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BIOCHEM > NUCLEIC ACIDS > Flashcards

NUCLEIC ACIDS Flashcards

1
Q

Discovered by Friedrich Mierscher in 1869 while studying the nucleus of WBC
pH of nucleus is because of nucleic acid found inside it
Name is derived from the sugar unit they have in structure
Unbranched polymer in which a monomer unit is a nucleotide

A

Nucleic Acids

Acidic property of the nucleus of the cell is attributed to the nucleic acid found inside it
Acidic in nature; complementary bases and backbone is usually checked
Sequencing: always 5’ — 3’

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2
Q

a three subunit molecule in which a pentose sugar is bonded to both phosphate group and nitrogen-containing heterocyclic base/ nitrogenous bases
Sub-unit: Pentose sugar, nitrogenous base, phosphate group
Pentose: ribose (RNA), deoxyribose (DNA)
Named first before nucleotide in general

A

Nucleotide

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3
Q

Name the nucleotide:
Sugar- ribose
Nitrogenous base- guanine
Phosphate- two phosphate

A

Guanosine diphosphate

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4
Q

Name the nucleotide:
Sugar- deoxyribose
Nitrogenous base- thymine
Phosphate- three phosphate

A

Deoxythymidine triphosphate

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5
Q

Types of Nucleic Acid:
Found within the cell nucleus and small amounts in mitochondria
Storage and transfer of genetic information
Pass from past existing to new cells during cell division
Replicated in the cell cycle; specifically S phase of interphase
Replicated DNA are the ones passed onto the new cells
Double stranded

A

DNA

deoxyribonucleic acid; deoxyribose

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6
Q 
Types of Nucleic Acid:
Occurs in all parts of a cell.
90% in cytoplasm
Free ribosomes in cytoplasm and ribosomes attached on RER
Ribosomes have RNA in structure 
10% on nucleolus
A

RNA

ribonucleic acid; ribose
Synthesizes some RNA/ ribosomes  
Synthesis of proteins
RNA are translated to form amino acid, once sequence is made, it could produce protein coded base on the amino acid sequence 
Single stranded
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7
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct

  1. DNA and RNA differ in the identity of sugar unit in nucleotides
  2. Microorganisms are classified based on the type of nucleic acid that could be found inside them
A

C

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8
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct

  1. Viruses are classified based on nucleic acid; DNA or RNA
  2. Cells in an organism do not have the exact replicas, have the info on how to make new cells, information are stored in the nucleic acids
A

A

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9
Q

Subunits of Nucleic Acid:
Basis of the name of nucleic acid types
either pentose ribose or pentose 2’-deoxyribose
Difference of both is side chain that are found on C-2 of the structure

A

Pentose Sugar

Deoxyribose: H side chain; has no O2 on C-2 side chain
Beta-D-deoxyribose (Haworth projection)
Ribose: OH side chain
Beta-D-ribose (Haworth projection)

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10
Q

Subunits of Nucleic Acid:
purine and pyrimidine
There are 5 (2:3) types of nitrogenous base, but not all 5 could occur in both types of Nucleotide/ nucleic acid
Basic in nature due to the functional group, amine (NH3), in their structure

A

Nitrogen-containing heterocyclic base/ nitrogenous base

Responsible for their basic behavior; accept protons (H ions)
All contain nitrogen in their structure
Responsible for the coding of sequence of nucleic acid

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11
Q

a bicyclic base with fused five and six- membered rings

2-cyclic ring

A

Purine

Adenine: amino (NH3) in the C-6
Guanine: amino (NH3) C-2, w/ =O as side chain
N-9: bond for sugar unit; during the formation of nucleotide/ nucleic acid
Occur both in DNA and RNA

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12
Q

a monocyclic base with a six-membered ring

1 cyclic ring, has =O in structure

A

Pyrimidine

Cytosine: only structure that has NH2; RNA and DNA
Thymine: CH3 (methyl) in structure; DNA only
Uracil: unmethylated thymine; RNA only
N-1: bond for sugar unit; during formation of nucleotide
Not all can occur in both DNA or RNA

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13
Q

Subunits of Nucleic Acid:
From phosphoric acid (H3PO4) —> looses 2 H atoms —> hydrogen phosphate ion
Hydrogen phosphate ion: one that will bond in the sugar to form nucleotide
Always bonded on C-5 of nucleoside, can also be bonded on C-3 when forming a branched polymer of nucleic acid

A

Phosphate

Phosphate group bonds at C-5: when 1 nucleotide is formed
Phosphate group bonds at C-3: when nucleotide bond together to form polymer of nucleic acid

