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M2: Biochemistry > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

▪️ Responsible for storage and expression of genetic information
▪️ Composed of DNA and RNA

A

Nucleic Acids

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2
Q

Fundamental Components of Nucleic Acids

A
  1. Pentose sugar
  2. Phosphate group
  3. Nitrogenous bases
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3
Q

Nitrogenous Bases
▪️under PURINE (9 membered ring)

A

Mnemonics PurGA

Adenine (Alang Oxygen)
Guanine (9 membered ring with 1 O)

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4
Q

Nitrogenous Bases
▪️under PYRIMIDINE (6 membered ring)

A

Mnemonics: PyCUT
Cytosine (1 Oxygen)
Uracil
Thymine (meTHYL)

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5
Q

H - DNA - Double Strand

A

Deoxyribose

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6
Q

OH - RNA - Single Strand

A

Ribose

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7
Q

Pentose Sugar + Nitrogenous Base

A

Nucleoside

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8
Q

Phosphate + Pentose Sugar + Nitrogenous Base

A

Nucleotide

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9
Q

Nucleoside of A, G, C,T, U

[named by changing the nitrogen base ending to -OSINE FOR PURINE and -IDINE FOR PYRIMIDINE]

A

Adenosine
Guanosine
Cytidine
Uridine
Thymidine

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10
Q

Nucleotide of A, G, C,T, U

[named using the name of nucleoside followed by phosphate]

A

Adenosine Phosphate
Guanosine Phosphate
Cytidine Phosphate
Uridine Phosphate
Thymidine Phosphate

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11
Q

STRUCTURAL ORGANIZATION OF PROTEINS
▪️Linear
▪️Sequence of AA
▪️Peptide Bond

A

Primary Structure

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12
Q

STRUCTURAL ORGANIZATION OF PROTEINS
▪️Alpha helix, Beta-pleated sheets
▪️H-Bond

A

Secondary Structure

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13
Q

STRUCTURAL ORGANIZATION OF PROTEINS
▪️3D Structure (“Conformation”)
▪️Supercoiling of DNA
▪️Pertains to 1 polypeptide chain only
▪️Disulfide, H-bond, Hydrophobic & Ionic Interaction,

A

Tertiary Structure

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14
Q

What facilitates supercoiling?

A

DNA gyrase / Topoisomerase II

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15
Q

STRUCTURAL ORGANIZATION OF PROTEINS
▪️Interaction or combination of at least 2 tertiary structures / polypeptide chain
▪️Specificity
▪️Electrostatic & Hydrophobic Interaction, H-Bond

A

Quaternary Structure

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16
Q

MAJOR groove

A

Adenine & Thymine (2 H Bonds)

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17
Q

MINOR Groove

A

Cytosine & Guanine (3 H Bonds)

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18
Q

The ability of certain anticodon to pair with codons that differ at the third base

A

Wobble

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19
Q

Concept by which a tRNA can recognize more than one codon for a specific amino acid by allowing movement in the first base of the anticodon

A

Wobble Hypothesis

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20
Q

It allows a single tRNA to recognize more than once codon

A

Wobble hypothesis

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21
Q

In the chains, each end of the helix contains the 5’ end of one strand and the 3’ end of the other

A

Antiparallelism

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22
Q

Destruction or breaking down of hydrogen bonds that holds the two complementary strands of DNA

A

Denaturation / Melting

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23
Q

What Protein Structure do not undergo Denaturation?

