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Defending the Christian Worlview, Creationism, and Intelligent Design

This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Defending the Christian Worlview, Creationism, and Intelligent Design » Molecular biology of the cell » Origins - what cause explains best our existence, and why? - INDEX & CHAPTERS

Origins - what cause explains best our existence, and why? - INDEX & CHAPTERS

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Otangelo


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Origins - what cause explains best our existence, and why? - INDEX & CHAPTERS  

https://reasonandscience.catsboard.com/t2820-origins-what-cause-explains-best-our-existence-and-why-index-chapters

Molecular biochemistry, biology, the origin of life and biodiversity, systematically analyzed from a universal perspective
https://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why

Content

Abiogenesis, and the origin of life
Crack the Genetic Code and Cipher
Current scientific models and attempts to explain the Origin of Life
Current scientific transition proposals from a supposed "progenote" to the last universal common ancestor (LUCA)
LUCA—The Last Universal Common Ancestor
Essential elements and building blocks for the origin of life
From DNA to Proteins
The Cell
Membrane Structure, Synthesis, and Transport
Energy, Enzymes, and Metabolism
Cellular respiration and fermentation
Photosynthesis
Cell Communication
Multicellularity
Gene expression at the molecular level
Gene Regulation
The Eukaryotic Cell Cycle, Mitosis, and Meiosis
Developmental Genetics
Amino Acids and peptide bonding
A common step determines the chirality of all amino acids
The amino acid sequences of polypeptides determine the structure and function of Proteins
Overview of the Nitrogenase enzyme complex
Breaking the N2 triple bond: insights into the nitrogenase mechanism 
Peptide bonding of amino acids to form proteins and its origins
What Is the Metabolic Fate of Ammonium?
Glutamine synthetase (GS), a incredible molecular super-computer which defies naturalistic explanations
How Do Organisms Synthesize Amino Acids?
The folate biosynthesis pathway
Cheating of secular science papers, claiming of evolutionary mechanisms in place prior to life fully setup and self-replication.


Origins - what cause explains best our existence, and why?

Contents
Historical sciences, and methodological naturalism
PROBABILITY AND SCIENCE
How to recognize the signature of (past) intelligent actions
Is the mind natural, or supernatural? and what does it tell us about the theory of intelligent design?
Paley's watchmaker argument

Abiogenesis

Abiogenesis, and the origin of life
What is life?
What can we know about how life began?
History of Origin of Life research
Charles Darwin and the Origin of Life
Abiogenesis research  from 1950 to 2000
The Miller Urey experiment
From Primordial Soup to the Prebiotic Beach
Formation of nucleobases in a Miller–Urey reducing atmosphere

What might be a Cell’s minimal requirement of parts ?
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts

Calculations of life beginning through unguided, natural, random events.
https://reasonandscience.catsboard.com/t2508-calculations-of-life-beginning-through-unguided-natural-random-events

Abiogenesis is extremely unlikely - this is recognized the more science advances
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-impossible

Are factories made by intelligent professionals, or unguided unconscious random processes ?
https://reasonandscience.catsboard.com/t2799-are-factories-made-by-intelligent-professionals-or-unguided-unconscious-random-processes

The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-the-possible-mechanisms-to-explain-the-origin-of-life

Thermodynamics, and the origin of life
https://reasonandscience.catsboard.com/t2718-thermodynamics-and-the-origin-of-life

Where did Glucose come from in a prebiotic world ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world

Crack the Genetic Code and Cipher
The RNA World hypothesis

THE RNA WORLD,  AND THE ORIGINS OF LIFE
https://reasonandscience.catsboard.com/t2024-the-rna-world-and-the-origins-of-life

No evidence that RNA molecules ever had the broad range of catalytic activities
https://reasonandscience.catsboard.com/t2243-no-evidence-that-rna-molecules-ever-had-the-broad-range-of-catalytic-activities

The origin of replication and translation and the RNA World
https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world

The impossibility of formation of RNA in a prebiotic world
http://reasonandscience.heavenforum.org/t2031-the-impossibility-of-formation-of-rna-in-a-prebiotic-world

