Biology

Ch.4.2

Nucleic Acids

Concepts/Ideas/Facts:

1. The nucleic acids of DNA and RNA store all the hereditary information cells need to reproduce themselves.
2. the degree of accuracy of DNA replication is on the order of one error per billion nucleotides.
3. It is the specificity of base-pair linkages that underlies the mechanism of DNA replication
4. amino acid coding is universal, every organism uses essentially the same genetic code.

Definitions:

1. Nucleic Acids – are linear, unbranched polymers of nucleotide, important complex organic molecules that store important information in the cell. 
1. DNA (deoxyribonucleic acid) – contains all the information that is essential for almost all cell activities, including cell division.  It consists of two long strands, each of which is a chain of nucleotide monomers
2. RNA (ribonucleic acid) – stores and transfers information essential for protein synthesis.
2. Nucleotides – molecular group having one sugar, at lest one phosphate group, and one nitrogen-containing base.  Both sugars have a 5-carbon ring structure (pentose).  Nucleotides are the repeating subunits in DNA and RNA.  Nucleotides consist of three parts:

     A.   Pentose – a five-carbon sugar

1. Deoxyribose – in DNA, it has a hydrogen atom attached to its #2 carbon atom(designated’2)
2. Ribose – in RNA, it has a hydroxyl group attached to its #2 carbon

            B.   Base – A nitrogen-containing ring structure which is attached to the 1” carbon atom of the pentose.  There are four bases.

1. In DNA – two purines, adenine (A) and guanine (G)
2. In DNA – two pyrimidines, thymine (T) and Cytosine (C)
3. In RNA – same two purines, adenine (A) and guanine (G)
4. In RNA – uses the pyrimidine cytosine (C), but instead of thymine, it uses the pyrimidine uracil (U)
5. In DNA, adenine always bonds with thymine, cytosine always bonds with guanine
6. Uracil takes the place of thymine in RNA and always bonds with adenine

3. Deoxyrinucleotides – deoxyribose nucleotides that are monomers of DNA
4. Ribonucleotides – Ribose-containing nucleotides that are monomers of RNA
5. Purines – organic molecules which have a double ring of carbon and nitrogen atoms
6. Pyrimidines – organic molecules which have a single ring of carbon and nitrogen atoms
7. Double Helix – the spiral ladder-like structure of DNA, which has a right-handed twist, with a full turn consisting of ten base pairs.
8. Replication – process of the duplication of DNA which begins when the enzyme DNA  helicase attaches to a DNA molecule, moves along the molecule, and “unzips” the complimentary strands of DNA.  Helicase breaks the hydrogen bonds between the nitrogen bases.
9. DNA Helicase – enzyme that breaks the hydrogen bonds between the nitrogen bases which begins the process of DNA replication.
10. DNA Polymerases – enzymes that synthesize new strands of DNA
11. Gene – a segment of a DNA molecule (ranging from fewer than 1 thousand bases to several million), located in a particular position on a specific chromosome, whose base sequence contains the information necessary for protein synthesis.
12. Genome – is an organism’s complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome.
13. Genetic Code – a series of codons that specify which amino acids are required to make up specific proteins.
14. Codon – a specific group of three sequential nitrogen bases of a mRNA molecule.  Each codon attracts a group of bases on tRNA, and each tRNA has a specific amino acid attached to it.
15. Transcription – the process in which RNA is made from DNA
16. Protein Synthesis – the formation of proteins using information coded on DNA and carried out by RNA.  The assembly of amino acids into specific proteins is the task accomplished during protein synthesis.
17. Protein – consisting of the elements C, H, O, and N, proteins are made up of one or more polymers called polypeptides, each of which consists of a specific sequence of amino acids linked together by peptide bonds.  Functional and structural characteristics of a protein are determined by its amino acid sequence.
18. Genetic Code – system that contains information needed by cells for proper functioning, which is built into the arrangement of the nitrogen bases in a particular sequence of DNA.
19. Translation – process of assembling protein molecules from information encoded in mRNA.  Translation begins when mRNA moves out of the nucleus by passing through the nuclear pores.  It then migrates to a group of ribosomes, where the actual synthesis of protein occurs.  Amino acids floating in the cytoplasm are transported to the ribosomes by tRNA.  The assembly of a polypeptide begins when a ribosome attaches at an AUG codon on the mRNA.  Basically translation involves the transfer of information from one language (nucleotides) to another (amino acids).
20. Stop Codon – brings the translation process to an end and the mRNA is releases completing the polypeptide.
21. Origin of Replication – specific nucleotide where DNA replication begins
22. DNA Replication Forks – localized areas of DNA replication that appear as Y-shaped structures
23. Leading Strand – first strand to form after DNA  “unzips” and is sequentially continuous.
24. Lagging Strand – second strand to form at a slower rate after DNA “unzips” and is discontinuous.
25. Okazaki Fragments – the short DNA fragments that synthesize on the lagging strand of DNA
26. DNA Ligase – enzyme that join Okazaki fragments to the growing DNA strand
27. Topoisomerases – enzymes that prevent DNA tangling during replication.
28. RNA primase – enzyme that synthesizes RNA primer which initiates the beginning of a new DNA strand

