Biochemistry Midterm 2.1 - DNA Flashcards
what is an irreversible inhibitor?
how does it affect Vmax and Km?
covalently link to enzyme to shut it off
ex. toxins, drugs (aspirin, penicillin
Vmax and Km decrease because of substrate competition and blocking enzyme itself
what is allosteric inhibition/regulation
small chemicals, non covalent modification of enzymes
can be up regulation or down regulation
covalent enzyme modifications
R groups that are often modified to become more or less reactive: serine threonine and histidine
phosphorylation by kinases can work like an allosteric regulator
what is a zymogen?
an inactive precursor molecule of an enzyme, which requires irreversible covalent modification to become active form
nucleic acids are (5)
polymers of nucleotides used in:
DNA - storage of genetic info
mRNA - transmission of genetic info
ribozymes - processing of genetic info
protein synthesis using tRNA and rRNA
nucleotide uses
ATP, cofactors (NAD+) and cAMP (signal transduction)
pyrimidine structure
purine structure
nitrogenous bases
pyrimidines are hexagonal, purines are bicyclic
nucleotide vs nucleoside structure and numbering
nucleotide: phosphate, pentose, nitrogenous base
nucleoside: nitrogenous base and pentose
pentose ring is numbered #’, nitrogenous base is just #
phosphate group in nucleotide
connected to 5’ end of the ribose (can be on other positions in other molecules)
PO4 is negatively charged at pH 7
phosphodiester bond between nucleotides
5’ phosphate and 3’ hydroxyl
what is beta furanose? which molecules have this structure?
beta furanose is a 5 ring with 1 oxygen, and 4 carbons
ribose and deoxyribose (H instead of OH on 2’) for RNA/DNA
nitrogenous base chemical structural properties
heteroaromatic, UV light absorbing (250 nm- 270nm), planar, good H acceptor and donor, neutral at pH 7
Nucleotide/nucleoside nomenclature
Adenine: Adenosine / Adenylate
Guanine: Guanosine / Guanylate
Cytosine: Cytidine / Cytidylate
Thymine: Thymidine / Thymidylate
Uracil: Uridine/Uridylate
phosphate group in nucleotide
connected to 5’ end of the pentose (can be on other positions in other molecules)
PO4 is negatively charged at pH 7
B-N-Glycosidic bond
bonds that connect nucleotides/nucleosides
1’ pentose connected to N1 on pyrimidines and N9 on purines
bond has rotation which allows helix to form
stable bond, especially in pyrimidines
conformations of N-glycosidic bond
number of bonds that affect nucleotide conformation
ring pucker
0° - syn conformation
180° - anti conformation (found in B DNA)
7 bonds
ring pucker (bond 4) limits torsion angle between nitrogenous base and pentose
nucleotide absorption measurement wavelength
260 nm
minor nucleosides that mark DNA to be transcribed
post synthesis modifications
in eukaryotes and bacteria: 5-methylcytosine
in bacteria: N^6-methyladenosine
used to mark one’s own DNA and genes to be transcribed
inosine
often in wobble position of anti-codon in tRNA
deaminated adenosine
wobble position
3rd nucleotide in a codon
allows for non-watson and crick pairing that is looser
pseudouridine
found in tRNA and rRNA
made from uridine (glycosylated uracil) after RNA synthesis
made stabilize tRNA and help folding rRNA
phosphodiester bonds in DNA/RNA
3’ carbon of pentose and the phosphate group 5’ carbon of deoxyribose/ribose
releases 1 water during formation
contributes to 5’ to 3’ orientation of DNA
Chargaff’s rule
base pairs bond via
ratio of base pairs in DNA
pyrimidines pair with purines (AT(U), GC)
hydrogen bonds
1:1 ratio of purines to pyrimidines
purines bases:
guanine and adenosine
pyrimidine bases:
cytosine and thymine and uracil
Friedrich Miescher
isolated “nuclein” from cell nuclei
hydrolyzed reveal phosphate, pentose and nitrogenous base
discovered phosphodiester bonds and pentose as a ribofuranoside
Franklin and Wilkins discovered
cross indicates helix structure
diamonds represent phosphate-sugar backbone on the outside
Watson and Crick discovered
missing layers indicate major and minor groove of helix and hydrogen pairing between bases
beta-DNA model - 36 Å (10.5 bases) between per turn of helix
3.4 Å between adjacent bases
20 Å wide
major and minor groove length
major - 22 Å
minor - 12 Å
forces that stabilize DNA helix
hydrogen bonds between complementary base pairs
van der waals interactions between adjacent base pairs
other forms of DNA structure
Beta form predominates in cells
A form (compressed) and Z form (squiggly)
semi conservative DNA replication
each strand serves as template for replication 5’ to 3’
new DNA has one daughter strand and one parent strand
mRNA produced from
mRNA can code
advantage of different base
genetic template
for more than 1 protein
differentiates between the genetic coding functions
why is RNA unstable compared to DNA?