From RNA to DNA impossible
https://reasonandscience.catsboard.com/t1784-from-rna-to-dna-impossible

How the discovery of ribozymes cast RNA in the roles of both chicken and egg in origin-of-life theories
Scientists discover double meaning in genetic code
From Primordial Soup to the Prebiotic Beach

Current scientific models and attempts to explain the Origin of Life

The “Prebiotic soup” theory
Hydrothermal origin of life
Extraterrestrial origin of life
Current origin of life proposals

Current scientific transition proposals from a supposed "progenote" to the last universal common ancestor (LUCA)

Systems chemistry synthesis of building blocks

LUCA—The Last Universal Common Ancestor

Essential elements and building blocks for the origin of life

Carbon
Oxygen
Chlorine
Hydrogen
Nitrogen
Potassium
Calcium
Molybdenum
Molybdate – Structure of molybdate
Sulfur
Iron
Magnesium
Phosphate
Sodium
Zinc
Chromium
Selenium
Lithium
Cobalt
Iodine
Boron  
Silicon
Functional groups
Essential Molecules for life
The stuff of life
Proteins
Carbohydrates

From DNA to Proteins

Nucleotides Are the Building Blocks of DNA and RNA
Water

From DNA to proteins

From DNA to Proteins
The DNA double helix

The DNA double helix, evidence of design
https://reasonandscience.catsboard.com/t2028-biosynthesis-of-the-dna-double-helix-evidence-of-design

The amazing DNA information storage capacity
https://reasonandscience.catsboard.com/t2052-the-amazing-dna-information-storage-capacity

Quantum entanglement holds and repairs together life’s blueprint
https://reasonandscience.catsboard.com/t2659-quantum-entanglement-holds-and-repairs-together-lifes-blueprint

The information stored in DNA is transcribed into messenger RNA
RNA Molecules Are Single-Stranded
Who had the "good idea" to exchange  Thymine to Uracil?
Transcription Produces RNA Complementary to One Strand of DNA
Overview of Transcription

The complexity of  transcription through RNA polymerase enzymes  and general transcription factors in eukaryotes
https://reasonandscience.catsboard.com/t2036-the-complexity-of-transcription-through-rna-polymerase-enzymes-and-general-transcription-factors-in-eukaryotes

The three stages of transcription are Initiation, Elongation, and Termination
RNA Transcripts Have Different Functions
Transcription in Bacteria
A Promoter Is a short sequence of DNA that is necessary to initiate transcription
Bacterial transcription is initiated when RNA Polymerase Holoenzyme binds at a promoter sequence
The RNA transcript Is synthesized during the elongation stage
Transcription Is terminated by either an RNA-binding protein or an intrinsic terminator

Transcription in eukaryotes
Eukaryotes have multiple RNA Polymerases that are structurally similar to the bacterial enzyme
Eukaryotic structural genes have a core promoter and regulatory elements
Transcription of eukaryotic structural genes is initiated when RNA Polymerase II and general transcription factors bind to a promoter sequence
Transcriptional termination of RNA Polymerase II occurs after the 3ʹ end of the transcript is cleaved near the PolyA signal sequence

DNA replication, and its mind-boggling nanotechnology  that defies naturalistic explanations
https://reasonandscience.catsboard.com/t1849-dna-replication-of-prokaryotes

DNA Replication in eukaryotes
https://reasonandscience.catsboard.com/t2233-dna-replication-of-eukaryotes

Lipids

Nucleic Acids
RNA modification

Messenger RNA is translated in the Ribosome to make proteins
Each Protein Is Encoded by a Specific Gene
How is the code translated?
During translation, the Genetic Code within mRNA is used to make a Polypeptide with a Specific Amino Acid sequence
Ribosome structure and assembly

Ribosomes amazing nano machines
https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines

Components of ribosomal subunits form functional sites for translation
Structure and function of tRNA
The function of a tRNA depends on the specificity between the amino acid it carries and its anticodon
Common structural features are shared by all tRNAs

