RNA Types and Structure

General Features of RNA

Structure

Ribonucleic acid (RNA) is a single-stranded polymer of nucleotides Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. Nucleic Acids that are linked through 3’–5’ phosphodiester bonds.

Nucleotides Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. Nucleic Acids are the basic unit of any nucleic acid. The nucleotides Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. Nucleic Acids in RNA are formed by the following parts:

1. Ribose Ribose A pentose active in biological systems usually in its d-form. Nucleic Acids (sugar): Carbon 2’ is bonded to hydroxyl (OH). 
   Note: In deoxyribonucleic acid Deoxyribonucleic acid A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure ( DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure), the word deoxyribose Deoxyribose Nucleic Acids means that there is no oxygen (O) attached to carbon 2’.
2. Phosphate group Phosphate group Nucleic Acids: bonded to the carbon 5’ of ribose Ribose A pentose active in biological systems usually in its d-form. Nucleic Acids; links to the OH of the carbon 3’ of the next nucleotide, forming a phosphodiester bond Phosphodiester bond DNA Types and Structure
3. Nitrogenous base: bonded to the carbon 1’ of ribose Ribose A pentose active in biological systems usually in its d-form. Nucleic Acids
   • Purine bases Bases Usually a hydroxide of lithium, sodium, potassium, rubidium or cesium, but also the carbonates of these metals, ammonia, and the amines. Acid-Base Balance:
     • Adenine Adenine A purine base and a fundamental unit of adenine nucleotides. Nucleic Acids
     • Guanine Guanine Nucleic Acids
   • Pyrimidine bases Bases Usually a hydroxide of lithium, sodium, potassium, rubidium or cesium, but also the carbonates of these metals, ammonia, and the amines. Acid-Base Balance:
     • Cytosine Cytosine A pyrimidine base that is a fundamental unit of nucleic acids. Nucleic Acids
     • Uracil Uracil One of four nucleotide bases in the nucleic acid RNA. Nucleic Acids (Note: Uracil Uracil One of four nucleotide bases in the nucleic acid RNA. Nucleic Acids differs from DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure, which has thymine Thymine One of four constituent bases of DNA. Nucleic Acids.)

Nucleic acid components:

• Nucleobase: nitrogenous base ( adenine Adenine A purine base and a fundamental unit of adenine nucleotides. Nucleic Acids)
• Nucleoside: nitrogenous base + sugar ( adenosine Adenosine A nucleoside that is composed of adenine and d-ribose. Adenosine or adenosine derivatives play many important biological roles in addition to being components of DNA and RNA. Adenosine itself is a neurotransmitter. Class 5 Antiarrhythmic Drugs)
• Nucleotide: nitrogenous base + sugar + phosphate Phosphate Inorganic salts of phosphoric acid. Electrolytes ( adenosine Adenosine A nucleoside that is composed of adenine and d-ribose. Adenosine or adenosine derivatives play many important biological roles in addition to being components of DNA and RNA. Adenosine itself is a neurotransmitter. Class 5 Antiarrhythmic Drugs monophosphate)
• Nucleic acid: polymer of nucleotide (RNA)

Function

• Protein synthesis Synthesis Polymerase Chain Reaction (PCR) (messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA))
• Gene Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. Basic Terms of Genetics expression regulation (micro RNA (miRNA), small regulatory RNA (sRNA), small interfering RNA (siRNA))
• Processing of other RNAs (small nuclear RNA (snRNA), small nucleolar RNA (snoRNA))
• Catalysis or metabolic function (ribozymes)
• Genetic material in some viruses Viruses Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. Virology
• Genome Genome The complete genetic complement contained in the DNA of a set of chromosomes in a human. The length of the human genome is about 3 billion base pairs. Basic Terms of Genetics defense (siRNA ( RNA interference RNA Interference A gene silencing phenomenon whereby specific dsRNAs (double-stranded RNA) trigger the degradation of homologous mRNA (messenger RNA). The specific dsrnas are processed into small interfering RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the rna-induced silencing complex. DNA methylation may also be triggered during this process. Stages and Regulation of Translation), PIWI-interacting RNA (piRNA) in eukaryotes, CRISPR in prokaryotes)

Coding versus non-coding RNA

• Coding RNA (translated into protein) such as:
  • mRNA
  • RNA of the viral genome Viral genome The complete genetic complement contained in a DNA or RNA molecule in a virus. Virology
• Non-coding RNA (other roles in the cell) such as:
  • tRNA
  • rRNA
  • miRNA
  • snoRNA
  • snRNA

Messenger RNA (mRNA)