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14
Q

reaction involved in nucleotide formation
Formation of water molecule between sugar-base and sugar-phosphate
H2O is yielded
Same reaction used in forming of peptide bonds in proteins and glycosidic linkage for carbohydrates

A

Condensation

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15
Q

Sugar and base (β-N) glycosidic linkage: (N-1 or N-9)
Purine:____
Pyrimidine:___

A

N-1

N-9

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16
Q

Phosphate to sugar is bonded on the ____ of sugar

A

C-5’

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17
Q

_____: phosphate group and sugar
_____: formed when phosphate group is bonded on another C-3 of a sugar unit

A

Phosphate-ester linkage

Phosphodiester bond

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18
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct
Primary Nucleic acid Structure

  1. Is the sequence in which molecules are linked together in a nucleic acid
  2. Does not depend on the sequence of bases present
A

A

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19
Q

Backbone: Phosphate-Sugar for _____
Backbone: Peptide bonds for _____

A

Nucleic Acids

Proteins

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20
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct
DNA Structure and Function

  1. Serves as genetic material for cells both prokaryotes and eukaryotes
  2. In eukaryotes, it is located in the plasma membrane separated from the cytoplasm by the nuclear membrane and is bounded by chromatin
A

A

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21
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct
DNA Structure and Function

  1. In prokaryotes, DNA is separated from the rest of the cellular contents; nucleoids, and is not scattered on the cytoplasm
  2. Chromatin is a complex of eukaryotic DNA bound to proteins where histone is the common protein bond on DNA, coiled on DNA structure forming chromatin
A

B

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22
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct
Structure of DNA

  1. DNA is a very short, thread like macromolecule made up of a large number of deoxyribonucleotides (N+S+P; 3 sub-units)
  2. Single helix or stranded: 2 polynucleotide strands coiled around each other
A

D

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23
Q

5’—3’ (___ strand) = 3’—5’ (____ strand; paired base on the bases present on the leading strand)

A

leading

complementary

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24
Q

How many hydrogen bonds?
A = T: ___ H-bonds

C = G:___ H-bonds

A

2

3

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25
Q

THE WHO?

Won a nobel prize in 1962
Attributed for the base composition patterns associated for DNA molecules

A

James Watson & Francis Crick

DNA Double-Helical Structure

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26
Q

States that :

In DNA structure, the content of A is equal to that of T and the contents of G equals to that of C

A

Chargaff’s Rule (Erwin Chargaff)
One member of a base pair in a DNA must always be a purine and the other a pyrimidine. Purines = Pyrimidines
Ratio of bases are always 1 (1:1)
Bases are located at the center and are known to be H bonded

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27
Q

THE WHO?

deduced that A must pair with T and G to C because of stearic and hydrogen bonding factors

A

James Watson & Francis Crick

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28
Q

Functions of DNA:
Source of information for the synthesis of all protein molecule of the cell
Not directly associated with protein sequence that will be produced
Responsible only for the information to synthesis the protein

A

Store genetic information

Provides the information inherited by the daughter cells or offsprings
DNA is replicated at the interphase; only replicated once regardless of cell division involves in cell cycle

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29
Q

A if only the first statement is correct
B if only the second statement is correct
C if both of the statements are correct
D if neither of the statements is correct
Comparison of DNA and RNA

  1. While DNA contains deoxyribose, RNA contains ribose
  2. Complementary base to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine
A

C

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30
Q

Backbone of molecular biology
DNA contains the genes that encode the information for the synthesis of a protein
Does not direct protein synthesis
Sequence of the bases in the DNA codes for the sequence of the amino acids in proteins
This dogma also includes the replication of DNA
It may start from RNA to DNA, and RNA can also be replicated

A

Flow of Biological Information: Central Dogma

The DNA does not direct protein synthesis.
RNA: there will be a changed in bases involved for protein synthesis
The genetic information in the DNA is decoded in the form of messenger RNA, which is then translated to Amino Acid sequence of a protein
According to Francis Crick, this information cannot be transferred from protein to either protein or nucleic acid

31
Q

3 Major Stages in Central Dogma:
Produces two identical molecules
Exact or identical copy

A

DNA Replication

32
Q

3 Major Stages in Central Dogma:
Produced mRNA
Genetic information in the DNA is copied in mRNA.
Sequence of the mRNA bases is the same as that of the DNA except for Thymine

A

Transcription

33
Q

3 Major Stages in Central Dogma:
Leads for the protein synthesis or production
Codons in the mRNA direct the sequence of amino acid in the protein

