DNA vs. RNA Structure and Nucleotides

RNA vs. DNA Structure

• RNA contains ribose sugar, while DNA contains deoxyribose
• RNA contains uracil (U) in place of DNA's thymine (T)
• RNA is single-stranded, whereas DNA is double-stranded

Nucleotide Structure

• Nucleotide structure is composed of a 5-carbon sugar, a nitrogenous base (A, T, G, C), and a phosphate group
• The nitrogenous base attaches to the 1' carbon
• The phosphate group attaches to the 5' carbon

DNA and RNA Bases

• DNA bases: cytosine (C), guanine (G), adenine (A), thymine (T)
• RNA bases: cytosine (C), guanine (G), adenine (A), uracil (U)
• Pyrimidines (single-ringed): cytosine, thymine, uracil
• Purines (double-ringed): guanine, adenine

DNA Nucleotide Linking

• DNA nucleotides are linked by phosphodiester bonds.
• These covalent bonds form between one nucleotide's phosphate group and another's 3' hydroxyl (-OH) group on the deoxyribose through a condensation reaction (aka dehydration synthesis).
• A continuous chain of sugar and phosphate groups linked by phosphodiester bonds forms the sugar-phosphate backbone.
• The resulting strands are polar

DNA Double Helix Formation

• Complementary DNA strands align antiparallel to one another
• Hydrogen bonds form between complementary bases:
• Adenine pairs with thymine (2 hydrogen bonds)
• Cytosine and guanine pair (3 hydrogen bonds)

3' and 5' Ends of Nucleic Acids

• The 5' end has a phosphate group attached to the 5' carbon of the sugar.
• The 3' end has a hydroxyl group attached to the 3' carbon of the sugar.
• DNA and RNA synthesis (replication) occurs from the 5' → 3' end:
• New nucleotides are added to the 3' end of existing DNA
• Synthesis starts with the 5' end of the new DNA strand

DNA Replication

• DNA replication involves the unwinding of the double helix and separation of strands by helicase, followed by the formation of new complementary strands by DNA polymerase.
• Helicase unwinds the double helix by breaking hydrogen bonds, separating the strands and creating a replication fork.
• Single-stranded binding proteins (SSBs) coat exposed single strands to keep them apart.
• DNA primase, an RNA polymerase, synthesizes RNA primers.
• These primers attach to the exposed strands.
• DNA gyrase (topoisomerase) of DNA replication relieves torsional strain and prevents supercoiling ahead of the replication fork.
• RNA primers help recruit DNA Polymerase III (DNA Pol III) to the strands, which adds nucleotides to the 3' end of growing DNA.
• The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously, creating Okazaki fragments.
• DNA Polymerase I (DNA Pol I) removes RNA primers and replaces them with DNA on the lagging strand.
• DNA ligase seals cuts between Okazaki fragments via the formation of a continuous strand.
• Telomerase adds telomeres to the ends of chromosomes, preventing shortening of chromosomes after each replication.

Significance of Complementary Base Pairing

• Complementary base pairing ensures that the DNA base sequence is conserved in replicated DNA.
• Each base on one of the parental strands pairs exclusively with its complementary base, resulting in a new copy identical to the initial parental strand.

Significance of Semi-Conservative DNA Replication

• Each new DNA molecule contains one original (parental) strand and one newly synthesized strand (semi-conservative model).
• Semiconservative replication ensures accurate replication of DNA, conserving the genetic information.

Alternative DNA Replication Models

• Conservative model: the original DNA remains intact, and an entirely new copy is synthesized.
• Dispersive model: new DNA strands are a combination of old and new DNA segments.

Experiments Confirming Semi-Conservative Replication

• Meselson and Stahl grew E. coli in a medium containing a heavy isotope of nitrogen (15N), incorporated into the DNA.
• They transferred the bacteria to a medium with a light isotope of nitrogen (14N) and extracted DNA samples after each replication.
• Ultracentrifugation separated strands by density (15N strands are denser than 14N strands).
  • After 1 replication, DNA had an intermediate density (one 15N and one 14N strand).
  • After 2 replications, DNA separated into two density classes: intermediate and light (14N).