A

Primary Structure

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24
Q

CENTRAL DOGMA OF THE MOLECULAR BIOLOGY

▪️DNA ➡️ RNA

A

Transcription

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25
CENTRAL DOGMA OF THE MOLECULAR BIOLOGY ▪️RNA ➡️ Proteins
Translation
26
CENTRAL DOGMA OF THE MOLECULAR BIOLOGY ▪️DNA ➡️ DNA
Replication
27
▪️ Process of transferring information to DNA for conservation of inherited traits ▪️ Process by which a "replica" or identical copy of DNA is made so that information can be preserved and handed down too offspring
Replication
28
▪️ Initiation by unwinding ▪️ Open the DNA double helix ▪️ unwinds the DNA
Helicase
29
Enzyme that connects Okazaki fragments
DNA ligase
30
Sequence of major events in Replication
1. DNA double helix is opened by HELICASES 2. Priming - PRIMASE creates template RNA primer for each strand 3. Polymerization - DNA POLYMERASE III synthesizes DNA in 5' to 3' direction 4. DNA POLYMERASE I removes the RNA primer and fills the gaps between Okazaki fragments 5. DNA LIGASE joins the DNA fragments of the lagging strand, creating a single DNA molecule
31
▪️ DNA Gyrase ▪️ Targeted by QUINOLONES
Topoisomerase Type 2
32
▪️Synthesis of RNA from DNA ▪️Enzyme use: Transcriptase / RNA polymerase
Transcription
33
▪️ Does not require a primer ▪️ Can initiate polymerization ▪️ Does not possess proofreading activity
RNA polymerase
34
Transcription Process
1. Initiation - DNA is transcribed by RNA polymerase 2. Elongation - transcription factors unwind the DNA strand 3. Termination - RNA polymerase reaches terminator sequence of DNA; Release of mRNA
35
Transcription Process: ▪️ DNA is transcribed by RNA polymerase ▪️ Binding of RNA polymerase to promoter region of gene
Initiation (Transcription)
36
Transcription Process: ▪️ Transcription factors unwind the DNA strand ▪️The antisense strands serves as the template
Elongation (Transcription)
37
Transcription Process: ▪️RNA polymerase reaches terminator sequence of DNA ▪️Release of mRNA ▪️Detachment of RNA polymerase from DNA
Termination (Transcription)
38
Produces the three basic types of RNA (?)
1. Messenger (mRNA) 2. Ribosomal (rRNA) 3. Transfer (tRNA)
39
▪️TEMPLATE of protein synthesis ▪️CARRIER of CODONS (sequence of three DNA or RNA) ▪️Carries genetic information
mRNA (RNA Polymerase II)
40
▪️ most abundant / most common form of RNA ▪️ Site of PROTEIN SYNTHESIS (catalytic or structural role) ▪️Ribosomal RNA
rRNA (RNA Polymerase I)
41
▪️ Carries activated amino acids and contains ANTI-CODON (opposite of codon) ▪️Transfer amino acid from cytosol to ribosomes ▪️At the 3' end, there is CAA sequence, which is where the amino acid attached
tRNA
42
▪️Enzyme use: Reverse Transcriptase (RNA-directed-DNA polymerase) ▪️ Synthesis of DNA from RNA ▪️ Oncogenic or tumor producing RNA viruses, also known as RETROVIRUSES ▪️Complementary DNA (cDNA) - product of reverse transcription
Reverse Transcription
43
▪️Synthesis of proteins based on the codons specified by the mRNA ▪️Formation of proteins from RNA
Translation
44
Three main steps in protein synthesis
1. Initiation 2. Elongation 3. Termination
45
STEPS IN PROTEIN SYNTHESIS ▪️Start Codon - AUG (Methionine in Eukaryote; Formyl Methionine in Prokaryote) 🔸️Eukaryote - Kozak sequence 🔹️Prokaryote - Shine-Dalgarno
Initiation
46
STEPS IN PROTEIN SYNTHESIS ▪️ Continuation of reading of codon by 3
Elongation
47
STEPS IN PROTEIN SYNTHESIS ▪️Stop Codon; UAG, UGA, UAA
Termination
48
▪️Deoxyribose ▪️CGAT ▪️Nucleus & Mitochondria ▪️Central repository of genetic information (Stores)
DNA
49
▪️Ribose ▪️CGAU ▪️Nucleus & Cytoplasm ▪️Helps in the expression of genetic information
RNA
50
▪️Hydrated (most stable) ▪️RIGHT-handed ▪️10 base pairs/turn ▪️MOST COMMON & MOST ABUNDANT; Described by Watson & Crick using X-ray diffraction
B-DNA
51
▪️Dehydrated ▪️RIGHT-handed ▪️11 base pairs/turn ▪️LESS COMMON
A-DNA
52
