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85 Cards in this Set

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What is a nucleic acid?

-macromolecule composed of chains of monomeric nucleotides


-located w/in cells and form structures

what is the basic unit of nucleic acid?

NUCLEOTIDE

Nucleic acid are based on what? And what two categories do Nucleic Acid fall in?

-Based on diff. pentose sugars & nitrogenous base


-1.) DNA Deoxyribonucleic acid


2.) RNA ribonucleic acid

What is DNA?

the genetic material that has all the info. to direct every cellular process is carried w/in DNA

What is RNA?

participate in several cellular processes involved in the formation transfer from the DNA to protein synthesis.


-the info. in DNA & RNA is encoded in the order of bases

Nucleic acid are based on functions, RNA falls into 3 categories which are?

1.) mRNA


2.) rRNA


3.) tRNA

What is mRNA, rRNA & tRNA?

-mRNA: template of DNA, carries info from DNA to ribosomes


-rRNA: protein manufacturer


-tRNA: rRNA & tRNA are involved in protein synthesis (transport genetic code)

Nucleic acid are composed in three parts name them?

1.) Nitrogenous base: aromatic ring of Carbon & nitrogen


2.) Pentose Sugar: 5 carbon sugar in ring form


3.) Phosphate group: acidic in nature

nitrogenouse base, pentose sugar & phosphate group make what?

nucleotide

Nitrogenous bases are in two categories which are?

1.) Purine


2.) Pyrimidine


What is a purine?

-fused 5-6 member ring


-AG (adenine & guanine)

What is pyrimidine?

-6 member ring


- C, U, T (cytosine, uracil, thymine)


What is the difference btw Thymine and Uracil?

-There is a METHYL group at C5 on Thymine, which uracil does not.

what are the two sugars?

Ribose & 2-deoxyribose


-2-Deoxoyrbions has no OH on C2'

What are phosphate groups?

-phosphorous occur mainly in the form of acidic phosphate groups, they are always negatively charged


-DNA & RNA are neg. charged cuz Phosphate is negatively charged.

Nitrogenous bases is linked to what?

1 ' carbon of sugar


Nucleoside includes what parts?

Nitrgoenous base + sugar


-glycosidic bond from N1 to pyrimidines or N9 of purines

Phosphate groups is attached to what?

5 ' carbon of sugar


Nucleotide include what parts?

nitrogenous base + sugar + phosphate

DNA is a long molecule made up of what?

polynucleotide

one nucleotide has three parts which are?

nitrogenous base + pentose sugar (2'-deoxyribose) + phosphate grp

DNA molecule contains 4 nitrogenous bases which are ?

A, T, C, G

What is the DNA structure?

-a polymer of nucleotides w/a long, flexible, threadlike structures


-constant diameter w/regulary spaced & repeated structures


-phosphodiester bonds link 5 ' phosphate of one nucleotide to the 3 ' OH of another


DNA is usually what?

-two single-stranded nucleic acids held together by base pairing through hydrogen bonds in anti-parallell orientation called double stranded, the DNA DOUBLE HELIX

What forms the backbones of the DNA structure?

-sugar & phosphate residues in each strand

How does the backbone of the DNA structure run?

-run anti-parallel (in opposite directions) to each in the 5' to 3'

The two strands of the double helix are held together by what?

base paring in anti-parallel orientation

1.) A : T are held together by what?


2.) C : G are held together by what?

1.) 2 hydrogen bonds


2.) 3 hydrogen bonds

The two chains of double helix have what?

-complementary sequences that goes 5' to 3' (on one chain) & 3' to 5" (opposite chain)

What is the fundamental feature of the double helix?

hydrogen bonds btw the complementary bases

Double helix has 2 external grooves called what?

major and minor grooves


What is a groove?

the space btw the strands

Each complete twist of DNA is how long in length?

3.4 nm

The major groove is _____ wider than the minor groove and rich in what?

50% ; chemical info.

The sugar-phosphate backbone circles around where?

outer surface of DNA

DNA is usually right-handed double helix or left handed helix?

Right handed double helix

Left handed double helix is only what?

alterative purine & pyrimidine

DNA structure image of right-handed vs left-handed doubles helix. Look at image!

Double helix has 3 forms which are?

1.) B DNA right handed (flower)


2.) A DNA right handed (donut)


3.) Z DNA left handed (ball)

Look at the pic of the 3 forms of DNA double helix.

which one is the most common double helical structure?

- B DNA


What is the B form DNA?

-observed at high humidity


-vast majority of the DNA in the cell = B form


-right-handed


- ~ 10 nucleotides per turn


-contains a major & minor groove


-Major groove is wider than minor groove

What is A form of DNA?

-observed under low humidity


-observed in certain DNA-protein complexes, RNA- DNA and RNA-RNA helices.