Structure

• Coding DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure sequence (CDS):
  • Broken into 3 base sequences known as codons (see mnemonic); correspond to specific amino acids Amino acids Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. Basics of Amino Acids
  • Begins with an initiation codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics (AUG)
  • Ends with a termination codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics (UGA, UAA, and UAG)
• Untranslated region (UTR) or non-coding sequences (see differences below):
  • 5’ cap
  • 3’ poly-A tail
  • Shine-Dalgarno sequence (in prokaryotes)

Mnemonic

To remember mRNA start codons, use the mnemonic AUG:

• InAUGurates protein synthesis Synthesis Polymerase Chain Reaction (PCR) 
• Are U Going

To remember mRNA stop codons, use the mnemonics UGA, UAA, and UAG:

• U Go Away
• U Are Away
• U Are Gone

Function

Messenger RNA (mRNA) serves as an amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids template for protein synthesis Synthesis Polymerase Chain Reaction (PCR).

• During transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription, mRNA has the following characteristics:
  • Complementary to the antisense or template strand (facilitated by the enzyme RNA polymerase)
  • Becomes a copy of the coding strand (sense strand)
• Messenger RNA is synthesized from the 5’ end to the 3’ end (because RNA polymerase can only add nucleotides Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. Nucleic Acids to the 3’ end of the mRNA chain).
• The initial transcript is known as heterogeneous nuclear RNA (hnRNA).
• Processed hnRNA, which has the addition of the 5’ cap and the 3’ poly-A tail followed by splicing, becomes mRNA.

Prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic versus eukaryotic Eukaryotic Eukaryotes can be single-celled or multicellular organisms and include plants, animals, fungi, and protozoa. Eukaryotic cells contain a well-organized nucleus contained by a membrane, along with other membrane-bound organelles. Cell Types: Eukaryotic versus Prokaryotic mRNA

Prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic mRNA

• Polycistronic: 
  • One mRNA = several polypeptides 
  • In bacteria Bacteria Bacteria are prokaryotic single-celled microorganisms that are metabolically active and divide by binary fission. Some of these organisms play a significant role in the pathogenesis of diseases. Bacteriology, clusters of related genes Genes A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. DNA Types and Structure or operons Operons In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic messenger RNA is under the control of an operator region. Regulation of Transcription are transcribed together in a single mRNA.
• The CDS is translated into proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis immediately after being synthesized (no post-transcriptional modifications Post-transcriptional Modifications Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein. Stages of Transcription).
• The 5’ UTR contains a Shine-Dalgarno sequence that helps recruit the ribosome to mRNA for protein synthesis Synthesis Polymerase Chain Reaction (PCR).

Eukaryotic Eukaryotic Eukaryotes can be single-celled or multicellular organisms and include plants, animals, fungi, and protozoa. Eukaryotic cells contain a well-organized nucleus contained by a membrane, along with other membrane-bound organelles. Cell Types: Eukaryotic versus Prokaryotic mRNA

• Monocistronic: 
  • One mRNA = single polypeptide 
  • One initiation and termination codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics producing one polypeptide chain
• Modified extensively before being translated into proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis:
  • Capping of 5’ end: linkage of 7-methylguanosine 
    • Aids AIDS Chronic HIV infection and depletion of CD4 cells eventually results in acquired immunodeficiency syndrome (AIDS), which can be diagnosed by the presence of certain opportunistic diseases called AIDS-defining conditions. These conditions include a wide spectrum of bacterial, viral, fungal, and parasitic infections as well as several malignancies and generalized conditions. HIV Infection and AIDS in recognition by the protein synthesis Synthesis Polymerase Chain Reaction (PCR) machinery 
    • Protects from degradation by exonucleases
  • The CDS undergoes modification or splicing of introns Introns Sequences of DNA in the genes that are located between the exons. They are transcribed along with the exons but are removed from the primary gene transcript by RNA splicing to leave mature RNA. Some introns code for separate genes. Post-transcriptional Modifications (RNA Processing) (non-coding segments).
  • Addition of the 3’ poly-A tail: chain of adenylate molecules (maintains the stability of mRNA as it exits the nucleus Nucleus Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (cell nucleolus). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the endoplasmic reticulum. A cell may contain more than one nucleus. The Cell: Organelles into the cytosol Cytosol A cell’s cytoskeleton is a network of intracellular protein fibers that provides structural support, anchors organelles, and aids intra- and extracellular movement. The Cell: Cytosol and Cytoskeleton)