Mechanisms of DNA Replication

• Initiation occurs via above steps 1-4.
• The leading strand is synthesized continuously in the 5' → 3' direction
• DNA Pol III can add nucleotides in the same direction the replication fork opens.
• The lagging strand is synthesized discontinuously (also in the 5' → 3' direction).
• DNA Pol III must work in the opposite direction of the replication fork, creating Okazaki fragments
• Each fragment requires a new RNA primer to recruit DNA Pol III and are later joined by DNA ligase.

Prokaryotic vs. Eukaryotic Replication

• Prokaryotes: replication occurs in cytoplasm, starting at a single origin of replication; usually faster due to the single circular DNA
• Eukaryotes: replication occurs in the nucleus, starting at multiple origins along a single chromosome; telomeres at the ends of chromosomes shorten after each replication

Polymerase Chain Reaction (PCR)

• In PCR, DNA is heated to denature double-stranded DNA
• It’s then cooled to allow primers (short DNA segments) to anneal to their complementary bases.
• DNA polymerase extends the primers, creating new DNA strands; this process repeats.
• In COVID testing, PCR is performed on nasal swabs to detect viral RNA, extracted, converted to DNA by reverse transcriptase, amplified by PCR, and analyzed.

Chromosome Structure

• DNA first wraps around histone proteins forming nucleosomes.
• Nucleosomes fold into chromatin fibers.
• Chromatin fibers loop around and interact with scaffold proteins, forming chromosomes.

Eukaryotic Chromosome Structure Advantages

• Compacts DNA in the nucleus
• Allows complex gene regulation
• Aids organized segregation in cell division

DNA Transcription

• RNA strand complimentary to the DNA strand forms, via RNA polymerase.
• mRNA synthesis correlates to DNA strand base pairs, forming mRNA with base sequence complementary to the template strand.

Processes During Transcription Phases

• Initiation: RNA polymerase binds to the promoter region of the gene and unwinds the DNA helix.
• Elongation: The transcription bubble forms and moves along the template strand.
• RNA polymerase synthesizes an RNA strand by adding complementary RNA nucleotides in the 5' → 3' direction.
• DNA in front of the enzyme is opened, while DNA behind it is rewound.
• Termination: RNA transcription stops.
• The newly-formed mRNA is released when the polymerase reaches the terminator region.
• In eukaryotes, pre-mRNA requires spicing to cut out introns.
• In prokaryotes, this mRNA proceeds directly to translation.

Molecular Factors Aiding Transcription

• A transcription factor first recognizes and binds to the TATA box sequence, part of the core promoter (in eukaryotes).
• It then attracts other transcription factors, building the initiation complex.
• Ultimately, the complex recruits RNA polymerase II, completing the initiation complex to start transcription.

Importance of DNA Sequences in Transcription

• Promoter region: found near the start of the gene; recognized by transcription factors, which help recruit RNA polymerase to begin transcription.
• In eukaryotes: it often includes the TATA box (a string of thymine and adenine, most commonly TATAAA).
• Terminator sequence: signals the end of transcription causing RNA polymerase to stop transcribing.
• Enhancer and silencer sequences: regulatory sequences that influence transcription, binding activators or repressors to increase or decrease transcription.

Eukaryotic vs. Prokaryotic Transcription

• Eukaryotes: occurs in the nucleus, involves RNA polymerase II, requires transcription factors and pre-mRNA splicing, regulated with enhancers and silencers.
• Prokaryotes: occurs in cytoplasm, involves a single RNA polymerase, regulated with operons, coupled with prokaryotic translation.

Translation Molecular Structures

• mRNA: carries the genetic code from the DNA to the ribosome
  • Message is read in triplets called codons, with each codon representing a specific amino acid
• tRNA: carries an amino acid with an appropriate anticodon, complementary to the mRNA codon
• Ribosome: site of translation, with large and small subunits consisting of rRNA and proteins
  • The small subunit decodes the transcribed message
  • The large subunit, which has peptidyl transferase, forms peptide bonds
  • Contains an A (aminoacyl) site, which binds to tRNA carrying the next amino acid
  • Contains a P (peptidyl) site, which binds to tRNA attached to the growing peptide chain
  • Contains an E (exit) site, which binds to tRNA that carried the previous amino acids
• Amino acids: the “building blocks” of proteins
• They link together in translation to form the polypeptide chain

Genetic Code

• The genetic code consists of 64 codon sequences, which are triplets of nucleotide bases (444 = 64)
• Each codon codes for a specific amino acid or a stop signal in translation.
• Because there are more codons than amino acids, some amino acids correspond to multiple codons.

