exam 3 lecture 9
Biochemistry 401 with Kaguni/kuo at Michigan State University
About this deck
By: Andrew Vallo
Textbook:
Biochemistry
Student Solutions Manual/Study Guide/Problems Book for Garrett/Grisham's Biochemistry, 3rd
Created: 2011-04-09
Size: 82 flashcards
Views: 14
Textbook:
BiochemistryStudent Solutions Manual/Study Guide/Problems Book for Garrett/Grisham's Biochemistry, 3rd
Created: 2011-04-09
Size: 82 flashcards
Views: 14
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3 steps of information transfer in cells
replication
transcription
translation
transcription
translation
transcription
sequence of bases in DNA is recorded as a complimentary series of bases on single stranded mRNA
translation
3 base condons on mRNA are recognized by tRNAs carrying specific amino acids, thus building proteins
pyrimidines
cytosine
uracil (only RNA)
thymine (only DNA)
uracil (only RNA)
thymine (only DNA)
purines
adenine
guanine
guanine
pyrimidine ring structure
single, 6 membered, 2 N ring
numbering begins with bottom N and goes clockwise
numbering begins with bottom N and goes clockwise
purine ring structure
2 N 6 member ring fused to a 2 N 5 member ring
numbering begins with furthest left N (on 6 member ring) and goes counterclockwise around 6 member ring, then clockwise starting at top of 5 member ring
numbering begins with furthest left N (on 6 member ring) and goes counterclockwise around 6 member ring, then clockwise starting at top of 5 member ring
cytosine structure
slide 9 lecture 9
pyrimidine with carbonyl group at 2 and amine group at 4
pyrimidine with carbonyl group at 2 and amine group at 4
uracil structure
pyrimidine with carbonyl groups at 2 and 4
thymine
pyrimidine with carbonyl groups at 2 and 4 and a methyl group at 5
adenine structure
purine with amine group on 6
guanine structure
purine with amine group on 2 and a carbonyl group on 6
other purines
hypoxathine- carbonyl group on 6 ( guanine w/o amine group on 2)
xanthine- carbonyl groups on 2 and 6
uric acid- carbonyl groups on 2,6, and 8
xanthine- carbonyl groups on 2 and 6
uric acid- carbonyl groups on 2,6, and 8
ketol-enol tautomerism
aromaticity and e- rich nature of purines and pyrimidines allows them to undergo ketol-enol tuatomerism
involves the movement of a proton and shifting of bonding e-
involves the movement of a proton and shifting of bonding e-
keto form
a ketone or aldehyde (with C=O)
enol form
an alcohol (with OH)
keto predominate nitrogenous bases
uracil, thymine, gaunine
enol predominate nitrogenous bases
cytosine
autacoid (what is it, and what nucleoside is one)
local hormone, adenosine
structure of adenosine
adenine attached to a ribose sugar
functions of adenosine
circulates in blood influencing blood vessel dilation, smooth muscle contraction, neurotransmitter release, and fat metabolism
also a sleep regulator (rises during wakefulness promoting eventual sleepiness)
also a sleep regulator (rises during wakefulness promoting eventual sleepiness)
what blocks the binding of adenosine promoting wakefulness
caffeine
linkage between base and sugar of nucleosides
glycosidic
the sugars of nucleosides are (C quantitative)
pentose
type of pentose in RNA nucleosides
D-ribose
type of pentose in DNA nucleosides
2-deoxy-D-ribose
difference b/t D-ribose and 2-deoxy-D-ribose
2'-OH (d-ribose) vs 2'-H (2-deoxy-d-ribose)
affects secondary structure and stability
affects secondary structure and stability
naming nucleosides: pyrimidines vs. purines
pyrimidines: add 'idine' to the root
purines: add 'osine' to the root
purines: add 'osine' to the root
advantage of nucleosides vs. free bases
sugars make nucleosides more water soluble
nucleotides
nucleoside phosphates
most are ribonucleotides
most are ribonucleotides
polyprotic acids
able to donate more than one proton
all nucleotides are polyprotic acids
all nucleotides are polyprotic acids
draw a nucleotide
slide 24, lecture 9
phosphate group linked to O on 5'C of ribose
phosphate group linked to O on 5'C of ribose
bond linking phosphate group to ribose
phosphoester bond
cyclic nucleotides
also links the O of phosphate to the 3'C of ribose
formation of ADP and ATP by addition of more P groups via _______ linkages
phosphoric anhydride
achieved by dehydration synthesis
achieved by dehydration synthesis
function of cyclic nucleotides
signal molecules
regulators of cellular metabolism and reproduction
regulators of cellular metabolism and reproduction
functioin of ATP
energy metabolism
function of GTP
drives protein synthesis
function of CTP
drives lipid synthesis
function of UTP
drives carbohydrate metabolism
major chemical reactions of nucleotides
phosphoryl transfer (1 phosphate group)
pyrophosphory transfer (2 phosphate groups)
nucleotidyl group transfer (base, sugar, phosphate group transfer)
pyrophosphory transfer (2 phosphate groups)
nucleotidyl group transfer (base, sugar, phosphate group transfer)
nucleic acids
linear polymers of nucleotides linked 3' to 5'
linkages bewteen nucleotides
phosphodiester bridges
the sequence of nucleotides is always read ___ to ____
5' to 3'
different classes of nucelic acids
DNA
RNA
-ribosomal RNA
-messenger RNA
-transfer RNA
also small nuclear RNA and small non-coding RNAs
RNA
-ribosomal RNA
-messenger RNA
-transfer RNA
also small nuclear RNA and small non-coding RNAs
ribosomal RNA
the basis of structure and function of ribosomes
messenger RNA
carries the message for protein synthesis
transfer RNA
carries the amino acids for protein synthesis
the DNA double helix is stabalized by
Hydrogen bonds
watson and crick
crick showed it was a helix
watson figured out the h bonds
watson figured out the h bonds
whose data held the clue to base pairing?