There is a long-held belief that prokaryotes lack the 5’ cap. Recently, however, some bacteria Bacteria Bacteria are prokaryotic single-celled microorganisms that are metabolically active and divide by binary fission. Some of these organisms play a significant role in the pathogenesis of diseases. Bacteriology have been found to have a 5’ nicotinamide adenine dinucleotide Nicotinamide adenine dinucleotide A coenzyme composed of ribosylnicotinamide 5′-diphosphate coupled to adenosine 5′-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). Pentose Phosphate Pathway ( NAD NAD+ A coenzyme composed of ribosylnicotinamide 5′-diphosphate coupled to adenosine 5′-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). Pentose Phosphate Pathway) cap:

• Appears to protect bacterial RNA from degradation
• The 5’ NAD NAD+ A coenzyme composed of ribosylnicotinamide 5′-diphosphate coupled to adenosine 5′-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). Pentose Phosphate Pathway cap found in some eukaryotes actually promotes decay rather than provide protection.
• 5’ 7-methylguanosine cap of eukaryotes: added post- transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription
• 5’ NAD NAD+ A coenzyme composed of ribosylnicotinamide 5′-diphosphate coupled to adenosine 5′-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). Pentose Phosphate Pathway cap in prokaryotes and eukaryotes: added in initiation step of transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription

Transfer RNA (tRNA)

Structure

• Transfer RNA is a single polynucleotide made up of an average of 75 nucleotides Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. Nucleic Acids.
• Has modified bases Bases Usually a hydroxide of lithium, sodium, potassium, rubidium or cesium, but also the carbonates of these metals, ammonia, and the amines. Acid-Base Balance such as inosine, dihydrouridine, and pseudouridine
• The distinctive fold creates a 2-dimensional 2-Dimensional Imaging of the Heart and Great Vessels shape resembling a cloverleaf.
• The 3-dimensional or tertiary structure of tRNA is actually L shaped.
• Parts of tRNA consist of:
  • Acceptor stem:
    • Contains the 3’ CCA (cytosine-cytosine-adenine) sequence: 
      • Amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids attachment site 
      • Forms a covalent bond to a specific amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids via aminoacyl-tRNA synthetase
    • The acceptor stem also contains parts of the 5’ end of tRNA.
  • Anti-codon loop:
    • The 3-base sequence is complementary to the mRNA triplet code for the specific amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids.
  • D-arm (contains dihydrouridine) and T-arm (pseudouridine loop) or TΨC arm Arm The arm, or “upper arm” in common usage, is the region of the upper limb that extends from the shoulder to the elbow joint and connects inferiorly to the forearm through the cubital fossa. It is divided into 2 fascial compartments (anterior and posterior). Arm: Anatomy (thymidine-pseudouridine-cytidine):
    • The D-arm is believed to be a recognition site for aminoacyl-tRNA synthetase.
    • The T-arm aids AIDS Chronic HIV infection and depletion of CD4 cells eventually results in acquired immunodeficiency syndrome (AIDS), which can be diagnosed by the presence of certain opportunistic diseases called AIDS-defining conditions. These conditions include a wide spectrum of bacterial, viral, fungal, and parasitic infections as well as several malignancies and generalized conditions. HIV Infection and AIDS in ribosome attachment.
  • Variable Variable Variables represent information about something that can change. The design of the measurement scales, or of the methods for obtaining information, will determine the data gathered and the characteristics of that data. As a result, a variable can be qualitative or quantitative, and may be further classified into subgroups. Types of Variables loop:
    • May or may not be present; allows for further classification of tRNA

Function

Transfer RNA transports amino acids Amino acids Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. Basics of Amino Acids to ribosomes Ribosomes Multicomponent ribonucleoprotein structures found in the cytoplasm of all cells, and in mitochondria, and plastids. They function in protein biosynthesis via genetic translation. The Cell: Organelles for assembly Assembly The assembly of viral structural proteins and nucleic acid (viral DNA or viral RNA) to form a virus particle. Virology into proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis. This process is carried out by these 2 main actions:

