Cell Properties & Nucleic Acids

Properties of Living Cells & Nucleic Acids

• Living cells can produce exact replicas of themselves
• Cellular instructions for creating organisms reside in nucleic acids.

Discovery of Nucleic Acids

• Friedrich Miescher discovered nucleic acids in 1869 while studying white blood cell nuclei
• Initially discovered in cell nuclei and found to be acidic, hence the name "nucleic acid"
• Though now known to exist throughout the cell, the name nucleic acid is still used

Types of Nucleic Acids

• Nucleic acids are unbranched polymers with nucleotides as monomer units
• Two main types in higher organisms are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

Deoxyribonucleic Acid (DNA)

• Primarily located in the cell nucleus
• Functions to store and transfer genetic information
• Used indirectly to control many living cell functions
• Passed from existing to new cells during division

Ribonucleic Acid (RNA)

• Present in all parts of a cell
• Key role is in synthesizing proteins, which carry out essential cell functions

Nucleotide Building Blocks

• Nucleotides contain three subunits: a pentose sugar, a phosphate group, and a nitrogen-containing heterocyclic base

Pentose Sugar Details

• Can be either pentose ribose or pentose 2'-deoxyribose
• The difference occurs at carbon 2'
• Ribose sugars have an -OH group on carbon 2', which is replaced by -H in 2'-deoxyribose
• Deoxy- prefix means "without oxygen"
• RNA contains ribose
• DNA contains 2'-deoxyribose

Nitrogen-Containing Heterocyclic Bases

• Five nitrogen-containing heterocyclic bases are components of nucleotides
• Adenine, guanine, and cytosine are present in both DNA and RNA
• Uracil is found only in RNA
• Thymine appears only in DNA

Phosphate Groups

• Phosphate is the third component of a nucleotide
• The phosphate is derived from phosphoric acid (H3PO4)
• Under cellular pH, it loses two hydrogen atoms, becoming a hydrogen phosphate ion (HPO42-)

Nucleotide Formation

• A nucleotide is assembled in two steps, from a sugar, a base and a phosphate
• First, a pentose sugar and a nitrogenous base form a nucleoside
• Next, the nucleoside reacts with a phosphate group to form a nucleotide
• Nucleotides are building blocks for nucleic acids

Nucleoside Formation

• A nucleoside contains a pentose sugar bonded to a nitrogen-containing heterocyclic base
• The bond linking the sugar and base is a 𝛽-N-glycosidic linkage

RNA and DNA Nucleosides

• RNA nucleosides: ribose-adenine, ribose-cytosine, ribose-guanine, ribose-uracil
• DNA nucleosides: deoxyribose-adenine, deoxyribose-cytosine, deoxyribose-guanine, deoxyribose-thymine

Structure of a Nucleic Acid

• Nucleic acids are polymers of nucleotide monomers
• Nucleotides are linked by sugar-phosphate bonds
• The chain has alternating sugar and phosphate groups, with a base group extending from the chain

Ribonucleic Acid (RNA) Polymer

• Nucleotide polymer with ribose, a phosphate group, and one of the heterocyclic bases (adenine, cytosine, guanine, or uracil)

Deoxyribonucleic Acid (DNA) Polymer

• A nucleotide polymer with deoxyribose, a phosphate group, and one of the heterocyclic bases (adenine, cytosine, guanine, or thymine)

Nucleic Acid Backbone

• Alternating sugar-phosphate chains

Base Sequence Variations

• RNA: adenine, guanine, cytosine, uracil
• DNA: adenine, guanine, cytosine, thymine

Primary Structure

• This is the order in which nucleotides are linked in a nucleic acid
• It depends only on the sequence of bases

Phosphodiester Linkage

• Each nonterminal phosphate group bonds to two sugar molecules via 3'-5' phosphodiester linkages
• A phosphoester bond links to the 5' carbon of one sugar and the 3' carbon of the other sugar

Directionality of Nucleic Acids

• Nucleotide chains have directionality
• The 5' end has a free phosphate group on the 5' carbon atom of the sugar
• The 3' end has a free hydroxyl group on the 3' carbon atom

Reading Base Sequences

• Convention dictate that base sequences are read from the 5' end to the 3' end

Key Points

• Specifies primary structure for a nucleic acid by listing nucleotide bases using one-letter codes in order, starting with the 5' end
• The primary structure of a four-nucleotide DNA segment can be written at 5' T-G-C-A 3'

