Ch. 9 - Mol structure and replication of genetuc material

exam 3

levels of complexity for nucleic acids: nucleotides, units

level 1

levels of complexity for nucleic acids: nucleotides are inked into a strand

level 2

levels of complexity for nucleic acids: two strands interact to form double helix

level 3

levels of complexity for nucleic acids: double helix folds, bends, and interacts with proteins to form 3-d structures in the form of chromosome

level 4`

RNA or DNA, a macromolecule that is composed of repeating nucleotide units

nucleic acids

nucleic acid term coined by

Miescher

RNA and DNA have a net ________________

negative charge

structure that results when two strands of DNA interact with each other to form a double strand helical strcuture

double helix structure

a nucleotide unit consists of

nitrogenous base, a sugar, and phosphate molecule

what sugar is found in DNA

deoxyribose

what sugar is found in RNA

ribose

the nitrogenous bases are divided into two categories: _________ and __________

purines and pyrimide

the nitrogenous bases that consists of a double ring

purines

nitrogenous bases that fall into the categories of purines

adenine (A) and guanine (G)

purine base that is found in RNA and DNA, pairs with either thymine or uracil

adenine

purine base found in either RNA or DNA, pairs with cytosine

guanine

nitrogenous base category in which the base consist of a single ring structure

pyrimide

what are the pyrimide bases

thymine (T), uracil (U), and Cytosine (C)

pyrimide base that is found in DNA, and pairs with adenine

thymine

pyrimide base that is found in RNA, and pairs with adenine

uracil

pyrimide base that is found in RNA and DNA and pairs with guanine

cytosine

what way is DNA synthesized

5’ to 3’

what carbon on the sugar, ribose or deoxyribose, does phosphate attach to?

carbon #5 of the sugar

what type of bond link nucleotide units together into a strand

phosphodiester bond

in phosphodiester bonds, the 5’ phosphate of one nucleotide connects to the other nucleotides _______

3’ hydroxyl

phosphodiester bond linkage forms

the strands backbone

structure where it simply consists of a base and sugar, there is no phosphate group

nucleoside

nucleoside structures in RNA change the names of the complex to

example: adenosine, guanosine, uranosine, and cytonosine

nucleoside structures in DNA change the names of the complex to

deoxyadenosine, deoxyguanosine, etc

three structural features that are used to describe nucleic acids units

• type of sugar

• type of base

• number of phosphate groups

carbon atoms are counted in a

clockwise direction

phosphate groups are always attached to ______ of the sugar

5’ carbon

nitrogenous base is always attached to ______ of the sugar

1’ carbon

who analyzed the base composition of DNA, from various diffraction from different organisms, images of DNA, providing clues the structure of DNA

Chargaff

they obtained the first high quality x-ray diffraction images of DNA, providing clues to its structure

Franklin and Wilkins

this types of linkage can be found in RNA and DNA, in which a phosphate group connects two sugar molecules via an ester bond

phosphodiester bond

DNA and RNA strand portion composed of covalently linked phosphates and sugar molecules

backbone

DNA and RNA backbone is _______ charged, due to ______

negatively; charges on phosphate group

refers to how in DNA and RNA, 5’ to 3’ orientation of nucleotides in a strand, all sugars have the same orientation

directionality

they solved the structure of DNA without performing any experiment, used Franklin and Chargaffs rules/data to uncover the double helix

Watson and Crick

who had captures the x-ray image that reveled DNA helical structure, with modifications and advancements in X-ray diffraction techniques

Franklin

abbreviation for how DNA and RNA strand structure contains specific sequences of bases to show directionality

5’-TACG-3’

sequences of bases in DNA strand remain the same over times expect in cases where a ______ occurs

mutation

• two strands of DNA form a right handed double helix

• turns in a clockwise direction

• two strands are antiparallel

• contain 10 b.p. per 360 turn

these are the key features of a double-helix shape

technique that proved to be important to the discovery of DNA double helix structure

Model Building

he proposed that regions of proteins can fold into a secondary structure known as alpha helix

Pauling

who were competing against each other to discover the structure of DNA

Pauling and Watson & Crick

Franklin DNA fibers suggested several key features of DNA

• patterns consistent with helical structure

• diameter being two wide to be a single strand

• suggested that helix contained 10 b.p. per complete turn

they assumed that DNA is composed of nucleotides linked together in a linear fashion and that linkage between two nucleotides were always the same

