Nucleic Acids Flashcards
Nucleic acids are found in
nucleus and are acidic in nature
True or false: a nucleic acid is a monomer
False
The monomer units of a nucleic acid are
nucleotides
What are the two types of nucleic acids?
DNA: Deoxyribonucleic Acid and RNA: Ribonucleic Acid
DNA :
Found
Function
Transportation
Found within cell nucleus
– Storage and transfer of genetic information
– Passed from one cell to other during cell division
RNA:
Occurs where
Primary function
Occurs in all parts of cell
– Primary function is to synthesize the proteins
*The components of a nucleotide
– Pentose Sugar - Monosaccharide – Phosphate Group (PO43-)
– Heterocyclic Base
Pentose Sugars – Ribose (RNA) vs. 2-Deoxyribose (DNA)
Ribose is present in RNA and 2-deoxyribose is present in DNA
• Structural difference:
– a —OH group present on carbon 2’ in ribose – a —H atom in 2-deoxyribose
• RNA and DNA differ in the identity of the sugar unit in their nucleotides.
Nitrogen-Containing Heterocyclic Bases
Bases
Pyrimidine derivatives
Purine derivatives
There are a total five bases (four of them in most of DNA and RNAs)
• Three pyrimidine derivatives - thymine (T), cytosine (C), and uracil (U)
• Two purine derivatives - adenine (A) and guanine (G)
• Adenine (A), guanine (G), and cytosine (C) are found in both DNA and RNA.
• Uracil (U): found only in RNA
• Thymine (T) found only in DNA.
Phosphate
Phosphate - third component of a nucleotide is derived from phosphoric acid (H3PO4)
• Under cellular pH conditions, the phosphoric acid is fully dissociated to give a hydrogen phosphate ion (HPO42-)
*Nucleotide Formation
The formation of a nucleotide from sugar, base, and phosphate can be visualized as a 2-step process
*The pentose sugar and nitrogenous base react to form a
Nucleoside
*The Nucleoside reacts with a phosphate group to form a
Nucleotide
*Nucleoside
A compound formed from a five-carbon monosaccharide and a purimone or pyrimidine base derivative. – The N9 of a purine or N1 of a pyrimidine base is attached to C- 1’ position of sugar (Beta-confirmation) – N-glycosidic linkage
– It is a condensation reaction (H2O released)
*There are 8 nucleosides associated with nucleic acid chemistry.
– Four ribonucleosides– RNA
– Four deoxyribonucleosides – DNA
*Nomenclature of nucleoside formation
– For pyrimidine bases – suffix -idine is used (cytidine, thymidine, uridine)
– For Purine bases – suffix -osine is used (adenosine, guanosine)
– Prefix “-deoxy” is used to indicate deoxyribose present (example: deoxythymidine)
*Nucleotide Formation
Addition of a phosphate group to a nucleoside
– Attached to C5” position through a phosphate-ester bond
– Condensationreaction(H2Oreleased)
– Named by appending 5’-monophosphate to nucleoside name
*Adenine DNA : Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: A
Nucleoside: Deoxyadenosine
Nucleotide: Deoxyadenosine 5’ monophosphate
Abbreviation: dAMP
*Guanine DNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: G
Nucleoside: Deoxyguanosine
Nucleotide : Deoxyguanosine 5’ monophosphate
Abbreviation: dGMP
*Cytosine DNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: C
Nucleoside: Deoxycytidine
Nucleotide: Deoxycytidine 5’ Monophosphate
Abbreviation: dCMP
*Thymine DNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: T
Nucleoside: deoxythymidine
Nucleotide: Deoxythymidine 5’ Monophosphate
Abbreviation: dTMP
*Adenine RNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: A
Nucleoside: Adenosine
Nucleotide: Adenosine 5’ Monophosphate
Abbreviation: AMP
*Guanine RNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: G
Nucleoside: Guanosine
Nucleotide: Guanosine 5’ Monophosphate
Abbreviation: GMP
*Cytosine RNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: C
Nucleoside: Cytidine
Nucleotide : Cytidine 5’ Monophosphate
Abbreviation : CMP
*Uracil RNA: Abbreviation Nucleoside Nucleotide Abbreviation
Abbreviation: U
Nucleoside: Uridine
Nucleotide: Uridine 5’ Monophosphate
Abbreviation: UMP
Sugar-phosphate groups are referred to as
nucleic acid backbone - Found in all nucleic acids
True or false: Sugars are different in DNA and RNA
True
ribonucleic acid (RNA)
a nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil
deoxyribonucleic acid (DNA)
a nucleotide polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine.
