Dna

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Smooth colony

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- secretes polysaccharides capsule - protects bacterium from the immune system of animals
-produces smooth colonies on solid media

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Rough colony

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- unable to secrete polysaccharide capsule
- produces colonies with rough appearance

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Transformation

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a process observed by griffith exp with mice. where dead type IIS transformed type IIR to type IIS
- it was unkknow at the time why this was happening or what was causing this

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Bacteriophage

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-is any one of a number of viruses that infect bacteria
-consist of an outer protein hull enclosing genetic material

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Bacteriophages T2

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simple
composed of two macromolecules-DNA and protein

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Capsid

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head structure of the phage, that contains the DNA

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Head

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head
-structure which can vary in size and shape
-icosahedral (20 sides) others are filamentous
-composed of many copies of one or more different proteins
-acts as the protective covering for the nucleic acid

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sheath

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contractile
contracts during infection of the bacterium- due to irreversible binding
- made up of proteins

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life cycle of a bacteriophage T2

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-phage injects Dna into host cell
-the phage DNA directs the synthesis of viral components
-the phage components are assembled
-host cell lyses and new phages are released

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radioisotopes

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are used in hershey and chase exp as a means of distinguishing DNA
- two labels
32P labels DNA
35S labels proteins

- labels infects nonradioactice Escherichia coli cells

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heat killed

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in the griffith exp. this was dont to the type IIS to kill the bacteria but did not kill the mice until it was mixed with live type IIR which did kill the mice

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polysacchride capsule and chem composition

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can differ significantly in their chemical composition

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lyses

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refers to the death of a cell by breaking of the cellular membrane, often by viral or osmotic mechanisms

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alpha helix

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- secondary structure that proteins can fold into proposed by linus pauling

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Pure DNA crystals

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used my x-ray diffraction

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complementary base pairs

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a-t by two h- bonds, large purine to smaller pyrimidine
c-g small pyrimidine with large purine

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base stacking

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within the DNA< the bases are oriented so that the flatten regions face one another

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hydrogen bonding

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occur between hydrogen bases

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phosphate group

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simplest sub sub unit, in simple diagram
- (structure) P aton of valence 5, 4 oxygens , one double bond

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pentose sugar

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next simplest - s in simple diagram
- structure - note the numbering of c atoms, 1-5

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nitrogenous base

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- code words for genes - such that every nucleotide has either one purine and pyrimidine
- consists of purines and pyrimidines

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adenine
thymine
guanine
cytosine

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a/g- purines
c/t- pryimidines

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covalent bond

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shared- all line of the DNA for this bond, with a 60-70 Kcal strength

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nucleotides

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- repeating , fundamental structural unit of DNA and RNA
- for polymers nucleotides are monomers and residue(digestion)
- has three subsub units
-P-S-B4

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nucleosides

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base + sugar
B -S
ex: adenine + ribose _ adenosine

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what form the noninformational backbone for railing for spiral staircase metaphor of DNA

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P-S , phosphate group-pentosegroup

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adenosine mono/di/tri - phosphate

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AMP, ADP, ATP- nucleotide

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phosphodiester bond

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covalently link nucleotides
-phosphate connects 5'C to 1 ntides sugar to the 3" C of another Ntide sugar

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strand directionality

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since 5' to 3' is asymmetrical which allow ecn side to be distinguished allowing for directionality

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name the secondary struct of DNA double helix

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-B- DNA, found in living cells
-A-DNA/ Z-DNA- in vitro conditions helices can form

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A- DNA

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right handed, 11bp per 360 turn ; lccurs in low humidity, very compacted, little bio importance

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z-Dna

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left handed, 12 bp per turn- cause 180 distortion
formations is favored by GC rich seq in high salt conc- in vitro
- or in cytosine methylation- low conc. in vivo
- may play role in transcription and recombination

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triplex DNA

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found by ALexander rich- during an in vitro where DNA pieces used to make synthetic strands
- natural double stranded DNA can form combine with synthetic strand to make triplex
- can bind to major groove of natural double stranded DNa

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sequence specifics of triplex

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T- AT
C- CG

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antiparallel strands

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strands are equidistant, assymmentrical due to positon of sugar on carbon, polar opposites

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handedness right and left

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-- heliz is right handed , due to how the bases are stacked due to bond agnles and bond distance

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major groove
minor groove

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widest groove
narrow groove
have alternating and continuous features

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denaturability

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when heated above 60 , the h bond that fold the bases of the DNA together cause the strands to be freed generating single strands

althernate case is when DNa is brought back to temp below 60 the h- bonds reform- renatured- this process will cause the bases to collide and reorganize untill finally zipping back up

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hybridization

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- renaturation of two complementary base seq
-implies common ancestry

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CG ratio

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the higer the Gc ratio the higher number of denaturation , there are 3 h bond between C and G and only 2 bond between A T

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topoismerase

type I/ type II

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- controls the topical state of DNA family of enyzmes
- DNa makes isomers by adding or subtracting supercoils
- type I - changes topical state by single strand breaks
- type II double strand breaks -

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catenate
decatenate

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add or induce supercoils
to subtract or remove supercoils

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example of protein DNA binders/ fucntion

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is leucine zippers, zinc fingers, and copper fist, P53
- when the proteins bind to DNA they alter activities of that binding region - control proteins

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positive info strands

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-sense strand watson strand
-coding region, important in studying viruses

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negative info strand

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- no info strand
- untranslated region

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palidrome

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same word forward and backward
-in genetics it is inverted, a repeat sequences which results in loops out or cruciform structures in the DNA

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methylation/ methylase

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degree controls transcription in ecukaryotes
- more methylation = inactive genes and vice versa
-protein enzy that add or subtract ch3 from the bases at the groove

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nucleases

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- a general name for protein enzymes class that digest nucleic acids

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retrovirus
gyrase

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- bad viruses
-is ex of type II it removes supercoils ahead of replication fork