ribose instead of deoxyribose is less stable
unstable un alkaline conditions or catalyzed by RNase
hydroxyl group acts as nucleophile
function of palindromic sequences
used as recognition sites
can form hairpins and cruciforms
RNA pairing
complex, unpredictable, many non-watson-crick pairs via H bonds
very folded to minimize energy
anneal
reforming of structure (DNA after replication)
why does UV absorption increase with DNA denaturation?
because base stacking is lost and aromatic bases are revealed
why is more heat/energy required to denature guanine/cytosine H bonds?
because G-C has 3 H bonds and A-T/U has only 2
Tm
higher C-G content in a sequence, the higher the midpoint of melting (Tm)
Longer DNA sequence increases Tm
pH and ionic strength affects Tm (salt increases Tm)
deamination
type of spontaneous mutagenesis
slow reaction that affects a large number of residues
C –> U (100 per day)
5-methylcytosine –> thymine
adenine –> hypoxanthine
G –> xanthine
depurination
type of spontaneous mutagenesis
removal of purine group involving breaking glycosidic bond
10000 per day!
Effect of UV light on pyrimidines
Effect of ionizing radiation (x rays)
pyrimidine dimers (stick together)
ring opening and strand breaking
NTP
nucleotide triphosphate
hydrolysis of these provides energy for enzymatic catalysis
nucleotide coenzymes
adenosine containing
coenzyme A, FAD (active form B2 riboflavin)
RNA and DNA pentose forms in solution and in nucleotides/nucleosides
in solution exists in equilibrium between aldehyde form and beta furanose
RNA exists as beta-d-ribofuranose
DNA exists as beta-2’-deoxy-d-ribofuranose
depurination of the N-glycosidic bond is often due to
frequency
hydrolysis under acidic conditions
10000 purines lost per day
A form DNA
right handed, 26 Å diameter
more condensed
anti glycosidic conformation
favors low hydration conditions
B form DNA
right handed, 20 Å diameter
less condensed than A form
anti glycosidic conformation
predominates in cells
Z form DNA
left handed, 18 Å diameter
least condensed DNA
anti for pyrimidines, syn for purines
predominates in high salt conditions
ATP is a
ribonucleoside triphosphate
What are nucleosides?
Nucleosides are important biological molecules that function as signaling molecules and as precursors to nucleotides needed for DNA and RNA synthesis.
groups participating in H bonds between A-T
A: N and NH
T: NH and =O (with another =O that doesn’t participate)
groups participating in H bonds between G-C
G: NH, NH and =O
C: =O, N, NH
difference between thymine and uracil?
thymine is methylated
what is 5-methylcytosine
minor nucleotide in eukaryotes and bacteria
can be spontaneous deaminated into thymine
what is xanthine and hypoxanthine?
xanthine - product of spontaneous deamination of guanine
hypoxanthine - product of spontaneous deamination of adenine
spontaneous deamination of cytosine forms
uracil
