4 | Nucleotides, Nucleic Acid, and Heredity Flashcards by Ssherwyn Lavarias

What are the 2 nucleic acid in cells?

◆ Ribonucleic acids (RNA)
◆ Deoxyribonucleic acids (DNA)

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Both RNA and DNA are polymers built from monomers called (___________) each of which consists of purine or pyrimidine bases, deoxyribose, ribose, and phosphate.

Nucleotides

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What are 3 substituents with nitrogen and their location?

Amino group is located at C6
Another Nitrogen is located at the 7th position.
Hydrogen is attached to the sugar moiety

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Adenine IUPAC naming?

6-Aminopurine.

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Guanine IUPAC naming?

2-Amino-6-Oxypurine

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N1, start counting clockwise or counterclockwise

counterclockwise

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Cytosine IUPAC naming?

2-Oxy-4-Aminopyrimidine

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Thymine IUPAC naming?

2,4-dioxy-5-methyl pyrimidine

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Uracil IUPAC naming?

2,4,-dioxy pyrimidine

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Uracil and Thymine are lookalikes, except that there
is no (____________) attached to the 5th position of
the pyrimidine ring.

methyl group

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Nucleosides is a compound that consists of D-ribose or
2-deoxy-D-ribose bonded to a purine or pyrimidine
base by?

β-N-glycosidic bond

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β means (?) direction

Upward direction

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The -OH group of the sugar is bonded to the (?) of sugar moiety of the pyrimidine bases?

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The -OH group of the sugar is bonded to the (?) of sugar moiety of the purine bases?

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Cytosine, Uracil, and Thymine is N1 or N9?

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Adenine and Guanine is N1 or N9?

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transcribe AMP?

Adenosine Monophosphate

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transcribe ADP?

Adenosine Diphosphat

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transcribe ATP?

Adenosine Triphosphate

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It is currency for energy?

ATP

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Thymine is present, it’s different from Uracil
because of the presence of methyl group at 5th
position of the pyrimidine ring, connected with N1C1
or NC glycosidic bond.

Deoxythymidine 3’-monophosphate (3’-dTMP)

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N9 is at the (?) aromatic ring

2nd aromatic ring

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It is the sequence of nucleotides, beginning with the nucleotide that has the free 5’ terminus.

Primary (1 ◌ํ) Structure

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It refers to the order of bases in the polynucleotide
sequences

Primary (1 ◌ํ) Structure

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The backbone of DNA can be seen here (sugar moiety and phosphate group). The backbone is constant, only the bases change

Schematic diagram of a nucleic acid molecule

The double helix model of DNA 2 ◌ํ structure was proposed by? and what year?

James Watson and Francis Cricks in 1953

Three dimensional structure of the DNA double helix. The blue and reddish ribbons represent the sugar phosphate “backbone.”

DNA Double Helix

What rule said that: For each adenine on one chain, a thymine is aligned opposite it on the other chain; Each guanine on one chain has a cytosine aligned with it on the other chain.

Chargaff’s rule

It is the most common and most stable form.

B-DNA

With B-DNA, a distinguishing feature is the presence of a (__________ and ___________), which arise because the two strands are not equally spaced around the helix.

major groove and a minor groove

Histones are rich in the basic amino acids Lys and Arg, whose side chains have a

Positive charge

The negatively-charged DNA molecules are provided by the?

phosphate ions depending if it is monophosphate, diphosphate, or triphosphate

The negatively-charged DNA molecules are provided by the phosphate ions depending if it is monophosphate, diphosphate, or triphosphate and positively-charged histones attract one another and form units called ?

nucleosomes

A core of with histone molecules around which the DNA helix is wrapped.

Nucleosome

Nucleosomes are further condense into

chromatin

DNA double helix nm?

2 nm

Nucleosome nm?

11 nm

"beads on a string" chromatin form nm?

11 nm

Loops (50 turns per loop) nm?

250 nm

Selonoid (6 nucleosomes per turn) nm?

30 nm

Chromosome (stacked minibands) nm?