Characteristics of Nucleic Acids

• Each nonterminal phosphate group has a -1 charge
• Phosphoric acid originally donating the phosphate had three -OH groups
• Two are involved in phosphodiester linkages
• Remaining -OH group exhibits acidic behavior and can produce a H+ ion
• Acidic properties result from phosphate groups in the backbone

Parallels Between Primary Nucleic Acid and Protein Structure

• DNA, RNA, and proteins all have consistent backbones
• The sequences that attach to the backbones vary
• They are nitrogenous bases in nucleic acids
• They are amino acid R groups in proteins, defining the molecule type
• Both nucleic acid and protein polymer chains have directionality

Base Pairing & the Double Helix

• James Watson and Francis Crick proposed the double-helix structure of DNA
• DNA carries genetic information.
• The double helix has two complementary strands
• The strands are linked by hydrogen bonds between adenine-thymine and guanine-cytosine base pairs

Chargaff's Base Ratio

• Purines and pyrimidines occur in equal amounts in DNA
• Adenine matches thymine, and cytosine aligns with guanine
• The ratio may vary between species but remains constant within a single species, aiding DNA identification

Watson and Cricks Model of DNA

• There are two polynucleotide chains
• The chains run antiparallel, meaning one chain runs in the 5' to 3' direction, while the other runs in the 3' to 5' direction
• Phosphate groups are on the outside, while nitrogenous bases point inward
• Hydrogen bonds link the bases of separate chains

Unique Features of Pairing Between Bases

• Purines pair with pyrimidines (adenine with thymine, and cytosine with guanine)
• Perfect match occurs between hydrogen donor and acceptor sites
• Adenine and thymine share two hydrogen atoms
• Cytosine and guanine are joined by three hydrogen bonds
• Constant diameter is supported by a two-ringed purine joining with a single-ringed pyrimidine

DNA Strands & Bonds

• Complementary strands feature bases opposite of each other and are reliant on hydrogen bonding for structural support
• Knowing a base sequence enables prediction of its paired strand

How to Write Base Sequences

• Base sequences are written in the 5' to 3' direction
• Without ends identified, it is assumed to start with a 5' end

Hydrogen Bonds & Base Stacking

• Hydrogen bonding stabilizes the DNA double-helix
• Base-stacking interactions also hold DNA double helix

Hydrophobic Properties

• Purine and pyrimidine bases are hydrophobic
• Stacking interactions involve London forces
• Hydrophobic interactions maintain cell membranes
• Nonpolar R groups contribute to protein stability

Replication of DNA

• DNA molecules transmit genetic data as units of heredity
• Parent cells must make exact copies of DNA for new daughter cells
• Process of how DNA molecules are generated is DNA replication

DNA Replication Process

• Biochemical process makes exact DNA duplicates
• Key to DNA replication is base pairing associated with the DNA double helix
• DNA replication occurs in a semi-conservative manner
• Each new molecule includes an original and newly synthesized strand

Enzymes of Replication

• DNA replication is enzyme-dependent
• DNA-dependent DNA polymerase is the main enzyme, but other enzymes aid such as helicase and ligase

DNA Polymerase

• Helps DNA strands to polymerize
• Catalyzes the whole replication procedure
• Nucleoside triphosphates provide substrate and energy
• Three types exist: DNA Polymerase I, II, and III

Types of DNA Polymerase

• DNA Polymerase I - A repair enzyme that has 5'-3' polymerase, 5'-3' exonuclease, and 3'-5' exonuclease activities
• DNA Polymerase II - Responsible for primer extension and proofreading
• DNA Polymerase III - Main one in bacteria that handles bulk synthesis along with proofreading

3 Key DNA Replication Enzymes

• Helicase unzips DNA strands by breaking hydrogen bonds and forming a replication fork
• Ligase joins Okazaki fragments of discontinuous DNA strands
• Primase synthesizes RNA primers for the DNA template strand
• Topoisomerases regulate DNA topology, relieving torsional strain/overwinding
• Endonucleases produce single/double-stranded cuts in DNA molecules
• Single-stranded Binding Proteins bind to single-stranded DNA to prevent secondary structure formation

Initiation of DNA Replication

• Specific initiation sites are termed origins of replication
• Prokaryotic cells have a single origin
• Eukaryotic cells have multiple origins
• Initiator proteins bind to the origin and unwind it into a bubble
• RNA primase acts as a starting point on the template

Elongation of DNA Replication

• The DNA polymerase enzymes add nucleotides to the growing DNA strand to form the new nucleic acid chain
• Synthesis goes from 5' to 3' bidirectionally from the origin
• The leading strand synthesizes continuously, with lagging strands synthesizing short Okazaki fragments with gaps
• Breaks in the daughter strand are called nicks

