NUCLEIC ACIDS Flashcards by Ady Cabalquinto

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

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’

How well did you know this?

Not at all

Perfectly

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

Nucleotide

How well did you know this?

Not at all

Perfectly

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

Guanosine diphosphate

How well did you know this?

Not at all

Perfectly

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

Deoxythymidine triphosphate

How well did you know this?

Not at all

Perfectly

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

DNA

deoxyribonucleic acid; deoxyribose

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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

Viruses are classified based on nucleic acid; DNA or RNA
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

How well did you know this?

Not at all

Perfectly

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

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)

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

a bicyclic base with fused five and six- membered rings

2-cyclic ring

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

How well did you know this?

Not at all

Perfectly

a monocyclic base with a six-membered ring

1 cyclic ring, has =O in structure

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

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

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

Condensation

How well did you know this?

Not at all

Perfectly

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

N-1

N-9

How well did you know this?

Not at all

Perfectly

Phosphate to sugar is bonded on the ____ of sugar

C-5’

How well did you know this?

Not at all

Perfectly

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

Phosphate-ester linkage

Phosphodiester bond

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

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

Nucleic Acids

Proteins

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

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

In prokaryotes, DNA is separated from the rest of the cellular contents; nucleoids, and is not scattered on the cytoplasm
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

How well did you know this?

Not at all

Perfectly

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

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

How well did you know this?

Not at all

Perfectly

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

leading

complementary

How well did you know this?

Not at all

Perfectly

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

C = G:___ H-bonds

How well did you know this?

Not at all

Perfectly

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

James Watson & Francis Crick DNA Double-Helical Structure

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

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

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

James Watson & Francis Crick

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

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

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

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

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

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

DNA Replication

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

Transcription

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

Translation

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

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

Replication Enzymes: ____ unzip the enzymes Processive unwinding of DNA

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

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

Topoisomerase

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

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

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)

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.

Replication Enzymes: | ____ Anchors DNA polymerase

Sliding clamp

Replication Enzymes: | ___ Prevents premature reannealing of ssDNA; prevents the forming of bonds of DNA during replication

Single-strand binding proteins (SBB)

Replication Enzymes: | ____ Removes RNA primers

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

Replication Enzymes: | ____ Links short DNA pieces together

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

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.

2. Proteins are transferred to the golgi complex

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

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

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

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

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

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

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

Sense strand

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

Anti-sense strand

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

hnRNA

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

mRNA

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

snRNA

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

rRNA

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

tRNA

Formation of mRNA | Involves conversion of hnRNA to mRNA via ‘splicing’

Post-Transcription Processing

Excision/ removal of introns and joining/ retaining of exons

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

a gene segment that codes for genetic information | Responsible for coding of genetic info

Exon

a DNA segments that interrupt a genetic message

Intron

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

Codon

anti-codon (3’-5’); complements the codon | Transfers the codon to the site of the protein synthesis

tRNA

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

Alternative splicing

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.

Transcriptome

Who proposed the Genetic Code Table?

Marshall Nirenberg Har Gobind Khorana Won a Nobel prize for chemistry; able to know how mRNA encodes for the protein

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.

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

Identify the stop codons:

UAA UGA UAG

Identify the start/ initiation codon:

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

codons that specify the same amino acid are called:

Synonyms

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.

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.

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

Anticodon

``` 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 ```

Translation

5 Steps of Translation Process: | addition of specific amino acids to the 3’-OH group of tRNA.

Activation of tRNA

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)

Initiation of protein synthesis

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.

Elongation

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

Termination

5 Steps of Translation Process: | gives the protein the final form it needs to be fully functional

Post-translational processing

NUCLEIC ACIDS Flashcards

(74 cards)