Primary Structure
Structure: Sequence of nucleotides in DNA or RNA
• Primary structure is due to changes in the bases
• Phosphodiester bond between 3’ and 5’ position
• 5’ end has free phosphate and 3’ end has a free OH group
• Sequence of bases read from 5’ to 3’
Comparison of the General Primary Structures of Nucleic Acids and Proteins
Backbone: -Phosphate-Sugar- Nucleic acids
• Backbone: -Peptide bonds - Proteins
the DNA Double Helix
Nucleic acids have secondary and tertiary structure
• The secondary structure involves two polynucleotide chains coiled around each other in a helical fashion
• The two polynucleotides run anti-parallel (opposite directions) to each other, i.e., 5’ - 3’ and 3’ - 5’
• The bases are located at the center and hydrogen bonded (A=T and GΞC) – # of H-bonds
• Base composition: %A = %T and %C = %G)
– Example: Human DNA contains 30% adenine, 30% thymine, 20% guanine and 20% cytosine
DNA Sequence:
the sequence of bases on one polynucleotide is complementary to the other polynucleotide
*true or false: Complementary bases are pairs of bases in a nucleic acid structure that can cavalently-bond to each other.
false - HYDROGEN BOND
*True or false: Complementary DNA strands are strands of DNA in a double helix with base pairing such that each base is located opposite to its complementary base
true
*Create a complimentary strand for:
5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’
Complementary strand of this sequence will be: 3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’
*A pyrimidine is always paired with a
purine
*true or false: A-T and G-C are called complementary bases
true
*Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below:
5’ A–A–T–G–C–A–G–C–T 3’
3’ T–T–A–C–G–T–C–G–A 5’
Replication:
Process by which DNA molecules produce exact duplicates of themselves, Old strands act as templates for the synthesis of new strands
DNA polymerase
checks the correct base pairing and catalyzes the formation of phosphodiester linkages
Replication:
true or false: The newly synthesized DNA has one new DNA strand and one old DNA strand
True
true or false:
DNA polymerase enzyme can only function in the 5’-to-3’ direction
true
true or false: The lagging strand grows in segments (Okazaki fragments) in the opposite direction
true
DNA ligase
connects the segments in replication
true or false: DNA replication one occurs in one site within a molecule (origin of replication)
false - occurs in many
true or false:
Multiple-site replication enables rapid DNA synthesis
true
Key Enzymes in Replication
DNA Helicase, Ligase and Polymerase
Upon DNA replication the large DNA molecules interacts with histone proteins to fold long DNA molecules.
true
The histone–DNA complexes are called chromosomes:
– A chromosome is about 15% by mass DNA and 85% by mass protein.
– Cells of different kinds of organisms have different numbers of chromosomes.
– Example: Number of chromosomes in a human cell 46, a mosquito 6, a frog 26, a dog 78, and a turkey 82
True or false: Chromosomes occur in unmatched (homologous) pairs.
false- they are matched
*Human chromosomes are present in…
the nucleus
Differences Between RNA and DNA Molecules:
The sugar unit in the backbone of RNA is ribose; it is deoxyribose in DNA.
• The base thymine found in DNA is replaced by uracil in RNA
• RNA is a single-stranded molecule; DNA is double- stranded (double helix)
• RNA molecules are much smaller than DNA molecules, ranging from 75 nucleotides to a few thousand nucleotides
Protein Synthesis
Protein synthesis involves RNA but is directly under the direction of DNA
• Proteins are responsible for the formation of skin, hair, enzymes, receptors, hormones, etc
Protein synthesis can be divided into…
transcription and translation
Transcription
A process by which DNA directs the synthesis of mRNA molecules
Translation
a process in which mRNA is deciphered to synthesize a protein molecule
Overview (drawing) of protein synthesis
DNA–> Transcription–> RNA–> Translation–> Protein
Heterogeneous nuclear RNA (hnRNA)
Formed directly by DNA transcription.
Post-transcription processing converts the hnRNA to
messenger RNA (mRNA)
Messenger RNA
Carries instructions for protein synthesis (genetic information) from DNA
– The molecular mass of mRNA varies with the length of the protein
Small nuclear RNA (snRNA):
Facilitates the conversion of hnRNA to mRNA.
