Exam 1 review Flashcards by Nora Schwartz

molecules recognize each other by

interactions

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van der waals interactions

give strong repulsions, weak “flickering” attractions

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dipole interactions

between molecules with hetero atoms

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hydrogen bonds

a type of dipole interaction with hydrogen that is important in biology

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strong interactions

covalent bonds and ionic interactions are responsible for stable, long-lived, structures

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water is the

ultimate hydrogen bonding liquid

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as ice, water forms how many bonds

4 h bonds
2 accept
2 donate
tetrahedral in shape

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as a liquid water forms how many bonds

4.5 h bonds
makes liquid more dense than ice

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life requires

water`

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water properties

liquid solvent
concentration gradients
biopolymers adopt unique shapes
hydrogen bonding networks
tetrahedral bonding
large void volume, dissolution of gasses
liquid from 273K to 373K
density maxima

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liquids and polymers are dominated by weak forces from potential interactions around RT in size. All of biology depends on using weak forces to allow

biological changes

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the purine groups are synthesized on the

ribophosphate
PRPP

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that displaces the phosphate at C1 on PRPP

the amide group of glutamine

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where is RNA hydrolyzed by water or base

2’OH

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RNA hydrolyzation creates

a 2’,3’ cyclic monophosphate nucleotide and a truncated RNA

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each base has a unique UV absorption spectrum due to the

electronic differences in the rings and substitutions

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for sequencing via UV, what wavelength is used

260nm
blue!

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tautomers for pyrimidine bases

lactam
lactim
double lactim

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tautomers are stabulized by different environments including

solvent polarity and pH

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pH causes different H-bonds to be stable and can

change the UV spectrum

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different electronic states are allowed due to the

number of hetero atoms in conjugation in the rings coupled to tautomers

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pH differences for UV are more prevelant in

pyrimidines

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in terms of the particle in a lox, pyrimidines have a

smaller box
greater % change

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attractive forces in DNA stability

base pair hydrogen bonds
base pi stacking

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repulsive forces in DNA stability

excluded volume phosphate-phosphate repulsions

2 molecules q1 and q2 interact with each other by

coulombs law for the potential energy U

water diminishes (screens) the interactions between two charges via

the dielectric constant of 80

water divides the interactions between to charges by

excess salt further diminishes (screens) interactions between charges as found by debye and huckel meaning that

it goes exponentially to zero with ionic strength

right handed form of DNA

A and B

left handed form of DNA

diameter of A form

26 A

diameter of B form

20A

diameter of z form

18A

base pairs per helical turn for A form

base pairs per helical turn for B form

10.5

base pairs per helical turn for Z form

base tilt normal to the helix axis for A form

20 degrees

base tilt normal to the helical axis for B and Z form

6-7 degrees

sugar pucker conformation for A form

C-3' endo north

sugar pucker conformation for B form

c-2' endo south

sugar pucker conformation for Z form

C-2' endo for pyrimidines C-3' endo for purines

DNA changes shape with respect to

salt concentration

at zero salt DNA

does not form a dimer

DNA shape with increasing salt concentration

single B A Z

there are many base pairing possibilities due to

the number of hydrogen bonding groups

triple helices

major groove binding base triple specific high salt requirement

quadruplex

g-quartets loops of 3-4 bases binds ions specifically in the core

if you add poly- a and poly - t to a solution,

TAT will form a triple helix A will go in solution (more soluble)

triplets of bases are reasonably

stable

common base triplets

TAT CGC

in a quadruplex, how many hydrogen bonds does each base have

4 h bonds per base

the center of a quadruplex is full of

oxygens and lone pairs

what ion goes in the middle of a quadruplex

K+ more stable than Na+

g tetrads can form in

any G-rich sequence

how to break a g tetrad

12M LiCl and boiling

many RNAs are inherently

single stranded

most RNAs fold up forming

secondary and tertiary structures

how do RNAs fold

each strands find complementary sections, often times short sections where complementary holds

structures in RNA

stems loops bulges try on MFOLD

mRNA carries the code from DNA to the

synthesis machinery

before mRNA can be read

it must be processed into a mature form by removing the introns

the genetic code has some redundancies in

the third slot of the codon

some species are specific in their codons requiring

codon optimization

domains in rRNA are more structurally varied than in

proteins

robosomal subunits

30S (lower) 50S (upper)

what ribosomal subunit holds the mRNA

30S

what subunit catalyses the peptide bond formation

50S

translocation and successive binding of tRNA are

GTP dependent

three sites of tRNA binding

APE

as the peptide is made it can either coil into an alpha helix or

await pickup by a chaperonin (beta sheets)

what signals the end of protein synthesis

release factor

release of the ribosome subunits allows for

ribosome recycling and energy conservation

what do helicases do

twist and untwist DNA

twisting a duplex can change

local and large scale structure

twist equation

L=T+W linking number = twist + writhe

what is twisting equilibrium

how an open transcription bubble is in equilibrium with the various shapes

twisting can lead to

strand separation

what can mechanically separate strands of DNA

gyrase topoisomerase helicase

what transcribed mRNA

RNA polymerase

the RNA DNA hybrid is known as

RNA-DNA double helix D-loop

DNA synthesis goes in a

5' to 3' direction

enzymes involved in the replication process

helicase DNA binding protein dnaB primase DNA polymerase DNA ligase