A

Translation

34
Q

Doubling/ duplication of DNA & occurs during the interphase (S) period of mitosis
Replicated only once; regardless of cell division
If replicated from a single ori (origin; where replication starts), with same rate as bacteria, this would take over 150 hours

A

DNA Replication

DNA to be copied is fed through the proteins of the replication factory
Duplex DNA to be copied is first split into single strands
Each of the two template strands is copied and becomes half of a new DNA double helix (semi-conservative)
Function: Provision of progeny with the genetic information possessed by the parent
Daughter cells will get the genetic info from parent

35
Q

Replication Enzymes:
____ unzip the enzymes
Processive unwinding of DNA

A

DNA Helicase

Break the hydrogen bonds between bases of the two antiparallel strands resulting in the unwinding of the helix/ unzip of DNA
Origin of replication: Ori
Region in the chromosome which is the initiation/ starting point for DNA replication
Replication fork: structure involved

36
Q

Replication Enzymes:
____relax DNA for local unwinding
Relieves torsional strain that results from helicase- induced unwinding

A

Topoisomerase

37
Q

Replication Enzymes:
____ attached to split DNA
Initiates synthesis of RNA primers

A

Primase
Binds the initiation point of the 5’—3’ parent chain and synthesizes the RNA primer
RNA primer: Has required 3’-OH end for the addition of a new nucleotide
Where it will start to bind or elongated sequence of parental DNA

38
Q

Replication Enzymes:
____ elongation
Polymerization of DNA
Elongates the new DNA strand at a 5’-3’ direction using the 3’-5’ template (complementary strand)
5’-3’ strand that proceeds to the direction of the replication fork (leading strand)

A

DNA polymerase
New strand using the 5’-3’ template is synthesize in a discontinuous manner (lagging strand)
There will be possible nicks formed during DNA replication
Nicks: dent or gaps found in short DNA fragments
Okazaki fragments: short DNA fragments added.

39
Q

Replication Enzymes:

____ Anchors DNA polymerase

A

Sliding clamp

40
Q

Replication Enzymes:

___ Prevents premature reannealing of ssDNA; prevents the forming of bonds of DNA during replication

A

Single-strand binding proteins (SBB)

41
Q

Replication Enzymes:

____ Removes RNA primers

A

RNase H/ DNA Polymerase I (E.coli)
Removes the primer in the lagging strand and fill the gap with appropriate nucleotides (using RNA primer)
Nicks will be removed and will feel the gaps

42
Q

Replication Enzymes:

____ Links short DNA pieces together

A

DNA Ligase

Gaps between the Okazaki fragments (short DNA fragments) are sealed

43
Q

ODD MAN OUT:
Replication Process

  1. Enzymes unwind the parental double helix (DNA)
  2. Proteins are transferred to the golgi complex
  3. Proteins stabilize the unwound parental DNA
  4. The leading strand is synthesized continuously by DNA polymerase
  5. The lagging strand is synthesized discontinuously where RNA polymerase synthesizes a short RNA primer which is then extended by DNA polymerase
  6. DNA polymerase digests RNA primer and replaces it with DNA
  7. DNA ligase joins the discontinuous fragments of the lagging strand.
A
  1. Proteins are transferred to the golgi complex
44
Q

Another type of nucleic acid
Made up of unbranched chain of nucleotides as in DNA
Dextro-ribose, Uracil instead of Thymine and single stranded.

A

RNA (Ribonucleic Acid)

Uracil is paired with Adenine (U = A)
75 to few thousand nucleotides
Involves the transcription and translation

45
Q

2nd stage of central dogma
Prior to this, unwinding the DNA double helix is needed for bases to be exposed via the topoisomerase and allow the RNA polymerase to access the DNA
Process of copying of a DNA template in the form of RNA

A

Transcription

DNA directs the synthesis of mRNA; 2 step process
1st: synthesizes hnRNA
2nd: yields mRNA
All RNAs are synthesized using DNA template
Process requires the enzyme RNA polymerase (has access in DNA)
Makes a complementary strand of the DNA

46
Q

segment of a DNA base sequence responsible to produce specific hnRNA or mRNA

A

Gene
Human genes: 20,000-25,000 genes= genome (complete set of genes)
Most/ each human genes have 1000-3500 nucleotide units long

47
Q

Sense strand or Anti-sense strand:

Codes for the sequence of the gene
Nucleotides found are the one responsible for the sequencing of the gene

A

Sense strand

48
Q

Sense strand or Anti-sense strand:

Opposite complementary strand that is used as the template for RNA synthesis
RNA base sequence is identical with that of the sense strand except for the presence of U and T
T —> U for A

A

Anti-sense strand

49
Q

Types of RNA Molecules:
formed directly by DNA transcription
Heterogenous nuclear RNA
Post-transcription processing: hnRNA —> ‘splicing’ —> mRNA