Relationship Between Genes and Polypeptides

• Each gene encodes the information to produce one specific polypeptide.

Mutation Types

• Germline mutations: occur in germ cells (sperm or eggs), and are inheritable.
• Somatic mutations: occur in somatic cells, thus only affect the individual cell and are not inherited.
• Coding region (exons) mutations: can impact the resulting protein after translation, altering structure and function.
• Non-coding region (promoters or introns) mutations: can affect gene regulation but do not affect exons or resulting proteins directly.

Mutation Effects on Gene Function

• Mutations affect gene function by changing the gene sequence, resulting in unintended production of certain amino acids and proteins with altered structures and functions.
• Point mutations (including missense and nonsense mutations) change single nucleotides, while frameshift mutations insert or delete nucleotides, which shift the reading frame of the codons.
• Missense mutations result in a single codon change, producing a different amino acid
• Nonsense mutations are missense that cause amino acid-producing codon to change to a stop codon, truncating the polypeptide.

Transcription and Translation

• Transcription transfers genetic information from DNA to mRNA in the nucleus.
• Translation converts the genetic information in mRNA to amino acids to build the protein.
• A gene is said to be expressed when it produces a protein.

Lac and Trp Operons

• Lac operon: inducible; normally inactive and only activates in specific conditions, breaking down lactose if there is no glucose.
• If there is no lactose/glucose, the repressor protein attaches to the operator and prevents transcription.
• If there is lactose, it binds to the repressor, releasing it from the operator.
• RNA polymerase can then bind and express the proteins on the operon.
• Trp operon: repressible; usually expressed unless unneeded; regulates synthesis of tryptophan.
• If tryptophan is absent, the cell makes it on its own.
• If there is tryptophan, it activates repressor protein and enables it to bind to the operator, inhibiting trp transcription.

Transcription Factors and Activators

• Transcription factors (TFs) are proteins that bind to specific DNA sequences.
• General transcription factors assemble transcription apparatus and recruit RNA Pol II to the promoter.
• Specific transcription factors (activators) increase level of transcription in certain cells or in response to signals.
• Transcription activators are regulatory proteins that bind to DNA at enhancer sites, which can interact with the complex to increase the rate of transcription.

Chromatin Structure

• Chromatin structure regulates DNA’s accessibility by controlling its compaction.
• Tightly-wound DNA is less accessible, thus preventing transcription.
• Various modifications: DNA methylation (less accessible), X-chromosome inactivation, Histone modifications (lysine acetylation and methylation; serine, threonine, and tyrosine phosphorylation)
• The modifications include chromatin-remodeling complexes.

RNA Processing

• RNA processing modifies pre-mRNA.
• 5' capping: adds a modified guanine nucleotide to the 5' end to facilitate ribosome binding in translation.
• Pre-mRNA slicing
• Removal of introns (non-coding sequences)
• 3' polyadenylation
• Addition of adenine nucleotides to the 3' end to help mRNA stability

Cell Communication

• Cells communicate through chemical and physical signaling, including direct contact, paracrine signaling, endocrine signaling, and synaptic signaling.
• Autocrine signaling is for cells to communicate with themselves

Types of Signaling

• Direct contact (juxtacrine signaling): two cells in direct contact send signals across gap junctions.
• Paracrine signaling: signal one cell gives off have an effect on nearby cells.
• Endocrine signaling: signal one cell gives off have an effect on distant cells in a different part of the organism.
• Synaptic signaling: nerve cells release neurotransmitter signals, which bind to receptors in nearby target cells.
• Occurs through the nervous system
• Autocrine signaling: a cell releases signaling molecules that bind to its own receptors.

Receptor Types in Cells

• Membrane receptors: transmembrane proteins on the membrane
• Channel-linked receptors (aka chemically gated ion channels): allow ions through specific ion channels that activate upon chemical binding
• Enzymatic receptors: act as enzymes or are directly linked to enzymes and activates upon signal molecule reception
• Protein kinases: phosphorylate proteins to activate them
• G protein-coupled receptors (GPCR): activate G protein when ligand binds and activates the receptor
• Effector proteins are activated by G proteins
• Intracellular receptors: located in the cell
• Nuclear receptors: receptors at the nucleus
• Steroid hormone receptors: act as regulators of gene expression with 3 functional domains: hormone-binding, DNA-binding, and one that interacts with coactivators.