– Contains from 100 to 200 nucleotides
Ribosomal RNA (rRNA):
Combines with specific proteins to form ribosomes - the physical site for protein synthesis
Ribosomes have molecular masses on the order of 3 million
Transfer RNA (tRNA):
Delivers amino acids to the sites for protein synthesis
– tRNAs are the smallest RNAs (75–90 nucleotide units)
Transcription:
A process by which DNA directs the synthesis of mRNA molecules
Two steps of transcription
Two-step process - (1) synthesis of hnRNA and (2) editing to yield mRNA molecule
*Gene:
A segment of a DNA base sequence responsible for the production of a specific hnRNA/mRNA molecule
– Most human genes are ~1000–3500 nucleotide units long
*Genome
All of the genetic material (the total DNA) contained in the chromosomes of an organism
– Human genome contains approximately 20,000 genes (as of 2014) : http://arxiv.org/abs/1312.7111
Steps in the Transcription Process(long)
Unwinding of DNA double helix to expose some bases (a gene):
– The unwinding process is governed by RNA polymerase
• Alignment of free ribonucleotides along the exposed DNA strand (template) forming new base pairs
• RNA polymerase catalyzes the linkage of ribonucleotides one by one to form mRNA molecule
• Transcription ends when the RNA polymerase enzyme encounters a stop signal on the DNA template:
– The newly formed RNA molecule and the RNA polymerase enzyme are released
Post-Transcription Processing: Formation of mRNA
nvolves conversion of hnRNA to mRNA
*Splicing
Excision of introns and joining of exons
*Exon
a gene segment that codes for genetic information
*Intron
a DNA segments that interrupt a genetic message
*The splicing process is driven by
snRNA
*Alternative splicing
A process that ultimately leads to the formation of several different protein variants from a single gene
– The process involves excision of one or more exons from hnRNA during splicing process.
– The process occurs in a splicesome (a complex protein-nucleic acid molecular structure responsible for splicing hnRNA)
Transcriptome
All of the mRNA molecules that can be generated from the genetic material in a genome.
– Transcriptome is different from a genome
– Responsible for the biochemical complexity created by splice variants obtained by hnRNA.
Proteome
All of the protein molecules generated from mRNAs
true or false: The base sequence in a mRNA determines the amino acid sequence for the protein synthesized
true
The base sequence of an mRNA molecule involves only 4 different bases -
A, G, C, U
*Codon
A three-nucleotide sequence in an mRNA molecule that codes for a specific amino acid
– Based on all possible combination of bases A, G, C, U there are 64 possible codes
Genetic code:
The assignment of the 64 mRNA codons to specific amino acids (or stop signals)
– 3 of the 64 codons are termination codons (“stop” signals)
Characteristics of Genetic Code
The genetic code is highly degenerate:
– Many amino acids are designated by more than one codon.
– Arg, Leu, and Ser - represented by six codons.
– Most other amino acids - represented by two codons
– Met and Trp - have only a single codon.
– Codons that specify the same amino acid are called synonyms
There is a pattern to the arrangement of synonyms in the genetic code table.
– All synonyms for an amino acid fall within a single box in unless there are more than four synonyms
– The significance of the “single box” pattern - the first two bases are the same
– For example, the four synonyms for Proline - CCU, CCC, CCA, and CCG.
The genetic code is almost universal:
– With minor exceptions the code is the same in all organisms
– The same codon specifies the same amino acid whether the cell is a bacterial cell, a corn plant cell, or a human cell.
An initiation codon exists:
– The existence of “stop” codons (UAG, UAA, and UGA)
suggests the existence of “start” codons.
*The codon
coding for the amino acid methionine (AUG) functions as initiation or “start” codon.
During protein synthesis amino acids directly interact with the codons of an mRNA molecule.
False
two important features of the tRNA structure
– 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.
*Anticodon -
a three-nucleotide sequence on a tRNA molecule that is complementary to a codon on an mRNA molecule.
true or false: tRNA and its anticodon bind to the enzyme aminoacyl-tRNA synthetase to give proper placement of an amino acid on a protein
true
Translation
a process in which mRNA codons are deciphered to synthesize a protein molecule
Ribosome
an rRNA–protein complex - serves as the site of protein synthesis:
– Contains 4 rRNA molecules and ~80 proteins - packed into two rRNA-protein subunits (one small and one large)
– ~65% rRNA and 35% protein by mass
– A ribosome’s active site – Large subunit
– The mRNA binds to the small subunit of the ribosome.
Activation of tRNA:
addition of specific amino acids to the 3’-OH group of tRNA.
Initiation of protein synthesis:
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)
Elongation
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. Peptidyl transferase links the A site and P site amino acids via a peptide bond.
Termination:
The polypeptide continues to grow via translocation until all necessary amino acids are in place and bonded to each other. The process stops when a stop codon is encountered.