A

hnRNA

50
Q

Types of RNA Molecules:
carries instructions for protein synthesis; genetic information from DNA
Messenger RNA
Molecular mass depends on the length of protein produced

A

mRNA

51
Q 
Types of RNA Molecules:
facilitates the conversion of hnRNA to mRNA
Small nuclear RNA
Contains little amount of nucleotide
100-200 nucleotides
A

snRNA

52
Q 
Types of RNA Molecules:
Structural component of the ribosomes 
Ribosomal RNA
rRNA + specific protein = ribosomes
Ribosomes: 3M molecular mass; (physical sites of protein synthesis)
A

rRNA

53
Q

Types of RNA Molecules:
delivers amino acids to the site for protein synthesis (ribosome)
Transfer RNA
Smallest type of RNA: 75-90 nucleotides unit
Acts as anti-codon to deliver amino acid to the protein synthesis site

A

tRNA

54
Q

Formation of mRNA

Involves conversion of hnRNA to mRNA via ‘splicing’

A

Post-Transcription Processing

55
Q

Excision/ removal of introns and joining/ retaining of exons

A

Splicing

Splicing process is driven by snRNA; facilitates the conversion of hnRNA to mRNA

56
Q

a gene segment that codes for genetic information

Responsible for coding of genetic info

A

Exon

57
Q

a DNA segments that interrupt a genetic message

A

Intron

58
Q

3 nucleotide sequence in a mRNA molecule that codes for specific amino acids

A

Codon

59
Q

anti-codon (3’-5’); complements the codon

Transfers the codon to the site of the protein synthesis

A

tRNA

60
Q

A process by which several different protein variants are produced from a single gene
The process involves excision of one or more exons

A

Alternative splicing

61
Q

All of the mRNA molecules that can be generated from the genetic material in a genome. It is different from a genome
Responsible for the biochemical complexity created by splice variants obtained by hnRNA.

A

Transcriptome

62
Q

Who proposed the Genetic Code Table?

A

Marshall Nirenberg
Har Gobind Khorana

Won a Nobel prize for chemistry; able to know how mRNA encodes for the protein

63
Q

It was discovered 1966
Scientists are now able to predict characteristics by studying DNA.
is the assignment of the 64 mRNA codons to specific amino acids.
Leads to genetic engineering, genetic counseling.

A

Genetic Code
Out of 64 codons, 61 codons can be translated into amino acid
Many amino acids are designated by more than one codon
3 are considered as stop/ termination codon; stops the translation of amino acid

64
Q

Identify the stop codons:

A

UAA
UGA
UAG

65
Q

Identify the start/ initiation codon:

A

AUG

(methionine), when it appears coding of amino acid can start, always at the start

66
Q

codons that specify the same amino acid are called:

A

Synonyms

67
Q

For delivering and transferring the amino acids
During protein synthesis amino acids do not directly interact with the codons of an mRNA molecule.
tRNA molecules as intermediaries deliver amino acids to mRNA.

A

Anticodons and tRNA Molecules

The 3’ end of tRNA is where an amino acid is covalently bonded to the tRNA.
The loop opposite to the open end of tRNA is the site for a sequence of three bases called an anticodon.

68
Q

a three-nucleotide sequence on a tRNA molecule that is complementary to a codon on a mRNA molecule.
Not to be translated, function only to deliver codon in protein synthesis site

A

Anticodon

69
Q 
Protein synthesis (ribosome; 65% rNA, 35% protein. rRNA-protein complex)
Process in which mRNA codons are now deciphered to synthesis a protein molecule 
Process by which the sequence of nucleotides in an mRNA molecule directs the incorporation of amino acid into protein
A

Translation

70
Q

5 Steps of Translation Process:

addition of specific amino acids to the 3’-OH group of tRNA.

A

Activation of tRNA

71
Q

5 Steps of Translation Process:
Begins with binding of mRNA to small ribosomal subunit such that its first codon (initiating codon AUG) occupies a site called the P site (peptidyl site in ribosome)

A

Initiation of protein synthesis

72
Q

5 Steps of Translation Process:
Adjacent to the P site in an mRNA–ribosome complex is A site (aminoacyl site) and the next tRNA with the appropriate anticodon binds to it.

A

Elongation

73
Q

5 Steps of Translation Process:
The polypeptide continues to grow via translocation until all necessary amino acids are in place and bonded to each other. End only when stop codon appears

A

Termination

74
Q

5 Steps of Translation Process:

gives the protein the final form it needs to be fully functional

A

Post-translational processing

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