Proofreading & Repair

• The DNA polymerases have proofreading activity to ensure replicated DNA
• Incorrect nucleotides are removed by exonuclease activity and replaced
• DNA repair mechanisms can fix damage/errors

Termination of DNA Replication

• Occurs when replication forks meet
• In prokaryotic cells it happens head-on
• Eukaryotic is more complex and the fusion occurs at forks from origins of replication

DNA and Histones

• Replicated DNA interacts with histones to form structural units
• Histone-DNA complexes are termed chromosomes
• Chromosomes are individual DNA molecules bound to proteins
• Chromosomes are composed of 15% DNA/85% protein

Nucleic Acids in Protein Synthesis

• Ribonucleic acids are nucleic acids, similar in structure to DNA
• RNA is often single-stranded
• RNA has a backbone of alternating phosphate groups and the sugar ribose (DNA has deoxyribose)
• Each sugar has one of four bases attached: adenine (A), uracil (U), cytosine (C), or guanine (G).

Feature Comparison of RNA and DNA

Types of Ribonucleic Acid (RNA)

• Heterogeneous nuclear RNA (hnRNA) that undergoes post-transcription conversion to mRNA
• Messenger RNA (mRNA) that carries instructions for protein manufacturing
• Small nuclear RNA (snRNA) facilitates hnRNA to mRNA conversion
• Ribosomal RNA (rRNA) combines with proteins to form ribosomes
• Transfer RNA (tRNA) that delivers the amino acids to sites for protein manufacturing

Heterogenous Nuclear RNA (hnRNA)

• Formed by DNA Transcription
• This then converts the hnRNA into messenger RNA

Messenger RNA (mRNA)

• Carries protein synthesis instructions to manufacturing sites
• Molecular mass varies on the length of protein it will direct
• The molecule's nucleotide base sequence is critical

Small Nuclear RNA (snRNA)

• Facilitates the conversion of hnRNA to mRNA
• Contains from 100 to 200 nucleotides

Ribosomal RNA (rRNA)

• Combines with proteins to form ribosomes
• Ribosomes have a molecular mass of 3 million amu
• Plays no informational role

Transfer RNA (tRNA)

• Delivers amino acids to protein manufacturing sites
• The smallest of the RNAs has only has 75-90 nucleotide units

A. Transcription Details

• It is an RNA synthesis by DNA for molecules carrying codes for protein synthesis

Summary Points

• RNA polymerase initiates transcription by binding to the promoter region on the DNA
• Portion of the DNA unwinds, exposing the strand of template to RNA polymerase
• Elongation starts with the addition of ribonucleotides by RNA polymerase that are complementary to the template, extending the chain
• Occurs with U pairing to A (instead of T)
• Termination occurs when RNA polymerase hits the termination signal, prompted to dissociate from DNA template

RNA and Transcription

• Transcription is an RNA synthesis by DNA to form hnRNA/mRNA with codes for protein synthesis

Transcription Points

• In eukaryotes, termination might involve cleaving an RNA transcript, then polyadenylate

Post-Transcriptional Processing

• Process of turning hnRNA into mature mRNA involving post-transcription processes such as splicing
• Splicing removes hnRNA portions (introns) with the remaining portions (exons) joining to become the mature mRNA
• Splicing involves small nuclear ribonucleoprotein particles (snRNPs)

Exons

• Gene segments (code for functional elements)
• Crucial for expressing the genetic message
• Contribute to the synthesis of functional proteins

Introns

• Segments that lack code for functional elements
• Interrupt the coding sequences
• Transcribed but removed before translation
• May provide regulatory/diversity functions

RNA Splicing

• Provides for several ways in which variations of single proteins can be produced

Important Terms in Translation Process

• Known as the triplet code, is the assignment of the 64 mRNA codons to specific amino acids or stop signals
• There are 64 possible codons (4 nucleotides having 3 positions), but only 20 standard amino acids including the stop codons
• Redundancy is the multiple codons that code a single amino acid with a degree of robustness for transcription/translation errors
• Genetic code is universal across all organisms
• Essential for passing on genetic information to synthesize specific proteins

Anticodons/tRNA Molecules

Structure

• It exhibits a cloverleaf-shaped structure of parallel strands/loops, twisted into 3D

Aminoacylation

• Site is on 3' end to connect amino acid molecules with ester bonds
• Synthetase enzymes can recognize specific types of tRNA to connect the proper chains

Anticodon

• Opposite the cloverleaf and has specific sequences acting as an anticodon complementary to the strand of mRNA
• Complementarity allows the correct amino acid to be placed into the growing peptide