Hormone Signal Mechanisms

• Water-soluble hormones bind to membrane-bound receptors b/c they can’t cross the lipid bilayer. since they are polar
• Lipid-soluble hormones diffuse through the cell membrane and bind to intracellular receptors, regulating gene transcription

Protein Kinase Receptors

• A ligand binds to a protein kinase receptor:
  • Receptor-ligand complexes associate (dimerization) and phosphorylate each other (autophosphorylation). Autophosphorylation transmits signal across the membrane
• It activates intracellular kinase domain of the receptor, proteins which phosphorylates target proteins for cellular response.

G Protein–Coupled Receptor Activation

• Upon ligand binding, the G protein undergoes a conformational change, causing GTP exhange for GDP on the G.
• This activates via split into beta gamma and alpha subunits
• Each interact w/ different effector proteins, which may trigger cellular responses.

Steps of Signal Transduction

• Signal reception occurs when a ligand binds to a receptor protein, which produces a cellular response or phosphorylates a protein.
• If phosphorylation occurs, a phosphorylation cascade or kinase cascade may occur amplifying the signal.
• Signals from multiple pathways are integrated to coordinate a cellular response.
• Once the signal is terminated: Phosphatases are used to dephosphorylate activated proteins.

Phosphorylation Cascade

• The activated protein phosphorylates multiple target proteins.
• Each activated protein then phosphorylates other target proteins, amplifying the signal.
• Eventually, the final proteins may activate other molecules that produce a cellular response.

Second Messengers

• Second messengers like cAMP amplify and distribute signals in the cell
• This enables a single receptor sending many signals and regulating multiple pathways without wasting resources.

Cellular Responses to Signal Transduction

• Gene expression
• Protein manufacture
• Enzyme activation
• Cell division
• Apoptosis

Nerve Impulse Progression

• Nerve impulses pass along as action potentials along every segment of the neuron.

Neuron Potential

• Resting potential: charge difference between the inside and out in a resting neuron, approximately -70 mV
• The inside of the neuron is more negative than the outside
• Action potential: rapid, temporary change to the membrane potential, which transmits a neuron impulse.

Ion Movement and Potential Creation

• Resting potential: maintained by NA/K (sodium potassium) pumps which actively transports 3 Na+ out and 2 K+ in. Action potential: the start when stimulus causes membrane protein to hit/near threshhold that opens+ NA+_ diffusion into the cell
• It depolarizes membranes which increases membrane pt until ~35+ mV w
• When Na+ Ch closes, the membrane potential rises, leading the K+ channels to open. K+ diffuses out.
• membrane repolarizes until around -80 mV, a hyperpolarization that restores the resting potential.

Action Potential

• When one area of the membrane depolarizes: adjacent regions depolarize (threshhold)
• Na+ channels open passing the action potential.
• The transfer of the new membrane pt causes hyperpolarization in sections as the neuron restores.

Synaptic Communication

• Signals by neurons move via synapses to other neurons/muscle/glands.
• Its in pt for all brain funcs that req memory/ muscle movement/etc.
• When presynaptic neurons absorbs them, enzymes degrade membrane PT and defuse.

Synaptic Transmission

• the neuron fires which triggers release or triggers openings of voltage channels which:
• causes synaptic vesicles to fuse presynaptic and releases neuro into the cleft through exocytosis

Signaling pt. 2.0 and the Post Synaptic Neuron

• NT diffuses until recepts in pt
• Leads to deplarizaiton EPSP
• hyperplarizaion (IPSP)
• Comb EPSP and IPSP the AP can start and carry an action potential
• presynaptic absoabs after

Variations in Post Synaptic Activity

• type in synapse.
• EPSPS= execitatory Glut -> binds rep -> opens a channels -> deplarizaiton.
• Glcine + binds Cl channels are more opened -> hyperpolarization (IPSP)

Other Points to Note

Nervous systems are made pt/

• neurons quick elec pulses diagrame neuron ->
• dendrytic nucleus Axon shielr and notor plate Chapter 44: what it all really is to state + outinept13 -> consist of horme relealse and transport. outiline- there all feedback
• ADU controls theyroid balcal