Transfer RNA, and its biogenesis, best explained through design
https://reasonandscience.catsboard.com/t2070-transfer-rna-and-its-biogenesis

Aminoacyl-tRNA Synthetases charge tRNAs by attaching the appropriate amino acid
Mismatches that follow the wobble rule can occur at the third position in codon-anticodon pairing
Stages of translation

Gene expression at the molecular level

Gene expression at the molecular level

Molecular gene expression involves the processes of transcription and translation
The protein products of genes largely determine an organism’s characteristics
At the molecular level, a gene is transcribed and produces a functional product
During transcription, RNA Polymerase Uses a DNA template to make RNA
Transcription in eukaryotes involves more proteins
RNA Modification in Eukaryotes
RNA modification involves the addition of a 5′ Cap and a 3′ Poly A tail to eukaryotic mRNAs

3'-end Cleavage and Polyadenylation through poly-A-binding proteins
https://reasonandscience.catsboard.com/t2022-3-end-cleavage-and-polyadenylationn

Splicing involves the removal of introns and the linkage of exons

Information

Information is regarded as the foundation on which physical reality is constructed
http://reasonandscience.heavenforum.org/t2392-information-is-regarded-as-the-foundation-on-which-physical-reality-is-constructed

Complex Specified/instructing Information – It’s not that hard to understand
https://reasonandscience.catsboard.com/t2374-complex-instructing-specified-information-its-not-that-hard-to-understand

DNA stores literally coded information
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information

Getting the message - Paul Davies
http://reasonandscience.heavenforum.org/t2274-getting-the-message-paul-davies

The language of the genetic code
https://reasonandscience.catsboard.com/t1472-the-language-of-the-genetic-code

Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind

The genetic code cannot arise through natural selection
https://reasonandscience.catsboard.com/t1405-the-genetic-code-cannot-arise-through-natural-selection

The five levels of information in DNA
https://reasonandscience.catsboard.com/t1311-the-five-levels-of-information-in-dna

The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-unsurmountable-problem-for-non-intelligent-origin

Wanna Build a Cell? A DVD Player Might Be Easier
https://reasonandscience.catsboard.com/t2404-wanna-build-a-cell-a-dvd-player-might-be-easier

The amazing DNA information storage capacity
https://reasonandscience.catsboard.com/t2052-the-amazing-dna-information-storage-capacity

The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes

The various codes in the cell
https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life

Is calling DNA code just a metaphor?
https://reasonandscience.catsboard.com/t1466-is-calling-dna-a-code-just-a-metaphor#2131

Origin of  translation of the 4 nucleic acid bases and the 20 amino acids, and the universal assignment of codons to amino acids
https://reasonandscience.catsboard.com/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids

The origin of the genetic cypher, the most perplexing problem in biology
http://reasonandscience.heavenforum.org/t2267-the-origin-of-the-genetic-cipher-the-most-perplexing-problem-in-biology

The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codeses

The various codes in the cell
https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

The Cell 

The Cell

Some History
Eukaryotic Cells
Surface area and volume are critical parameters that affect cell sizes and shapes
The Cytosol
Synthesis and breakdown of Molecules occur in the cytosol
The Cytoskeleton

The dramatic cellular morphology of the Microvillar Cytoskeleton
https://reasonandscience.catsboard.com/t2141-the-dramatic-cellular-morphology-of-the-microvillar-cytoskeleton

The astonishing  language written on microtubules, amazing evidence of  design
https://reasonandscience.catsboard.com/t2096-the-astonishing-language-written-on-microtubules-amazing-evidence-of-design

Motor proteins interact with cytoskeletal filaments to promote movements

Kinesin and myosin motor proteins - amazing cargo carriers in the cell
http://reasonandscience.heavenforum.org/t1448-kinesin-and-myosin-motor-proteins-amazing-cargo-carriers-in-the-cell

Primary Cilium a Cell’s Antenna or Its Brain
http://reasonandscience.heavenforum.org/t2089-primary-cilium-a-cells-antenna-or-its-brain