Chargaff's
eukaryotic DNA is wrapped around _____ proteins to form _______
histone; nucleosomes
practical applications of DNA
DNA chains have been used to nanomachines capable of simple movements
more elaborate DNA devices can act as motors walking along DNA tracts
more elaborate DNA devices can act as motors walking along DNA tracts
mRNA: prokaryotes vs. eukaryotes
prokaryotes: a single mRNA contains the information for synthesis of many proteins
eukaryotes: a single mRNA codes for just one protein, contains introns and extrons with Poly A tail
eukaryotes: a single mRNA codes for just one protein, contains introns and extrons with Poly A tail
extron
coding sequence of mRNA
intron
non-coding intervening sequence that must be removed
splicing
the process of removing introns
produces final mRNA
produces final mRNA
ratio of RNA and proteins in ribosomes
RNA 2/3
proteins 1/3
proteins 1/3
different species of rRNA are referred to according to their
sedimentation coefficients
rRNAs typically contained modified nucleotides such as
pseudouridine and ribothymidylic acid
prokaryotic ribosomes and subunits
70S ribosomes
30S and 50S subunits
30S and 50S subunits
eukaryotic ribsomes and subunits
80S ribosomes
40S and 60S subunits
40S and 60S subunits
unusual bases in DNA
4-thiouridine
inosine
ribothymidine
pseudouridine
dihydrouridine
inosine
ribothymidine
pseudouridine
dihydrouridine
tRNA structure
small polynucleotide chains (73-94 residues each)
several bases methylated
several bases methylated
substrate of protein synthesis
aminoacyl tRNA
Cech and Altman showed that RNA molecules are not only information, they can also be__
catalytic
gave evidence to the postulate by Watson and Crick that prebiotic evolution depended on self-replicating, catalytic RNAs
gave evidence to the postulate by Watson and Crick that prebiotic evolution depended on self-replicating, catalytic RNAs
likely origin of nucleotides
conversion of aminoamidazolecarbonitrile to adenine
and glycoaldehyde could have formed ribose
adenine and glycoaldehyde exist in outerspace
and glycoaldehyde could have formed ribose
adenine and glycoaldehyde exist in outerspace
aminoamidazolecarbonitrile structure
pentamer of HCN
glycoaldehyde structure
an aldehyde with a hydroxyl group on the alpha C
2 fundamental differences between DNA and RNA
DNA has 2-deoxyribose instead of ribose
DNA contains thymine instead of uracil
DNA contains thymine instead of uracil
why does DNA contain thymine
cytosine spontaneously deaminates to form uracil
repair enzymes in DNA recognize these mutations and replace Us with Cs
but how would repair enzymes recognize these mutatant Us from normal Us?
hence DNA uses thymine instead of uracil
repair enzymes in DNA recognize these mutations and replace Us with Cs
but how would repair enzymes recognize these mutatant Us from normal Us?
hence DNA uses thymine instead of uracil
structural difference b/t thymine and uracil
thymine has a methyl group at the 5 position
they both have carbonyl groups at 2 and 4
they both have carbonyl groups at 2 and 4
why do DNA and RNA use different sugars?
additional OH group in RNA makes it subject to hydrolysis (meant to be used and broken down)
DNA (genetic material) must be more stable
DNA (genetic material) must be more stable
effect of dilute acid on DNA and RNA
DNA is depurinated
RNA is resistant
RNA is resistant
effect of dilute base on DNA and RNA
DNA is resistant
RNA is hydrolyzed
RNA is hydrolyzed
random base hydrolysis of RNA gives what products
mixture of 2' and 3' nucleoside monophosphates
alpha side of phosphodiester
3' side
b side of phosphodiester
5' side
cleavage on the a side
leaves the phosphate attached to the 5' end of the adjacent nucleotide
b side hydrolysis
yields 3' phosphate products
restriction enzymes
restrict foreign DNA
types I and II cleave DNA chains at selected sites
types I and II cleave DNA chains at selected sites
six cutter
an enzyme that recognizes a 6-base sequence
About this deck
By: Andrew Vallo
Textbook: Biochemistry
Student Solutions Manual/Study Guide/Problems Book for Garrett/Grisham's Biochemistry, 3rd
Created: 2011-04-09
Size: 82 flashcards
Views: 14
Textbook:
BiochemistryStudent Solutions Manual/Study Guide/Problems Book for Garrett/Grisham's Biochemistry, 3rd
Created: 2011-04-09
Size: 82 flashcards
Views: 14
About StudyBlue
STUDYBLUE makes things that make you better at school.
Things like online flashcards with photos and audio.
Things like personalized quizzes and friendly reminders about when (and what) to study next.
Think of it as a digital backpack™: access to all of your study materials online and on your phone.
STUDYBLUE exists to make studying efficient and effective for every student, for free. Join us.
“I have been getting MUCH better grades on all my tests for school. Flash cards, notes, and quizzes are great on here. Thanks!”
Kathy
Kathy