Watson & Crick

____________ allows for precise base pairing between the strands

antiparallel orientation

how many hydrogens bonds are between adenine and thymine (uracil in RNA) base pairing

two hydrogen bonds

how many hydrogens bonds are between guanine and cytosine base pairing

three hydrogen bonds

term used to describe the indentations where atoms of the bases are in contact with surrounding cellular fluid

groove

narrow indentation

minor groove

wide indentation

major groove

grooves are important for

providing access for proteins to bind and regulate genes, allows for gene processes like transcription and repair

how wide is the major groove

22 nm

how wide is the minor groove

12 nm

linear distance along a strand through a complete turn

3.4 nm

linear distance along a strand between each base pair

0.34 nm

in DNA, phenomenon in which adenine base always pairs with thymine, and guanine always pairs with cytosine via hydrogen bonds

AT/GC Rule

this rule allows us to predict the sequence in one DNA strand if the sequence in the opposite strand is known

AT/CG rule

refers to an arrangement in a double helix in which one strand is running 5’ to 3’ direction, while the other strand in 3’ to 5’ direction

antiparallel arrangement

in DNA, the orientation of base pairs in which flat sides of the bases are facing eachother

base stacking

stability of helical structure of DNA backbone/double-strand structure is stabilized by

hydrogen bonding and base stacking

the standard structure of DNA

B-DNA

DNA can adopt other double helical forms depending on

environmental conditions

• predominant form of DNA

• right-handed helix

• 10 bp per turn

• 20 A diameter or 2 nm

• prevalent under aqueous, low salt conditions

B-DNA

• not predominant form of DNA

• left handed helix

• backbone appears zig zag formation

• 12 bp per turn

• prevalent in DNA with altering repeating C-G sequences

• involved in transcription regulation and innate immune defenses

• can exists in B-DNA regions

• 18 A diameter, 1.8 nm

Z-DNA

• 11 bp per turn

• 23 A diameter, 2.3 nm

• prevalent under high salt concentrations

• right handed

• doesnt really occur, not known to exists in living cells

A-DNA

negative DNA supercoiling favors which conformation

Z-DNA

who report that the Z-DNA binding region of on such protein played a role in regulating the transcription of particular genes

Rich

this form of DNA is the most stable, supports replication and gene regulation

B-DNA

this form of DNA may play a role in regulating gene expression and recombination

Z-DNA

DNA secondary structures are also called

non-canonical structure

what are the non-canonical structures of DNA

hairpins, cruciform, triplex, and G-quadruplex

DNA form when a single DNA strand folds back on itself to crate a stem loop stucture

Hairpin

DNA form from a double helix where both strands fold into two opposite hairpins, creating a cross like structure stabilized via DNA supercoiling

cruciform

these secondary structures are due to standard watson-crick base pairing

hairpin and cruciform

DNA form where cell puts three strands together to form a

triplex

DNA form where cell puts four strands together to form a

quadruplex

these DNA forms require more than normal watson-crick base pairing

triplex and quadruplex

hoogsteen base pair is a type of non watson-crick base pairing where purine base material rotates 180 with respect to axis and adopts a conformation with different bonding capabilities

hoogsteen hydrogen bonding

is a structure made of 4 guanine bases arranged in a square plane and held together by 8 hoogsteen hydrogen bonds

G-tetrad or G-quartex

multiple g-tetrads stacked on top of each other, forming a four stranded DNA or RNA structure, are called

G-quadruplex

what is the significance of non-canonical DNA structures

alternative DNA structure play a role in various cellular processes, they have been recently implicated in human genetic diseases like cancer

• contains uracil instead of thymine

• contains ribose instead of deoxyribose

• carries an extra OH group in carbon #2

RNA differences from DNA

RNA is ______ stable than DNA, but ______ flexible in structure and function

less; more

strands of RNA are usually a few _________ nucleotides in length

hundred to thousands

strands of DNA are usually a few _________ nucleotides in length

million

• bulge loop

• internal loop

• multibranched junction

• stem loop

different RNA arrangements

in RNA, complementary regions via different arrangements, are held together by

hydrogen bonds

in RNA, non complementary regions are ____________ from double stranded regions

projecting away

RNA is typically

single stranded

RNA that carry instructions or code for making proteins they are known as

coding RNA

RNA that do not carry instructions or code for making proteins they are known as

non coding RNA

RNA double helix tend to adapt what form

A-helix

A-RNA has a _______ major groove than B-DNA

deeper, narrower

radioisotope used to label proteins

³⁵S

radioisotope used to label DNA

³²P