Process of DNA Replication: DNA replication occurs simultaneously at many points on the molecule and individual segments are joined to each other as the process proceeds.  Each strand of the double helix serves as a template for the synthesis of a new strand, the nucleotide sequence of which is strictly determined. Replication thus produces twin daughter helices, each an exact replica of its sole parent.

1. begins when the DNA enzyme helicase attaches to a DNA molecule, moves along the molecule, and “unzips” the complimentary strands of DNA.  Helicase breaks the hydrogen bonds between the nitrogen bases.
2. separated unpaired DNA strands now react with complimentary bases of nucleotides that are floating in the nucleus.
3. new hydrogen bonds form between the free floating bases and the unpaired DNA strands
4. DNA polymerase enzyme now catalyzes the formation of the sugar-to-phosphorous bonds that connect one nucleotide to the next one.  Two new DNA molecules are created, which consists of one “old” DNA separated strand and one “new” strand of DNA.  The sequence of nucleotides in each new strand exactly matches that in the original molecule.

Ribonucleic Acid (RNA) and Protein Synthesis

1. Messenger RNA (mRNA) – single, uncoiled strand that transmits information from DNA for use during protein synthesis.  After DNA is transcribed into the mRNA within the nucleus, it exits the nucleus through the nuclear pores and within the cytoplasm delivers the coded genetic message to ribosomal RNA (rRNA).   mRNA carries the genetic message from the nucleus to the ribosomes, where protein synthesis takes place.  In prokaryotic cells, most proteins are encoded by a continuous segment of DNA from which a functional mRNA molecule is copied.  In eukaryotic cells there is a gene coding sequence, called exons, interrupted by non-coding sequences, called introns
2. Ribosomal (rRNA) – globular form of RNA, is the major constituent of ribosomes.   rRNA reads the delivered code from the mRNA and translates it into the appropriate amino acid sequence for the designated protein being synthesized.  .
3. Transfer RNA (tRNA) – single strand of RNA folded back on itself in hairpin fashion, allowing complimentary bases to pair.  tRNA exists in 20 or more varieties, each with the ability to bond to only specific type of amino acids.  tRNA transfers the appropriate amino acids within the cytoplasm to their designated site in the protein under construction.  It puts the amino acids in their proper places next to one another.  tRNA translates mRNA into the language of proteins.  The tRNA chain always terminates in a CCA sequence (codon).
4. RNA Polymerases – enzymes that transcribe RNA synthesis
5. Uracil – the amino acid  which replaces thymine in RNA transcription
6. Promoters – specific nucleotide sequences of DNA act as start signals for RNA transcription
7. Terminators – specific nucleotide sequences of DNA that stop RNA transcription.
8. Introns – segments of DNA of a eukaryote gene, which are transcribed into mRNA and then are excised from the RNA, leaving behind exons to be translated into proteins.
9. Exons – segments of DNA of a eukaryote gene, which are transcribed into mRNA and then into proteins
10. Primary Transcription – the entire copied gene in RNA transcription with both intron and exon sequences
11. RNA Splicing – the removal of introns by special RNA processing enzymes and the splicing of the remaining exons together before the molecule leaves the nucleus.
12. Anticodons- bind the codon of a mRNA to the anticodon of tRNA.  Anticodons serve to “plug in” the tRNA molecule to an mRNA codon.  It is basically the opposite (complimentary) amino acids.
13. Aminoacyl-tRNA synthetases – enzyme that attaches tRNA molecules to a particular amino acid.
14. Ribosomal RNA (rRNA) – the RNA that manipulates protein synthesis and is associated with ribosomes.
15. Ribosomes – large protein-synthesizing machines on which tRNA molecules position themselves in precise relationship to mRNA molecules so as to read accurately the genetic message encoded in the mRNA.   Two sites involved in protein synthesis:

1. A site (aminoacyl site) – the binding site for incoming tRNA, with its amino acid
2. P site (peptidyl site) – site to which the growing polypeptide chain is attached.  The   enzyme peptidyl transferase forges the peptide bond between the first amino acid and the second amino acid.