-right handed


- ~ 11 nucleotides per turn


-contains a major & minor groove


-Major groove is narrower, much deeper than B form


-minor groove is broader & shallower


What is the Z form of DNA?

-observed in DNA containing alterative purine & pyrimidine


-left handed


-helix w/ zigzag look


DNA double helix can separate which is called, define it?

Denature/ DNA melting


-heat to near 100 C


-High PH

DNA double helix can reassociate is called, define it?

renature


-single strands often meet their complementary strands & reform regular double helixes when heated solution of denatured DNA are slowly cooled.

What is hybridization?

-artificial hybrid DNA to be formed by slowly cooling mixtures of denatured DNA from 2 diff. Sources. (the basis of several molecular techniques)

(Denature of DNA )


-when DNA is heated to 80 degrees and up, its UV absorbance is what and increases to what?

260 nm ; 30-40%

(DENATURE of DNA)


The hyper chromic shift reflects on what?

the unwinding of the DNA double helix

(denature of DNA)


When temperature is lowered, the ______ drops, reflecting the ___________.

absorbance ; re-estabilishment of stacking

(Denature of DNA)


What is Tm?

melting temperature: a point which exactly half of a double stranded sequence becomes single-stranded.

What is DNA supercoiling structure?

-occurs in closed structure when ends are not free to release torsion on molecule


-in duplex, DNA 10 bp per turn of helix, circular DNA sometimes has more or less than 10 bp per turn.


What are topoisomerase or gyrases?

-removes supercoils

DNA has type types of supercoiling which are?

1.) positive supercoiling


2.) negative supercoiling

What is positive supercoiling?

- when DNA is supercoiled in the same direction as the intrinsic winding of helix


-tightens the structure


-increase the rotation per base pair


-overwound


DNA is said to be overwound is called?


DNA is said to be underwound is called?

-Positive supercoiling


-negative supercoiling


Microorganisms that lived under high extreme high temps such as hot springs have what kinda of supercoiled DNA?

-positive supercoiled DNA


what is DNA negative supercoiling?

-twists dada about its axis in the opposite direction rom the clockwise turn of the right-handed double helix


-loosens the winding of the 2 strands


-reduces the rotation per base pair


Circular DNA from bacterial and eukaryotes are usually what type of supercoiling?

-negative supercoiling

look at the structures of DNA supercoiling?

DNA supercoiling requires what?

-energy to introduce supercoil and to separate DNA strands for replication or transcription


-does not occur spontaenously


Molecules without supercoiling is said to be what?

relaxed

DNA supercoiling is important for what? and required for what?

-DNA packaging w/in the cell


-DNA/RNA synthesis

Supercoils results as....

result of the undwinding of DNA for DNA/RNA polymerase action


-Topoisomerases

DNA supercoiling structure can be separated by what technique?

-gel electrophoreiss


- the more compact the Dna, the fasted it is able to migrate through the gel

what is topoisomerase?

-enzyme that catalyzes the reversible breaking and rejoining of DNA strands (relieves the strain of twisting)


-maintains supercoling by acting as a swivel

what are the two types of topoiosomerase?

1.) Type 1: make transient single-strand breaks (NO ATP)



2.) Type 2: make transient double-strand breaks ( REQUIRE ATP)

what topoisomerase type is this?

what topoisomerase type is this?

Type 1

what topisomerase type is this?

what topisomerase type is this?

type 2

What is RNA?

-long molecule made up of polynucleotide


-single stranded


- nucleotide w/ 3 parts


- 4 nitrogen bases: A, U, G, C


-contains 10 times more RNA than DNA


-URACIL in place of THYMINE


RNA has 3 primary classes which are?

1.) rRNA- 3-4 different types


2.) tRNA - 50 different types


3.) mRNA - > 1000 different types

For RNA, a nucleotide contains what?

nitrogenous base


sugar (RIBOSE)


phoshpate group

RNA chains fold back on themselves to form diff. structures what are they?

a. hairpin


b. bulge


c. Loop

late these.

label these.

a. hairpin


b. bulge


c. loop


-Theses are stem-loop structures

what is a stem-loop structure?

non complementary sequences become "looped out" to form different structure.

what is this?

what is this?

pseudoknot

what is a psedoknot?

formed by base pairing take place btw noncontiguous complementary sequences

what is this?

what is this?

C(UUCGG)G TETRALOOP

what is a C(UUCG)G TETRALOOP?

SPECIAL bise stacking interactions in the loops

what is this?

what is this?

tertiary structure G : U

what is this?

what is this?

tertiary structure, U : A : U base triple

what is this?

what is this?

-secondary structure, enzyme


-Hammer head ribozyme

What does hammer head ribozyme do?

cleavesRNA by the formation of 2', 3' cyclic phosphate

Some RNA's can be what?

enzymes (RIBOZYMES) ex: RNase P & RNA Self-splicing

what is this?

what is this?

tertiary strcture