▪️Rare (in prokaryote) ▪️LEFT-handed ▪️12 base pairs/turn ▪️MOST STABLE in vitro during methylation or negative supercoiling
Z-DNA
53
Wide & Deep MAJOR GROOVE
B-DNA
54
Narrow & Deep MAJOR GROOVE
A-DNA
55
Flat MAJOR GROOVE
Z-DNA
56
Narrow & Shallow MINOR GROOVE
B-DNA
57
Broad & Shallow MINOR GROOVE
A-DNA
58
Narrow & Deep MINOR GROOVE
Z-DNA
59
Most common type of DNA in humans
B-DNA
60
Sleeping / dormant form of DNA
Z-DNA
61
One parent strand and one daughter strand appear in the final product. New DNA is made by using the original DNA as template
Semi-conservative
62
When 2 strands of the DNA double helix are separated, each strand can serve as a template for the replication of a new complementary strand
Semi-conservative Replication
63
Two parents strands stay together and two daughter strands stay together
Conservative
64
▪️Segments of DNA that specify or code proteins ▪️Basic unit of genetic information ▪️ Represent the genetic information transcribed into a single RNA molecule, which is in turn into a single protein ▪️All genes are translated except for genes for RNA molecules (rRNA & tRNA)
Genes
65
PARTS OF A GENE ▪️Coding regions ▪️Informational DNA segments that makeup genes
Exons
66
PARTS OF A GENE ▪️non-coding regions ▪️intruder
Introns
67
Before the mRNA molecule leaves the nucleus nonsense bases that make up the INTRONS ARE CUT OUT and the informationally useful exons are joined together
RNA Splicing
68
▪️Total genetic makeup of an organism ▪️Human genome is composed of 30,000 genes
Genome
69
▪️Groups of three bases called CODOND control the production of a particular amino acid in the cytoplasm of the cell ▪️Different amino acids and the order in which they are joined up determines the sort of protein being produced
Genetic Code
70
▪️Permanent change in the base sequence of DNA ▪️Unwanted changes in the DNA sequence
Mutations
71
Agent in the environment that brought about mutation
Mutagen
72
Absence of mutagen; occasional mistakes during the DNA replication
Spontaneous mutation
73
Presence of mutagen
Induce mutagen
74
TYPES OF MUTATION
1. Point Mutation 2. Frameshift Mutation
75
TYPES OF MUTATION There is substitution of a single base
Point Mutation
76
TYPES OF MUTATION Addition or removal/deletion of bases Intercalation
Frameshift Mutation
77
What aromatic compounds cause Frameshift Mutation (2)
Acridines & Ethidium bromide
78
Types of Point Mutation ▪️SAME chemical class ▪️ Purine replaced by Purine ▪️ Pyrimidine replaces Pyrimidine
Transitional / Transition
79
Types of Point Mutation ▪️DIFFERENT chemical class ▪️ Purine replaced by Pyrimidine base and vice versa
Transversional / Transversion
80
RESULT OF POINT MUTATION (3)
1. Silent (SAME) 2. Missense (DIFFERENT) 3. Nonsense (STOP)
81
RESULT OF POINT MUTATION ▪️result to still the SAME amino acid ▪️Does not result in any change in protein sequence ▪️Ex. UCA (Serine) -> UCU (Serine)
Silent
82
RESULT OF POINT MUTATION ▪️DIFFERENT amino acid ▪️Ex. UCA (Serine) -> ACA (Proline)
Missense
83
RESULT OF POINT MUTATION ▪️result in STOP codon ▪️Ex. UCA (Serine) -> Stop Codon
Nonsense
84
End product of purine metabolism
Allantoin
85
End product of purine metabolism in humans
Uric Acid
86
DEGENERACY OF THE GENETIC CODE ▪️Several codons may code for the amino acids ▪️1 AA = ?
▪️1 AA = 6 codons
87
DNA-dependent RNA synthesis
Transcription
88
DNA-dependent DNA synthesis
Replication
89
Conversion of RNA to Proteins
Translation
90
RNA Polymerase Attaches to consensus sequences: ▪️Eukaryotes - CAAT box (aka?)
Hogness box
91
RNA Polymerase Attaches to consensus sequences: ▪️Prokaryotes - TATA box (aka?)
Pribnow box
92
▪️Triplets sequences of nucleotides ▪️See in RNA only
Codons
93
Post-translational modification happens in Involves glycosylation & proteolytic cleavage
Golgi apparatus
94
The bond between the oxygen part of the phosphate group and the pentose sugar is called
Phosphodiester bond

M2: Biochemistry (22 decks)

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