16. Polyribosome or Polysome – a group of ribosomes translating the same mRNA molecule

RNA Transcription: synthesis of RNA along an “unzipped” DNA strand which during transcription the genetic code of DNA becomes inherent in the sequence of bases in RNA.

1. RNA polymerase first binds to a DNA molecule causing the separation of the complimentary strand of DNA.
2. enzyme directs the formation of hydrogen bonds between basses of a DNA strand an complimentary bases of RNA nucleotides that are floating in the nucleus.
3. RNAS polymerase then moves along the section of DNA, establishing the sugar-to-phosphorous bonds between the RNA nucleotides similar to the way DNA replicates
4. when RNA polymerase reaches the sequence of bases on the DNA that acts as a termination signal, the enzyme triggers the release of the newly made RNA

Three differences between RNA and DNA:

1. RNA molecule consists of a single strand of nucleotides, DNA as double strand.
2. RNA has a ribose as its five-carbon sugar, DNA has deoxiribose.
3. RNA has the nitrogen base uracil instead of thymine.

Stages in Translation:

1. Initiation – begins when smaller ribosomal units attach to a strand of mRNA exposing its first codon, the initiation codon.  The first tRNA then pairs with the initiation codon of the mRNA in an anti-parallel fashion.
2. Initiation Codon – where translation begins
3. Initiation Complex – combination of the small ribosomal subunit, mRNA, and the initiator tRNA.
4. Elongation – period of the growth of the polypeptide chain as amino acids are added to the chain
5. Chain Termination – the encountering of a stop codon on mRNA which terminates the translation of a polypeptide.  Once a stop codon is encountered, no tRNA recognizes these codons, so translation ceases.  At this point a release factor from the cytoplasm binds to the stop codon and translation is complete.  

Enzyme Biosynthesis Regulation:

1. Operon – consists of a promoter, one or more structural genes, and an operator
2. Structural Genes – genes that code for proteins, often enzymes that work sequentially in a particular reaction pathway.
3. Operator – sequence of nucleotides located between the promoter and the structural genes.  It may overlap the promoter, and /or the structural gene(s).  It is the site at which a repressor protein can bind.
4. Regulator – located anywhere on the bacterial chromosome, it codes for a protein called the repressor, which binds to the operator, obstructing the promoter.  No mRNA transcription can occur if this occurs.
5. Effector – depending on the operon, an effector can either activate or inactivate the repressor for that particular operon.
6. Repressor – protein that precedes the operator, that binds to the operator and obstructs (inhibits) the promoter.  It is the binding site for RNA polymerase.

“Central Dogma” of Genetics:

Gene à mRNA àproteins

                    or

Gene à primary transcription à mRNA à protein

Process by which non-coding sequences of base pairs (introns) are subtracted from the coding sequences (exons) of a gene in order to transcribe DNA into messenger RNA (mRNA.)

In chromosomes, DNA acts as a template for the synthesis of RNA in a process called transcription. In most mammalian cells, only 1% of the DNA sequence is copied into a functional RNA (mRNA). Only one part of the DNA is transcribed to produce nuclear RNA, and only a minor portion of the nuclear RNA survives the RNA processing steps.

One of the most important stages in RNA processing is RNA splicing. In many genes, the DNA sequence coding for proteins, or "exons", may be interrupted by stretches of non-coding DNA, called "introns". In the cell nucleus, the DNA that includes all the exons and introns of the gene is first transcribed into a complementary RNA copy called "nuclear RNA," or nRNA. In a second step, introns are removed from nRNA by a process called RNA splicing. The edited sequence is called "messenger RNA," or mRNA.

The mRNA leaves the nucleus and travels to the cytoplasm, where it encounters cellular bodies called ribosomes. The mRNA, which carries the gene's instructions, dictates the production of proteins by the ribosomes.

http://www.johnkyrk.com/DNAtranscription.html

The majority of genes are expressed as the proteins they encode. The process occurs in two steps:

• Transcription = DNA → RNA
• Translation = RNA → protein

Taken together, they make up the "central dogma" of biology: DNA → RNA → protein.

The majority of genes are expressed as the proteins they encode. The process occurs in two steps:

• Transcription = DNA → RNA
• Translation = RNA → protein

Taken together, they make up the "central dogma" of biology: DNA → RNA → protein.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html