840 nm

Transfer RNA molecules contain not only cytosine, guanine, adenine, and uracil, but also several other modified nucleotides, such as

1-methylguanosine

Miniband nm?

840 nm

Transports amino acids to site of protein synthesis

Transfer (tRNA)

Size of Transfer (tRNA)

Small

Combines with proteins to form ribosomes, the site of protein synthesis

Ribosomal RNA (rRNA)

Size of rRNA

several kinds-variable in size

Directs amino acid sequence of proteins

messenger RNA (mRNA)

SIZE OF messenger RNA (mRNA)

small

Processes initial mRNA to its mature form in eukaryotes

small nuclear RNA (snRNA)

SIZE OF small nuclear RNA (snRNA)

small

PROTECTS ANIMAL GENOMES AGAINST TRANSPOSONS

- Piwi-associated RNA(piRNA)

Affects gene expression; important in growth and development

micro RNA (miRNA)

Affects gene expression; used by scientists to knock out a gene being studied

small interfering RNA(siRNA)

SIZE OF small interfering RNA(siRNA)

SMALL

SIZE OF micro RNA (miRNA)

SMALL

Involved in activating or silencing specific genes

Long non-coding RNA (IncRNA)

SIZE OF Long non-coding RNA (IncRNA)

- VARIABLE

Acts as miRNA sponge, controlling the effects of miRNA

- CIRCULAR RNA

SIZE OF Piwi-associated RNA(piRNA)

- Small

SIZE OF CIRCULAR RNA

- VARIABLE

The BER pathway contains two parts:

- 1. A specific DNA glycolase (1) recognizes the damaged base and catalyzes the hydrolysis of the glycosidic bond between that base and the deoxyribose, then releases the damaged base completing the excision. The sugar-phosphate backbone is still intact. At the AP site (apurinic or apyrimidinic site) created in this way, (2) the backbone is cleaved by a second enzyme, endonuclease. A third enzyme, exonuclease (3), liberates the sugar-phosphate unit of the damaged site. - 2. In the synthesis step, the enzyme DNA polymerase (4) inserts the correct nucleotide, cytidine, and the enzyme DNA ligase seals (5) the backbone to complete the repair.

Nucleotide of Adenine(DNA)

- Deoxyadenosine 5'-monophosphate

Nucleoside of Guanine(DNA)

- Deoxyguanosine

Nucleotide of Cytosine(DNA)

- Deoxycytidine 5'-monophosphate

Nucleotide of Guanine(DNA)

- Deoxyguanosine 5'-monophosphate

Nucleoside of Thymine(DNA)

- Deoxythymidine

Nucleotide of Thymine(DNA)

- Deoxythymidine 5'-monophosphate

Nucleoside of Guanine(RNA)

- guanosine

Nucleoside of Cytosine (DNA)

- Deoxycytidine

Nucleotide of Adenine(RNA)

- adenosine 5'-monophosphate

Nucleoside of Adenine(RNA)

- adenosine

Nucleotide of Guanine(RNA)

- guanosine 5'-monophosphate

Nucleoside of Uracil (RNA)

- Uridine

Nucleotide of Cytosine(RNA)

- cytidine 5'-monophosphate

Nucleotide of Uracil (RNA)

- Uridine 5'-monophosphate

Nucleoside of Cytosine (RNA)

- cytidine

It temporarily introduce either single or double strand breaks in DNA.

- Topoisomerases (also called gyrases)

The structure of a typical prokaryotic ribosome. The individual components can be mixed, producing functional subunits. Reassociation of subunits gives rise to an intact ribosome. The designation S refers to Svedberg, a unit of relative size determined when molecules are separated by centrifugation.

- Structure of rRNA

The designation S refers to _______, a unit of relative size determined when molecules are separated by centrifugation.

- Svedberg

a segment of DNA that carries a base sequence that directs the synthesis of a particular protein, tRNA, or mRNA

- gene

a unit of relative size determined when molecules are separated by centrifugation

Svedberg

In bacteria, the gene is ______ (continuous or discontinuous)

- continuous

a section of DNA that, when transcribed, codes for a protein or RNA

- Exon

In higher organisms, the gene is ______ (continuous or discontinuous)

- discontinuous

a section of DNA that does not code for anything functional.

