Biochem exam 4 Flashcards
What are the functions of nucleic acids?
Storage and transmission of genetic information(DNA and RNA),processing of genetic information(ribosomes-catalytic mRNA),protein synthesis(tRNA, rRNA)
What are the functions of nucleotides?
Provide energy for metabolism(ATP), enzyme cofactors(NAD),signal transduction(cAMP)
What is the full name for DNA?
Deoxyribonucleic acid
What determines the amino acid sequence of proteins and nucleotide sequence of RNA molecules?
The nucleotide sequence in the cell’s DNA
What is the function of RNA
Carries genetic information from the site of DNA to the location of protein synthesis
Describe RNA
Components of ribosomes which is location of protein synthesis
What are the components of a nucleotide
a five carbon sugar,phosphate group,and nitrogenous base
What are the four nitrogenous bases present in deoxyribonucleic acids?
Adenine, guanine, cytosine, thymine
nucleotides are linked together by
dehydration synthesis or polymerization reactions between the sugar of one nucleotide and the phosphate group of another
Describe the sugar phosphate backbone
linkage of one nucleotide’s sugar and the phosphate group of another nucleotide
The strands of the DNA double helix are
antiparallel(opposite directions)
The two stands of DNA are held together by —–
hydrogen bonds between the nitrogenous bases of each strand
Cytosine bonds with
guanine
Thymine bonds with
adenine
What re the differences between DNA and RNA?
RNA contains the sugar ribose, the nitrogenous base uracil instead of thymine ,RNA is single stranded
Describe messenger RNA (mRNA)
Carry DNA primarily from nucleus to the ribosomes to serve as template for protein synthesis
Describe the function of transfer DNA (tRNA)
translates mRNA into a specific nucleotide sequence
What is the sugar found in DNA
beta-deoxy-D-ribosse
What is the sugar found in RNA?
Beta-d-ribose
What is a nucleoside?
A nucleotide without the phosphate group
What is a ribozyme
An RNA molecule capable of acting as a catalytic enzyme
What are the two types of nitrogenous bases present in nucleotides
pyrimidine and purine
What are the four nitrogenous bases in DNA
Adenine,Guanine, Thymine,Cytosine
What are the four nitrogenous bases in RNA?
Adenine,Guanine,Uracil,Cytosine
What makes the pyrimidine and purine bases?
The nitrogen contains lone pair of electrons which allows them to act as proton acceptors
Which are the pyrimidine bases?
Cytosine,Thymine, Uracil
Which are the purine bases?
Adenine,Guanine
Adenine pairs with?
Thymine in DNA and Uracil in RNA
Guanine pairs with?
cytosine
Thymine pairs with?
Adenine
Uracil in RNA pairs with?
Adenine
Cytosine pairs with?
Guanine
Cytosine pKa at N3 is
4.5
Thymine pKa at N3 is
9.5
Adenine pKa at N1
3.8
Guanine pKa at N7
2.4
Purines and pyrimidines are hydrophobic, and relatively insoluble in
Water at cellular pH
All nucleotide bases absorb UV light (strong absorption near —- resulting in electronic excitation
260nm
Do nucleic acids experience fluorescence?
no
The N-glycosidic bond is formed between the anomeric carbon of
the sugar in 𝛽 configuration and what position of the pyrimidine and purine?
N! of the pyrimidine, N9 of the purine
In nucleotides the pentose ring is attached to the base via a —- bond which is product of a — rxn
N-glycosidic bond, condensation
Can free rotation acoss the n-glycosidic bond occur in free nucleotides?
yess
The torsion angle about the N-glycosidic bond is defined by —- in purine
O4’-C1’-N9-C4
The torsion angle about the N-glycosidic bond is defined by — in pyrimidine
O4’-C1’-N1-C2
Angle near 0 degrees in the glycosidic corresponds to syn conformation
syn conformation
Angle near 180 degrees in the glycosidic bond corresponds to
anti conformation
the —- conformation of the glycosidic bond is most common in DNA
anti
Nitrogeneous base + Pentose + Phosphate and name ends in ylate
nucleotide
Nitrogeneous base + Pentose and name ends in osine
nucleoside
Epigenetic marker in prokaryotic cells
identifies own cell DNA to allow for destruction of foreign DNA
Epigenetic marker in eukaryotic cells
signals which genes should be active
Inosine sometimes found in the
“wobble position
” of the
anticodon in tRNA can be produced by —-
deaminating adenosine
Pseudouridine found widely in
tRNA and rRNA can be generated by
enzymatic isomerization of uridine after RNA synthesis
nucleotides are held together by
phosphodiester bonds
Why is RNA unstable?
