biochem unit 3

for bacteria we dont have

introns

bacteria has a _____ structure

polycistronic mRNA

eukaryotic mrna requires splicing and

polyadenylation

prokaryotic ribosomes are ____ compared to eukaryotic

smaller and consist of distinct subunits.

rRNAS can be separated by

gel electrophoresis

the three components of nucleotides

heterocyclic nitrogenous base, a pentose sugar, and phosphate

dna is the ____ of genetic information and ____ is central to its expression

repository; RNA

nucleotides are essential _____ in virtually all cellular metabolism

intermediates 

nitrogenous bases derive from

purines and pyrimidines

pyrimidines are

single six membered rings with two nitrogen atoms

purines are

fused rings resembling pyrimidine and imidazole

nitrogenous bases are relatively insoluble due to 

pronounced aromatic character 

pyrimidine ring

purine ring system

cytosine uracil and thymine are 

pyrimidines (cytosine and thymine for dna) and cytosine and uracil for rna 

guanine

adenine

cytosine 

uracil

thymine

purine bases for dna and rna 

Adenine and guanine for dna and rna 

nitrogenous bases undergo ____ shifts

keto-enol

bases have the ____ form at neutral ph

keto tautomer

this is an example of 

keto-enol tautomerization 

tautomeric form determines ______ possibilities which are key to nucleic acid function

H-bonding possibilities

bases strongly absorb UV light around 260 nm this is useful for ______

qualitative and qualitative analysis

nucleosides link a base to a pentose sugar in the ____ form 

furanose 

nucleoside bases and pentose form what linkage

beta-configuration glycosidic bond

after nucleosides form from bases and pentose the new names are

“idine” for pyrimidines and “osine” for purines

in naming nucleosides of deoxyribose 

we use the prefix deoxy - ex, deoxyadenosine 

describe adenosine

• local hormone and neuromodulator

• regulates heartbreak, blood vessel dilation, sleepiness

• caffeine blocks receptors

• low levels after sleep, high levels when being awake for long

a nucleotide is from when phosphoric acid is ____ usually at the 5’ of the sugar

esterified

due to the ____ group nucleotides are strong acids 

phosphate

this is an example of

a formed nucleotide

nucleoside diphosphate (NDPs) and triphosphate (NTOs) contain additional phosphates linked by ______ linkages

phosphoric anhydride

nucleoside diphosphate are indispensable carriers of 

chemical energy 

ADP

ATP

transfer of ________ groups drive biological work 

phosphoric, pyrophosphoryl or nucleotide (NMP)

in high energy nucleotides the different bases (AGCU) Chanel energy into _____ pathways

different metabolic

cyclic nucleotides are cyclic

phosphodiesters

examples of cyclic nucleotides 

3’,5’ cyclic amp (camp) and 3’,5’ cyclic GMP c(GMP)

the importance of cyclic and regulatory nucleotides

• important regulators of cellular metabolism

cGAMP is a cyclic

dinucleotide

cGAMP is synthesized by 

cyclic GMP-AMO synthase (cGAS) when dsDNA is sensed in the cytosol 

rising levels of cGAMP levels trigger ______

STING and an immune response

glucagon signaling leads to the activation of the enzyme _____ which converts ATP to cAMP

adenylate cyclase

functions of nucleotides

• triphosphate energy intermediates 

• carriers of metabolic intermediates

• chemical signaling aka secondary messengers

example of triphosphate as energy intermediates

triphosphate = major energy currency

GTP involved in driving protein synthesis

examples of nucleotides being carriers of metabolic intermediates

UDP in sugar metabolism, CDP in lipid, NAD and CoA are ADP intermediates

example of nucleotides in chemical signaling as secondary messengers

cyclic AMP and cyclic GMP

nucleic acids are polynucleotides formed by nucleotides linked ____ via ____ bridges

3’ to 5’, phosphodiester 

what forms a directional sugar phosphate backbone

polynucleotides structure

the sequence of nucleic acids is read from which direction

5’ to 3’

the unique nucleic acid identity is determined solely by 

sequence of bases 

DNAs singular role

preserving the information for all functional macromolecules

DNA consists of 

two antiparallel polynucleotide strands wound together in a double helix 

DNA strands are held together by

interchain hydrogen bonds aka base pairing

chargaffs rules

A=T and T=G, purines=pyrimidines

who discovered that A=T and C=G

watson and crick 

The A : T and G : C pairs form units, giving the helix uniform dimensions

spatially equivalent

the complementary relationship in DNA means information is conserved in _____

the opposing strand

base pairing ensures

replication 

dna encodes information using four bases

A C G T

Eukaryotic DNA is condensed by

wrapping around histone proteins to form nucleosomes

cellular RNA is usually ___ but forms double stranded regions through _____ base pairing 

single stranded, intra-stand 

mRNA

carries gene information for protein synthesis

Eukaryotic mRNA requires

intron removal (splicing) and polyadenylation

rRNA is the structural and function core of _____ playing a crucial role in _____

ribosomes, protein synthesis.

tRNA transports

amino acids

exons are protein coding regions that must be joined by removing

introns

rRNA has complex secondary structure due to many 

intrastrand hydrogen bonds 

rRNAs can be separated by

electrophoresis

all tRNAs possess the 3’ terminal sequence ____ where the amino acid attaches

C C A

small nuclear RNAs form complexes with proteins (snRNPs) that mediate splicing of 

hnRNA into mRNA 

mRNA function

encodes proteins

tRNA functions

acts as adaptor between mRNA and amino acids 

rRNA function

forms ribosome

rnRNA function

various processes (gene splicing)

snoRNA 

facilitates chemical modification of RNAs

miRNA

regulates gene expression

siRNA

silences gene expression

IncRNA

regulates gene expression 

how dna differs chemically from rna

• deoxyribose instead of ribose

• thymine instead of uracil

in DNA which is “long lived” compared to RNA, the deamination of cytosine to uridine occurs spontaeously at a ____ rate

low

As DNA contains Thymine instead of Uracil, the DNA repair recognition/repair system substitutes the wrong base (Uracil) for the right base ______, thereby correcting the sequence

(Cytosine)

The absence of the 2'-OH group in DNA confers greater resistance to _____

alkaline hydrolysis

alkali liable means

readily hydrolyzed by hydroxide ions

RNA is alkali labile because 

the 2’ OH group promotes nucleophilic cleavage at the phosphodiester bond

DNA is acid labile meaning

purine glycosidic bonds hydrolyze in dilute acid

nucleases are enzymes called _____ that hydrolyze phosphodiester bonds 

phosphodiesterase

cleavage in phosphodiesterase are categorized as either

internal - endo or terminal - exo

cleavage in nucleases is labeled as ___ side or ___ of the phosphodiester bridge

a 3’ or b' 5’

nucleases exhibit specificity for 

single vs double strands 

______ are bacterial enzymes that cleave dsDNA at specific recognition sequences, typically four or six nucleotides long

Type II restriction endonucleases

in type II restriction endonucleases recognition sites often have ____ symmetry

twofold

EcoRI cleaves ____ leaving single stranded sticky ends 

staggered

the sticky ends from EcoRI cleavage allow for ____. they are essential tools for manipulating DNA and restriction mapping 

recombinant DNA formation 

______ give rise to nucleic acid structures

7 rotational degrees of freedom