Amino Acid Delivery

• Interaction occurs thanks to the anticodon of the mRNA and tRNA with accuracy due to the bonding of the complements

Protein Synthesis

• Translation is where the mRNA codons are translated to produce protein molecules
• Components needed are tRNA and mRNA molecules, as well as enzymes, ribosomes and amino acids
• Ribosomes are made of proteins combining with rRNA for synthesis translation

tRNA Activation

• First an amino acid interacts with ATP to become activated
• Next, bonding occurs at the 3' end with enzymes involved

Initiation

• The mRNA first attaches itself to the surface of a ribosomal subunit, namely as an AUG codon in the proper section
• Anticodon that properly complements itself to the AUG, base pairs to create an initiation complex

Elongation

• Chain shifts form on P and A sites, enzyme transferring a binding of amino acid at P site to acid at A site
• tRNA at A site bears the dipeptide that leaves the initial P site
• Ribosome then shifts thanks to tRNA release, moving next codon of the mRNA

Translocation

• Ribosomes move one mRNA molecule causing the translocation where one codon can be occupied by each molecule

Termination

• Chain grows thanks to translocation
• Bond all together until stop codons arrive/create no tRna site, cleaving resulting polypeptide

Post-translation Details

• Protein modification proceeds usually after all processing is completed and polypeptide is made
• After which, there can be removal of methionine (Met) residues thanks to the specialized enzyme, or addition to cysteine residue
• Folding/completion occurs during elongation on ribosome with various components assembled together

Mutagens and Mutations

• Mutation is an error in gene sequence reproduced with error to genetic transcription/translation
• Mutagen is an agent of changed gene/structre

Examples of Mutation

Types of Mutation

• A nucleotide can changed to another, resulting in possible subcategories
• Missense mutations create a change somewhere in the amino-acid's encoded protein sequence
• Silent mutation has no effect on sequence thanks to genetics
• Nonsense mutation has premature stop, leaving to truncation

Frameshift

• With insertions, there is an addition shift of nucleotide for the code with it changing the amino acid sequence
• With a deletion, that also shifts the code and changes what is written

Repeat Expansion

• Repeats occur, especially expansion for nucleotide
• Increased expansion can cause genetic problems

Chromosomal Aberrations

• Deletions are a segment lost from the chromosome with genetic loss included
• Duplications have chromosome copies with genetic and dosage increase
• Inversions happen when segments break with opposite orientation and disruption

Translocations:

• Occurs through a transfer of one chromosome to another non homologously speaking with gene disruption

Direct Repair

• This refers to situations with reversal possible without nucleotide change

Photoreactivation

• uses light to reverse specific dimers

Alkyltransferases

• Remove the specific aklyl groups

Mutation Repair Mechanisms

• Base Excision Repair (BER): Used to correct certain helix distortions on the DNA with involved steps listed

1. Removal is conducted of damaged base by glycosylase
2. Incision with AP endonuclease
3. DNA is synthesized for a fill
4. Ligation seals up nick

Nucleotide Excision Repair (NER)

• NER handles adducts and dimers with help

1. Damaged segments get removed with a nucleases
2. Replication conducted with strand serving as proper template This is followed up by:
3. DNA ligation sealing each nick

Mismatch Repair or (MMR): Used to correct replication for small instances, and involves:

1. Recognition with MutS protein
2. Recruitment of MutL protein
3. Excision of proper nucleotide to resolve error

In this scenario, there is also the steps used for homologous recombination (HR) or with non-homologous end joining (NHEJ)

Additional Readings: Nucleic Acids and Viruses

• Considered simplest agents and can't replicate with proper organisms
• The structure is made of proteins to create capsids as genetic material gets surrounded, be it DNA or RNA with lipid present
• Lack machinery for reproduction thus rely on hosts
• Viral invasion occurs, attaching to cell where enzyme facilitates genetic material getting ready

Steps for Replication

• First using host machinery (if it contains DNA) with the host used replicatation
• Retroviruses change RNA using transcriptase and viral integrates after replicating

Diseases and Vaccines

• Viruses cause disease across organisms like flu and hepatitis

• Vaccines use inactive virus forms for artificial immunity for prevention

• Retroviruses are responsible for causing AIDS (HIV) using transcriptase reverse to convert genomic code for integration

Recombinant DNA (rDNA)

• rDNA, genetic modification is made possible thanks to technology with specific exhibited traits
• This has lead to significant genetic advancements

Process Overview

• Procedures involve DNA that has organisms mixed with one another