single stranded, ribose makes it more susceptible to degradation
Hydrolysis of RNA is catalyzed by
RNases
How many H-bonds does a A-T form?
two
How many H-bonds does C-G form
three
Adenosine is part of many —— such as FAD and NAD
enzyme cofactors
What is the role of adenosine as a cofactore
provide binding energy and stabilize intermediates
What does FAD stand for?
Flavin adenine dinucleotide
What does NAD stand for?
Nicotinamide adenine dinucleotide
Some variations of nucleotide may serve as —- on the surface of cell prompting the production of a —-
second messenger
Some variations of nucleotide may serve as —-
second messenger
Inosine function
provides richer genetic code
Pseudouridine
stabilize tRNa and may help in folding of rRNA
primary structure of a nucleic acid
nucleotide sequence
secondary structure of nucleic acid
stable 3-D structure of a short polynucleotide segment(piece of DNA)
Tertiary structure of nucleic acid
folding of a nucleic acid into a chromosome or folding of large tRNA and rRNA molecules
A segment of 10 nucleotide pairs is approximately —- long
3.4 nm or 34 Angstrum
DNA is a —– —— helix
right handed double
the deoxyribose-phosphate back bone of DNA is
hydrophilic
nitrogenous base interactions are important for DNA stability and occur
perpendicular to the helical axis
The two strands of DNA run —- to each other
anti parallel
During DNA replication what occurs first?
Strand separation
Each separated DNA strand
serves as —- for synthesizing the new
strand based on ——-
a template, complementary pairing
Each new DNA Molecule consists of one — strand and one — strand
parent, daughter
Every 10 base pairs is a —- degree rotation in the DNA double helix
360
The form is the most stable
structure for a random sequence DNA
molecule under physiological conditions
B-DNA
Asymmetric attachment of the base pairs to the
sugar rings gives rise to
major and minor grooves
—– found in the major and minor grooves on the DNA helix can aid in determining sequence due to interactions with proteins
hydrogen bonding patterns
sequence specific interactions between DNA and proteins typically occur in the —
major grooves
sequence specific interactions between DNA and proteins typically occur in the —
major grooves
What are the three forms of DNA?
A,B.Z
Which type of DNA is left handed?
Z
how many base pairs per helical turn in the A form of DNA
11
how many base pairs per helical turn in the B form of DNA
10.5
how many base pairs per helical turn in the z form of DNA
12
What is the diameter of the B-DNA helix
20 angstrom
What is the helix rise per base pair in A-DNA
2.6 angstrom
What is the helix rise per base pair in B-DNA
3.4 angstrum
What is the helix rise per base pair in Z-DNA
3.7 angstrom
What is the glycosidic bond conformation for A-DNA?
anti (180 degree torsion angle)
What is the glycosidic bond conformation for B-DNA?
Anti(180 degree torsion angle)
What is the glycosidic bond conformation for Z-DNA?
anti for pyrimidines and syn for purines
A-DNA is favored in many solutions that lack
water
A DNA is a right-handed double helix, but
—— compared to B-DNA
wider
Is there evidence of A-DNA in cells?
no
Describe the shape of Z-DNA
left handed, thin, elongated
Z-DNA has a — shaped back bone
zig zag
Short stretches (tracts) of Z-DNA are found in
bacteria and eukaryotic cells
What are possible roles of Z-DNA
regulation of gene expression and gene recombination
Poly (A) tract
the appearance of four consecutive adenine in one strand may cause a slight bend in the DNA helix
Palindromic sequence
nucleic acid sequence in RNA or DNA that is identical to the complementary strand when they are both read in the same direction
What shapes may a palindromic sequence lead to
hair pin or cruciform shape