• Chemically links to a specific amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids:
  • Specificity is due to the enzyme aminoacyl-tRNA synthetase: 
    • Each enzyme recognizes only one amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids and the corresponding tRNA.
    • 20 aminoacyl-tRNA synthetase enzymes Enzymes Enzymes are complex protein biocatalysts that accelerate chemical reactions without being consumed by them. Due to the body’s constant metabolic needs, the absence of enzymes would make life unsustainable, as reactions would occur too slowly without these molecules. Basics of Enzymes correspond to each of the 20 amino acids Amino acids Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. Basics of Amino Acids.
    • Uncharged tRNA: no amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids attached
    • Charged tRNA: amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids attached
  • Aminoacyl-tRNA synthetase links the amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids to the 3’ terminal of the tRNA acceptor stem. 
• Forms base pairs with the codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics in the mRNA:
  • Via tRNA anti-codon loop
  • Determines the amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids to carry to the ribosome for protein assembly Assembly The assembly of viral structural proteins and nucleic acid (viral DNA or viral RNA) to form a virus particle. Virology
  • One tRNA carries one specific amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids but one tRNA can read more than one codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics.
  • More than one codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics can code for one amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids ( codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics degeneracy):
    • Example: 1 tRNA = 1 amino acid Amino acid Amino acids (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). Basics of Amino Acids (Phe) = different codons, but the same first 2 bases Bases Usually a hydroxide of lithium, sodium, potassium, rubidium or cesium, but also the carbonates of these metals, ammonia, and the amines. Acid-Base Balance: UUU, UUC
  • The first 2 codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics bases Bases Usually a hydroxide of lithium, sodium, potassium, rubidium or cesium, but also the carbonates of these metals, ammonia, and the amines. Acid-Base Balance: main determining bases Bases Usually a hydroxide of lithium, sodium, potassium, rubidium or cesium, but also the carbonates of these metals, ammonia, and the amines. Acid-Base Balance for amino acids Amino acids Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. Basics of Amino Acids
  • Between the 3rd codon Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal. Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons. Basic Terms of Genetics base and the complementary 1st anti-codon base of the tRNA, more than one base pair is possible: 
    • Can follow atypical base-pairing (wobbling)
    • Example: Inosine (I), a modified base found in tRNA, pairs with the uracil Uracil One of four nucleotide bases in the nucleic acid RNA. Nucleic Acids (U), adenine Adenine A purine base and a fundamental unit of adenine nucleotides. Nucleic Acids (A), and cytosine Cytosine A pyrimidine base that is a fundamental unit of nucleic acids. Nucleic Acids (C).

Ribosomal RNA (rRNA)

Structure

Ribosomes consist of 2 subunits of unequally sized rRNA, and the sizes are measured in terms of an “S” value (Svedberg or sedimentation unit):

• Based on a measure of sedimentation velocity in a centrifuge (higher “S” value = faster sedimentation = greater mass)
• Therefore, “S” values are not additive.
• Prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic ribosomes Ribosomes Multicomponent ribonucleoprotein structures found in the cytoplasm of all cells, and in mitochondria, and plastids. They function in protein biosynthesis via genetic translation. The Cell: Organelles: 70S consisting of 50S (large subunit) and 30S (small subunit)
• Eukaryotic Eukaryotic Eukaryotes can be single-celled or multicellular organisms and include plants, animals, fungi, and protozoa. Eukaryotic cells contain a well-organized nucleus contained by a membrane, along with other membrane-bound organelles. Cell Types: Eukaryotic versus Prokaryotic ribosomes Ribosomes Multicomponent ribonucleoprotein structures found in the cytoplasm of all cells, and in mitochondria, and plastids. They function in protein biosynthesis via genetic translation. The Cell: Organelles: 80S consisting of 60S (large subunit)  and 40S (small subunit)
• Has 3 functionally distinct tRNA binding sites:
  • Amino acyl (A) site (accepts incoming aminoacyl tRNA)
  • Peptidyl (P) site (for the peptidyl tRNA to which the growing peptide chain is attached)
  • Exit (E) site (where the deacylated tRNA exits the ribosome)

Function

• Most abundant form of RNA in living cells (about 80% of total RNA in a cell)
• Serves as a scaffold of the ribosomal subunits
• Ribosomal RNA associates with proteins to form ribosomes (the site of protein synthesis).
• Catalyzes specific chemical reactions (ribozymes: “ribo-” that acts like en-“zymes”)
• Largest rRNA 23S (prokaryotes) and 28S (eukaryotes) in the large subunit of the ribosome:
  • The most important ribozyme
  • Ribosomal RNA is a peptidyl transferase Peptidyl Transferase Chloramphenicol (it catalyzes peptide bond Peptide bond A peptide bond is formed when the alpha carboxyl group of one amino acid reacts with the alpha-amino group of another amino acid. Proteins and Peptides formation between amino acids Amino acids Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. Basics of Amino Acids to form proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis).
• Note the differences:
  • Ribosomal RNA: rRNA
  • Ribosome: rRNA + proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis
  • Ribozyme: rRNA with enzyme-like activity, catalyzing protein synthesis Synthesis Polymerase Chain Reaction (PCR) in ribosomes Ribosomes Multicomponent ribonucleoprotein structures found in the cytoplasm of all cells, and in mitochondria, and plastids. They function in protein biosynthesis via genetic translation. The Cell: Organelles