Post-translational processing:
Gives the protein the final form it needs to be fully functional
Polysome (polyribosome):
The complex of a mRNA and several ribosomes
Mutation
An error in base sequence reproduced during DNA replication
• Errors in genetic information is passed on during transcription.
• The altered information can cause changes in amino acid sequence during protein synthesis and thereby alter protein function
External Mutagens
Mutations are caused by mutagens
• A mutagen is a substance or agent that causes a change in the structure of a gene:
– Radiation and chemical agents are two important types of mutagens
– Ultraviolet, X-ray, radioactivity and cosmic radiation are mutagenic –cause cancers
– Chemical agents can also have mutagenic effects
*Viruses
Tiny disease causing agents with outer protein envelope and inner nucleic acid core
• They can not reproduce outside their host cells (living organisms)
• Invade their host cells to reproduce and in the process disrupt the
normal cell’s operation
• Virus invade bacteria, plants animals, and humans
*Zika Virus
Known to cause microcephaly in children born to mothers infected with Zika
Transduction
Use of viral vectors to deliver genes to cells – Used in the lab: Genetically modified animals used in
research
Gene therapy
Hope to cure genetic diseases in patients
Ex: Gene therapy techniques being developed to treat Hemophila A. Insert gene for factor VIII synthesis
*Vaccines
riginally discovered by Jenner in 1798: Inactive virus or bacterial envelope (injection or oral dose)
• Antibodies produced against inactive viral or bacterial envelopes will kill the active bacteria and viruses
• Types: Influenza; Measles, Mumps, Rubella (MMR), Polio, Smallpox, Tetanus, Hepatitis B, Human Papilloma Virus (HPV), etc.
• Vaccines – When used by everyone; wiped out several serious diseases such as polio
*Vaccines now
Resurgence in some diseases – decreased use of vaccines due to fear of side effects.
– Vaccines work most effectively when most of the population receive them
– Ex: Autism: No credible science to connect Autism with vaccines or the preservatives in vaccines.
Recombinant DNA:
DNA molecules that have been synthesized by splicing a sequence of segment DNA (usually a gene) from one organism to the DNA of another organism.
*Genetic Engineering (Biotechnology):
A process in which an organism is intentionally changed at the molecular (DNA) level so that it exhibits different traits
*Recombinant DNA and Genetic Engineering
Applications
First genetically engineered organisms are bacteria (1973) and mice (1974)
• Insulin producing bacteria - commercialized in 1982.
– Bacteria act as protein factories
– Genetically modified (transgenic) animals used in drug development: Ex: knockout mice.
*Many plants have now been genetically engineered
– Disease resistance – increased crop yield
– Drought resistance – consumption of less water
– Predator resistance – less insecticide use
– Frost resistance – resist changes in temps below freezing.
– Deterioration resistance – long shelf-life.
Transgenic Animals: Knock-out mice
Used to study importance of a gene in vivo.
recombinant DNA Production using a Bacterial Plasmid
Dissolution of cells:
– E. coli cells of a specific strain containing the plasmid of interest are treated with chemicals to dissolve their membranes and release the cellular contents
• Isolation of plasmid fraction:
– The cellular contents are fractionated to obtain plasmids
• Cleavage of plasmid DNA:
– Restriction enzymes are used to cleave the double-stranded DNA
• Gene removal from another organism:
– Using the same restriction enzyme the gene of interest is removed from a chromosome of another organism
• Gene–plasmid splicing:
– The gene (from Step 4) and the opened plasmid (from Step 3) are mixed in the presence of the enzyme DNA ligase to splice them together.
• Uptake of recombinant DNA:
– The recombinant DNA prepared in step 5 are transferred to a live E. coli culture where they can be replicated, transcribed and translated.
Transformed cell can reproduce a large number of identical cells:
clones
true or false: Clones are the cells that have descended from a single cell and have identical DNA
true
true or false: Bacteria grows very slow
FALSE
Can accelerate process using PCR – Polymerase Chain Reaction
true
*The polymerase chain reaction (PCR):
A method for rapidly producing multiple copies of a DNA nucleotide sequence (gene).
• This method allows to produce billions of copies of a specific gene in a few hours.
*PCR is very easy to carryout and the requirements are:
– Source of gene to be copied
– Thermostable DNA polymerase
– Deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP)
– A set of two oligonucleotides with complementary sequence to the gene (primers)
– Thermostable plastic container and source of heat
– Used in biomedical research, manufacturing, forensics, etc.
