carried genes for the chracters he was crossing. After his original cross produced all purple flowers, he selfed those, and got some progeny who were white, which led him to conclude that the white allele was present in the purple flower, but unexpressed. This is when he coined the terms dominant and recessive.

 
 

From the pure line, one phenotype would disappear from the F1 but then return for the F2 in the ration of 1:4

anthocyanin is the end-product of a biochemical pathway which gives pea-plants their purple color (psium savitum)

Know what the Chi square and its uses

Know what the Chi square and its uses

Pedigree

incomplete dominance when neither allele can express itself completely (blending pink flower)

wild type + prevalent type observed in nature

mutant usually recesive, and is the least observed phenotype in a species

gene complementation (cinnabar 1 / 2 x scarlet)

lethal mutation, sterile mutation

central dogma

polydactyly is dominant

penetrance is the rate at which the gene is expressed, even if it's dominant.

(variable) expressivity the degree to which the trait is developed (formed)

Epistasis The presence of an allele can influence whether other genes are expressed or not

pleiotropy one gene can have several effects

hybrid vigor stronger than the parent

hybrid depression sometimes can also be weaker, or even unable to reproduce

(heterosis)

Chapter 5 – bold words

hemizygous – only one copy of the gene (males only)

autosomes

homologue

barr body random inactivation of an X chromosome in females, which can reactivate [how?]

 
 

gimesa, quinone dyes