Other Forms of RNA

RNA processing

Small nuclear RNA:

• Non-coding RNA (eukaryotes) 
• Associates with proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis to form small nuclear ribonucleoproteins (snRNPs):
  • Small nuclear ribonucleoproteins (snRNPs) + protein = spliceosome
  • Spliceosomes excise introns Introns Sequences of DNA in the genes that are located between the exons. They are transcribed along with the exons but are removed from the primary gene transcript by RNA splicing to leave mature RNA. Some introns code for separate genes. Post-transcriptional Modifications (RNA Processing) from a transcribed pre-mRNA (splicing).
  • Key for rRNA and mRNA processing and gene Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. Basic Terms of Genetics regulation

Small nucleolar RNA:

• Non-coding RNA (eukaryotes)
• Modifies RNA nucleotides Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. Nucleic Acids

Gene Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. Basic Terms of Genetics regulation

Micro RNA:

• Non-coding RNA (eukaryotes)
• Regulates degradation and translation Translation Translation is the process of synthesizing a protein from a messenger RNA (mRNA) transcript. This process is divided into three primary stages: initiation, elongation, and termination. Translation is catalyzed by structures known as ribosomes, which are large complexes of proteins and ribosomal RNA (rRNA). Stages and Regulation of Translation of mRNA
• Abnormal expression of miRNA can contribute to malignancy Malignancy Hemothorax development (functioning as oncogenes Oncogenes Genes whose gain-of-function alterations lead to neoplastic cell transformation. They include, for example, genes for activators or stimulators of cell proliferation such as growth factors, growth factor receptors, protein kinases, signal transducers, nuclear phosphoproteins, and transcription factors. A prefix of ‘v-‘ before oncogene symbols indicates oncogenes captured and transmitted by retroviruses; the prefix ‘c-‘ before the gene symbol of an oncogene indicates it is the cellular homolog (proto-oncogenes) of a v-oncogene. Carcinogenesis or tumor Tumor Inflammation suppressors).

Small regulatory RNA:

• Non-coding RNA (prokaryotes)
• Gene Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. Basic Terms of Genetics regulation

6sRNA:

• Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription regulation

Genome Genome The complete genetic complement contained in the DNA of a set of chromosomes in a human. The length of the human genome is about 3 billion base pairs. Basic Terms of Genetics defense

Small interfering RNA:

• Non-coding RNA (eukaryotes)
• Silencing RNA
• Operates within the RNA interference RNA Interference A gene silencing phenomenon whereby specific dsRNAs (double-stranded RNA) trigger the degradation of homologous mRNA (messenger RNA). The specific dsrnas are processed into small interfering RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the rna-induced silencing complex. DNA methylation may also be triggered during this process. Stages and Regulation of Translation (RNAi) pathway (with miRNA)
• Defense against foreign RNA

PIWI-interacting RNA:

• Non-coding RNA (eukaryotes)
• Regulates gene Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. Basic Terms of Genetics expression and fights viral infection

CRISPR (crRNA):

• Non-coding RNA (prokaryotes)
• Defense against foreign DNA DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA Types and Structure and RNA

Other ribozymes

Ribonuclease Ribonuclease Enzymes that catalyze the hydrolysis of ester bonds within RNA. Interferons P (RNAse P):

• Cleaves pre-tRNA to generate the 5’ free end of mature tRNA

Self-splicing introns Introns Sequences of DNA in the genes that are located between the exons. They are transcribed along with the exons but are removed from the primary gene transcript by RNA splicing to leave mature RNA. Some introns code for separate genes. Post-transcriptional Modifications (RNA Processing):

• Introns Introns Sequences of DNA in the genes that are located between the exons. They are transcribed along with the exons but are removed from the primary gene transcript by RNA splicing to leave mature RNA. Some introns code for separate genes. Post-transcriptional Modifications (RNA Processing) in the genes Genes A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. DNA Types and Structure act as ribozymes with nuclease activity.

Viroid:

• Non-coding RNA
• Naked RNA in plants Plants Cell Types: Eukaryotic versus Prokaryotic
• Cleaves itself during the viroid replicative cycle Cycle The type of signal that ends the inspiratory phase delivered by the ventilator Invasive Mechanical Ventilation