Biochem 2280 Final Exam UPDATED
ACTUAL Questions and CORRECT
Answers
what is a nucleoside, what are the components to it, and how are the carbons numbered -
CORRECT ANSWER✔✔- -this is when there is a sugar and a nitrogenous based attached to
each other
-the N that is added to a ribose sugar is labelled 1, then the C and N in the ring are labelled
going counter clockwise
so N1 is connected to 1' of the ribose sugar with a N-glycosidic bond
-this bond is connected to the anomeric carbon to, the sugar can no longer switch between
alpha and beta, al sugars in RNA and DNA are in beta configuration
-so C connected to base is called 1' then label carbon going clockwise, put a prine (') on the
number
-if the base is cytosine, then the whole molecule w the sugar and base is called cytidine, this
is the ribonucleoside
what is a ribonucleotide, its components, and other ways to say the name - CORRECT
ANSWER✔✔- -this is a nucleoside (so a base and sugar), but there is also at least 1
phosphate group added or maybe more
-phosphate are attached to the 5' position of ribose or deoxyribose by a phosphoester linkage
-so when the phosphate is attached to the nucleoside, a nucleotide is formed
-phosphate groups are normally negatively charged at cellular pH
-ex molecule that has cytosine as base and 3 phosphates would be called cytidine triphosphate
-or just called it a nucleotide (implied that there are phosphates on it) or a nucleoside
triphosphate
what is the difference between a ribonucleotide and a deoxyribonucleotide - CORRECT
ANSWER✔✔- -both are composed of a base connected to a sugar by n-glycodific bond to
C1', then also have phopshate groups attached to the 5' C of the sugar
-but the 2' C of the deoxyribose has lost an oxygen, so has 2 H connected instead of an H and
an OH group on ribose
,what are the two bases that are purines and basic characteristics - CORRECT ANSWER✔✔-
the two bases found in DNA and RNA are adenine and guanine, and they make the
nucleosides adenosine and guanosine
-they are made form a 6 member ring attached to a 5 member ring, then tehy have soem extra
stuff added on
-its important to note that they have hydrogen donors and acceptors, this comes into play w
base pairing
-structures are pretty flat in their ring structure and have quite a few pi electrons in their
double bonds
-the planar surfaces of these purines are fairly hydrophobic, even though they have some
hydorgen bonding partners
what are the based of pyrimidines that are found in DNA and RNA, and their basic structures
and characteristics - CORRECT ANSWER✔✔- -there is cytosine, found in DNA and RNA
-Thymine, found in DNA but not RNA
-Uracil, found in RNA but not DNA
-thymine and uracil are very similar, but U is missing a methyl group
-the nucleosides these make are cytidine, thymidine, and uridine
-the overall structure of a pyrimidine is a 6 member ring, then has stuff added depending on
the based
-these also have polar groups good for H binding, and the flat surfaces are pretty hydrophobic
how are polynucleotides formed? - CORRECT ANSWER✔✔- -this is when multiple
nucleotides come together in longer strings
-the phosphate group attached to 5'C of one sugar forms bond w the hydroxyl group at the 3'
end of another sugar, this is called the phosphodiester bond
-so joins the 3'C of 1 sugar to 5" c of the next sugar, and there is phosphate group in middle to
make covalent linkage
how are sequences of polynucleotides named - CORRECT ANSWER✔✔- -the sequence
name is presented by the letter of each nucleotide base, starting from the 5' end
-so this created a sugar phosphate backbone that is repeated, then the dif based on each
nucleotide make up the seuqnece name
-the 5' end means that C is not attached to any other C, may or may not have a phosphate
attached, and this is same w 3' end
,what is the evidence that DNA is in a double helix - CORRECT ANSWER✔✔- 1. Chargaffs
rule: the amount of A and T in DNA matched each other and the amount of C and G match, so
this suggests they are paired together
2. X ray diffraction of DNA by Franklin showed us the structure of the helix
3. correct tautomeric forms of bases, so two dif structures of the based, but one is better for H
bonding is the one that occurs in the double helix
explain the double helix of DNA - CORRECT ANSWER✔✔- -a single starnd of DNA is not
normally found in cell, it is usually 2 polynucleotides DNA strands tightly but not covalently
associated w each other in antiparallel orientation, so the 5' end connects to 3' of the other
strand
-the double helix is called B-DNA, this is the most stable form
-so basically there are 2 sugar phosphate backbones and the bases come together and twist
around so that each base interacts w its complimentary one
-this arrangement w the based on the inside and phosphates on outside minimizes charge
repulsion between the phosphates and allows for salt stabilization of the phosphates negative
charge
explain handiness of the double helix - CORRECT ANSWER✔✔- -this is the way that the
double helix twists around itself
-it does so in a right handed fashion
-thing about which why you would turn if you are walking down a staircase
forces that stabilize the double helix: base stacking - CORRECT ANSWER✔✔- 1. there is
base stacking, which is the major contributor for stability of the double helix, beacuse
remember that the bases are planar aromatic rings that are nearly perpendicular to the helical
axis, so they can stack on top of each other
-so this force refers to interactions that occur between the bases that are ight next to each
other, so stack on top since they are flat and hydrophobic
-there are london forces that attract each other, and also hydrophobic effect
-any base pair can stack on any other base pair
forces that stabilize the double helix: base pairing - CORRECT ANSWER✔✔- -this is not as
big of a contributor compared to base stacking
, -this is across the strands, so one bas forms H bodning q the base of the other sytrands
between chemical groups on edges of yheir ring structures
-they are always monogamous, so alwsys go with that specifc base pair, so its sequence
specific
-each base pair consists of one purine and one pyrimidine, each base pair size is uniform and
the two sugar phosphate backbones stay the same distance apart, water cant compete w the
bases for H bonding positions
-so A and T go together and form 2 H bonds
-C and G go together and form 3 H bonds
-all of the base pairs have constant length, so fits well inside teh double helix structure
what are the different dimensions of the double helix we need to know and what are the
grooves in the helix - CORRECT ANSWER✔✔- -the width of the double helix is 20 A or
2nm
-the length of 10 bp is 34 A or 3.4 nm, so 0.34 nm per bp
-because 1 A = 0.1nm
-there is the major groove, which is where sugar phosphate backbone goes in to the centre
axis, so there is space in between the ridges
-the major groove is the perfect size for alpha helix od a protein to fit in perfectly to react
with the DNA
-the minor groove is there too, but its smaller
-when looking down the helix, the sugar phosphate backbone is not totally symmetrical, there
is more space on one side bc the other bc this is how the bases bond to the sugars
nucleic acid stability and what is Tm - CORRECT ANSWER✔✔- -Double helix strands
separate (denature) when heated and anneal (renature) when cooled
-so when you increase temp, DNa starts to unwind and there is denaturation, there is
transition period where melting starts and as temp increases, there is bigger proportion of
single strand DNA
-single strand absorbs more light than double strand, so can figure out ration of denautued
DNA by looking at absorbance
-the Tm is when 50% have melted or denatured
what are the different factors affect Tm in DNA (7) - CORRECT ANSWER✔✔- -dif pieces
of DNA have different Tm, there are intrinsic factors and extrinsic factors