- Intron

The DNA in the chromosomes carries out two functions:

- 1) It reproduces itself. This process is called replication. - 2) It supplies the information necessary to make all the RNA and the proteins in the body, including enzymes.

What are the 6 distinct steps in replication of DNA

- 1) Opening up of the superstructure of the chromosomes. - 2) Relaxation of Higher-Order Structures of DNA. - 3) Unwinding the DNA Double Helix - 4) Primers/Primases - 5) DNA Polymerase - 6) Ligation

One key step in this process is _______________. This reaction eliminates some of the positive charges on histones and weakens the strength of the DNA-histone interaction.

- acetylation-deacetylation of lysine residues on histones

Replication begins at a point in the DNA called

- the origin of replication or a replication fork

One key step in this process is acetylation-deacetylation of lysine residues on histones. This reaction eliminates some of the positive charges on histones and weakens the strength of the DNA-histone interaction.

- Opening up of the superstructure of the chromosomes.

Topoisomerases (also called gyrases) temporarily introduce either single or double strand breaks in DNA. Once the supercoiling is relaxed, the broken strands are joined together and the topoisomerase diffuses from the location of the replication fork.

- Relaxation of Higher-Order Structures of DNA.

Replication of DNA molecules starts with the unwinding of the double helix which can occur at either end or in the middle. Special unwinding proteins called helicases attach themselves to one DNA strand and cause the separation of the double helix.

- Unwinding the DNA Double Helix

Special unwinding proteins called ____

- Helicases

They are short 4 to 15 nucleotides long oligonucleotides synthesized from ribonucleoside triphosphates. They are needed to initiate the primase-catalyzed synthesis of both daughter strands.

- Primers/primases

Once the two strands are separated at the replication fork, the DNA nucleotides must be lined up. In the absence of DNA polymerases, this alignment is extremely slow. The enzyme enables complementary base pairing with high specificity. While bases are being hydrogen bonded to their partners, polymerases join the nucleotide backbones. Along the lagging strand 3’—>5”, the enzymes can synthesize only short fragments, because the only way they can work is from 5’ to 3’. These resulting short fragments consist of about 200 nucleotides each, named Okazaki fragments after their discoverer.

- DNA Polymerase

They are short DNA segments made of about 200 nucleotides in higher organisms (eukaryotes) and of 2000 nucleotides in prokaryotes.

- Okazaki fragments

The 39-hydroxyl group at the end of the growing DNA chain is a

- nucleophile

The Okazaki fragments and any nicks remaining are eventually joined by DNA ligase.

- Ligation

It attacks at the phosphorus adjacent to the sugar in the nucleotide, which will be added to the growing chain.

- 39-hydroxyl group at the end of the growing DNA chain

Millions of copies of selected DNA fragments can be made within a few hours with high precision by a technique called ______

- polymerase chain reaction (PCR)

What temperature is required to unwind the double helix to hybridize the primer to the target DNA.

- 95°

How many cycles are there in PCR?

- 3 CYCLES

What cycle is this- Oligonucleotides complementary to a given DNA sequence prime the synthesis of only that sequence.

- Cycle 1&2

What cycle is this–Heat-stable Taq DNA polymerase survives many cycles of heating. Theoretically, the amount of the specific primed sequence is doubled in each cycle.

- Cycle 2&3

How Is DNA Repaired?

➔ The viability of cells depends on DNA repair enzymes that can detect, recognize, and remove mutations from DNA. ➔ Externally, UV radiation or highly reactive oxidizing agents, such as superoxide, may damage a base. ➔ Errors in copying or internal chemical reactions, such as deamination of a base, can create damage internally deamination of cytosine turns it into uracil, which creates a mismatch. The former C-G base pair becomes a U-G mispairing that must be removed.

One of the most common base repair preparation means.

- BER (Base Excision Repair)

The BER pathway contains two parts: