Nucleic Acid Structures Flashcards
1
Q
join the 3’-carbon of one sugar to the 5’-carbon of the next sugar
A
Phosphodiester bonds
2
Q
DNA chains are ______ meaning on side runs from 5’ to 3’ while the other side runs from 3’ to 5’ end
A
antiparallel
3
Q
located on the outside of the double helix
A
phosphate groups. Used in phosphodiester bonds
4
Q
is right-handed and contains ______ per turn.
A
B form of DNA; 10 base pairs
5
Q
Alkali or heat causes the strands of DNA to separate but does not break phosphodiester bonds.
A
Denaturing
6
Q
If strands of DNA are separated by heat and then the temperature is slowly decreased under the appropriate conditions, base pairs reform, and complementary strands of DNA come back together.
A
Renaturing/annealing
7
Q
A single strand of DNA or RNA pairs with complementary base sequen- ces on another strand of DNA or RNA.
A
Hybridization
8
Q
a segment of a DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA
A
gene
9
Q
only known functions of DNA:
A
storage of biological information transmission of that information to the next generation
10
Q
Pneumococcus type:
- Live (smooth bacteria):
- Heat-killed (smooth bacteria:
- Live (rough bacteria)
- Mixture of Heat-killed (smooth bacteria) + Live (rough bacteria)
Mouse fate?
A
- Mouse dies
- Mouse lives
- Mouse lives
- Mouse dies
11
Q
- protein injection:
- lipids injection:
- carbohydrates injection:
- nucleic acids fraction:
A
- mouse lives
- mouse lives
- mouse lives
- mouse dies
12
Q
Gene flow
A
replication (DNA) transcription/reverse transcription (RNA) translation protein
13
Q
associated with gene silencing
A
methylation (5-methylcytosine)
14
Q
A
15
Q
Catalyzes the formation of DNA chains
A
DNA Polymerase
16
Q
short (typically < 50 nucleotides) nucleic acid
A
oligonucleotide
17
Q
longer nucleic acid
A
polynucleotide
18
Q
All nucleic acid sequences are written in a ________ direction
A
5’ to 3’ direction
19
Q
Severs p-type linkage
A
Endonuclease
20
Q
severs d-type linkage
A
exonucleases (cleavage on the edges of the strand)
21
Q
Classes of RNA:
A
- ribosomal RNAs (rRNAs) = components of ribosomes
- messenger RNAs (mRNAs) = intermediates in protein synthesis
- transfer RNAs (tRNAs) = adapter molecules that translate the information in mRNA into a specific amino acid sequence
- noncoding RNAs (ncRNAs) = wide variety of functions
22
Q
4 Basic Molecular Genetic Processes
A
- Transcription
- RNA Processing
- mRNA translation
- Replication
23
Q
Formation of 3’ to 5’ Linkage
A
How phoshodiester bonds are linked 3’ to 5’ dispite the strand still going from 5’ to 3’ end.
24
Q
The normal form of DNA found in mammals
Most stable for a random-sequence DNA molecule under physiological conditions
characteristic:
A
B form
perpendicular bases
25
right-handed double helix with a wider helix, 11 bp/turn, and a tilted plane
favored in solutions devoid of water
A-form DNA
26
left-handed helix with 12 bp/turn and a backbone with a zig-zag appearance
appears more slender and elongated
Z-form DNA
27
Comparison of A, B, and Z forms of DNA
28
Stabilizing Forces of DNA
* Hydrophobic Interactions Among the Bases
* Electrostatic Interactions of the Negatively Charged Phosphate Groups; Counter-ions Such as Mg++; and Basic Proteins
* Hydrogen Bonds (weak forces)
29
the observed decrease in the absorption of UV light when complementary strands are paired
hypochromic effect
30
Stabilization of the DNA Double Helix
* metal cations that shield the negative charges of backbone phosphates
* base stacking interactions between successive base pairs
* successive G≡C or C≡G are stronger than successive A=T or T=A
* duplexes with higher G≡C context are more stable
31
the observed increase in the absorption of UV light when a double-stranded nucleic acid is denatured
hyperchromic effect
32
monitoring UV absorption at \_\_\_\_\_\_nmcan detect the transition from double-stranded to single-stranded DNA
260 nm
33
Absorption of light in different forms of DNA
Describe the graph for the following
* Single stranded DNA
* Double stranded DNA
* linear graph
* sigmoidal curve
34
An increase in the percentage of C + G bonds _______ the melting point.
increases
35
Consists of short (~20 nts or less) that are repeated many thousands or several million times. Located mostly in centromeres. Sometimes called satellite DNA
Highly Repetitive DNA
36
DNA sequences that are repeated from 100 - 1000x times. The sequences are several hundred to several thousands bps long. Usually found in tandem arrays among transcribed single-copy DNA
Moderately Repetitive DNA
37
DNA sequences that are present in only one copy are referred to an unique or single copy DNA. Usually, code for proteins; pseudogenes (not expressed) and introns (found within functional genes)/spacers (between genes).
Single - Copy DNA
38
Defined Order Sequences
39
region of DNA that is identical when read either forward or backward
applied to regions of DNA with inverted repeats
palindrome
40
sequence when the inverted repeat occurs within each individual strand
mirror repeat
41
Secondary Structures of DNA
* Hairpin
* Stem-Loop
42
Tertiary Structure or DNA
* Pseudoknot
43
Types of Histones
* H1
* H2A
* H2B
* H3
* H4
evolutionary conserved
44
Histone octamer
2 copies of H2A, H2B, H3, and H4 bound up in an octet and tied by one copy of HI
45
Histones
* Genes are highly conserved
* Expressed during the S-phase of the cell cycle
* The mRNAs contain no poly-A tails
* Genes have no introns and occur in tandem repeats
* NOT associated with bacterial or mitochondrial DNAs
46
Organization of chromatin in the cell
47
48
The linear chromosomes of eukaryotes have many origins of replication usually spaced about _________ kilobase pairs (kb) apart.
30-100 kb
49
At each replication fork synthesis of the leading strand is ________ and synthesis of the lagging strand is \_\_\_\_\_\_\_\_\_.
continuous; discontinuous
50
Short discontinuous segments, which later are joined
Okazaki fragments
51
BAsic principles that apply to DNA synthesis in every organism
* DNA replication is semiconservative
* replication begins at an origin and usually proceeds bidirectionally
* DNA synthesis proceeds in a 5′→3′ direction and is semidiscontinuous
52
each DNA strand serves as a template for the synthesis of a new strand
produces two new DNA molecules, each with one new strand and one old strand
established by Meselson and Stahl in 1957
semiconservative replication
53
DNA replication and histone synthesis in the mammalian cell cycle takes place during the
S Phase
54
The programmed suicide of cells
apoptosis
55
General Characteristics of DNA Replication
1. Occurs in a 5' ----\> 3' direction
2. DNA repln. requires:
1. a DNA template
2. Mg++
3. all 4 dNTPs
4. ATP
5. many proteins
6. RNA primers
7. most importantly, DNA-dependent DNA polymerases.
56
a structure that would allow molecules to be lined up in a specific order and joined to create a macromolecule with a unique sequence and function
template
## Footnote
the structure of DNA revealed one strand is the complement of the other.
each strand provides the template for a new strand
57
a strand segment with a free 3′-OH group to which a nucleotide can be added
must be complementary to the template
many are RNA oligonucleotides
primer
58
the free 3′ end of the primer
primer terminus
59
DNA Polymerases
60
removes RNA until it gets to a single RNA nucleotide
Rnase H
61
Removes single RNA nucleotide after RNase H removal of RNA
Flap endonuclease 1
62
# fill in the gaps in the removal of RNA primers
a reverse transcriptase that has its own RNA template
telomerase
63
Characteristics of Coronavirus Virion
~125 nm diameter, 30 Kb (+) RNA genome
with :
* Ribonucleoprotein complex (RNP)
* Membrane Glycoprotein (M)
* Envelope protein (E)
* Spike protein (S)
* C-terminal and Transmembrane domains
64
Coronavirus Replication
RNA-dependent RNA Polymerase or Replicase
## Footnote
The CoV replicase requires functional integration of RNA polymerase, capping and proof-reading.
65
Unusual/Modified RNA Bases
66
process by which an enzyme system converts the genetic information in dsDNA into an RNA strand with a complementary base sequence
transcription
67
RNA is synthesized by RNA polymerases using
DNA templates and ribonucleoside 5'-triphosphates
68
RNA can be used as a template for synthesis of DNA by
reverse transcriptases
69
RNA can act as both a
catalyst and carrier of genetic information
70
Major types of RNAs
71
72
73
responsible for cleavage in tRNA processing
Nucleotidyl transferase
74
In prokaryotes, messenger RNA undergo ________ processing at all
little or no
75
Formation of the 5′ Cap
formed by condensation of a molecule of GTP with the triphosphate at the 5′ end of the transcript
methylation occurs at the N-7 guanine and often the 2′-OH groups of the two nucleotides adjacent to the cap
methyl groups are derived from S-adenosylmethionine
76
A single polypeptide protein with 3 different catalytic domains
DNA Polymerase I
77
Palindrome & Palindrome-like Sequences
1. EcoRI restriction site
2. Single and double stranded inverted repeats
1. Hairpin
2. Cruciform
3. Mirror repeat
78
separate double-stranded DNA into single strands allowing each strand to be copied
helicase
79
catalyze and guide the unknotting or unlinking of DNA by creating transient breaks in the DNA using a conserved tyrosine as the catalytic residue
topoisomerase
80
* RNase D cuts at the :
* RNase P cuts at the :
* Nucleotidyl transferase:
* Final structure of Transfer RNA is ______ long
* RNase D cuts at the 3’ end
* RNase P cuts at the 5’ end
* Nucleotidyl transferase adds the 3’-CCA to all mature tRNA
* Final structure is 70-90 nucleotides long
81
As DNA polmerase extends the strand, it does so by
releasing a pyrophosphate molecule