The nucleus and endomembrane system

The Endoplasmic Reticulum
https://reasonandscience.catsboard.com/t2197-the-endoplasmic-reticulum

The eukaryotic nucleus contains chromosomes

Chromatin dance in the nucleus through extensile motors contribute to another higher order, promoting gene regulation and expression. Design, or evolution?
https://reasonandscience.catsboard.com/t2746-chromatin-dance-in-the-nucleus-through-extensile-motors-contribute-to-another-higher-order-promoting-gene-regulation-and-expression-design-or-evolution

Nuclear pore complexes. Design, or evolution ?
https://reasonandscience.catsboard.com/t2117-nuclear-pore-complexes-design-or-evolution

The endoplasmic reticulum (ER)

The Endoplasmic Reticulum
https://reasonandscience.catsboard.com/t2197-the-endoplasmic-reticulum

The golgi apparatus directs the processing, sorting, and secretion of cellular molecules
Lysosomes are involved in the intracellular digestion of macromolecules
Peroxisomes catalyze detoxifying reactions

Peroxisome origins - another unsolved problem of an essential organelle
http://reasonandscience.heavenforum.org/t2645-peroxisome-origins-another-unsolved-problem-of-an-essential-organelle

The plasma membrane Is the interface between a cell and its environment
Mitochondria supply cells with most of their ATP

THE MITOCHONDRION
https://reasonandscience.catsboard.com/t2131-the-mitochondrion

The Transport of Proteins into Mitochondria is a interdependent complex system
https://reasonandscience.catsboard.com/t2157-the-transport-of-proteins-into-mitochondria-is-a-interdependent-complex-system

The Transport of Proteins into Mitochondria
https://reasonandscience.catsboard.com/t2155-the-transport-of-proteins-into-mitochondria

The Fission and Fusion of Mitochondria
https://reasonandscience.catsboard.com/t2368-the-fission-and-fusion-of-mitochondria

The Role of the Mitochondrion in Aerobic Respiration
https://reasonandscience.catsboard.com/t2154-the-role-of-the-mitochondrion-in-aerobic-respiration

Your Inner Locomotive Revealed
https://reasonandscience.catsboard.com/t2140-nadh-dehydrogenase-complex-i-in-mitochondria

Chloroplasts carry out photosynthesis

Mitochondria and chloroplasts contain their own genetic material and divide by binary fission
Protein Sorting to Organelles
The cotranslational sorting of some proteins occurs at the endoplasmic reticulum membrane
Proteins are sorted post-translationally to the nucleus, peroxisomes, mitochondria, and chloroplasts

Membrane Structure, Synthesis, and Transport

Membrane Structure, Synthesis, and Transport
Membrane Structure
Lipids
Biological membranes are a mosaic of lipids, proteins, and carbohydrates
Proteins associate with membranes in three different ways
Proteins
Membranes Are Semifluid
Synthesis of Membrane Components in Eukaryotic Cells
Most transmembrane proteins are first inserted into the ER membrane
The attachment of carbohydrates to proteins occurs in the ER and golgi apparatus
The phospholipid bilayer is a barrier to the movement of hydrophilic solutes
Cells maintain gradients across their membranes
Osmosis is the movement of water across membranes to balance solute concentrations
Transport Proteins
Channels provide open passageways for solute movement
Transporters bind their solutes and undergo conformational changes
Active transport is the movement of solutes against a gradient
ATP-driven ion pumps generate ion electrochemical gradients
Exocytosis and Endocytosis

Energy, Enzymes, and Metabolism

Major metabolic pathways and their inadequacy for origin of life proposals
https://reasonandscience.catsboard.com/t2004-major-metabolic-pathways-and-their-inadequacy-for-origin-of-life-proposals

Chloroplasts and mitochondria: Completing an energy cycle
https://reasonandscience.catsboard.com/t1607-chloroplasts-and-mitochondria-completing-an-energy-cycle

Energy Exists in Different Forms
The change in free energy determines the direction of a chemical reaction
Cells use ATP to drive endergonic reactions
Enzymes and Ribozymes
Enzymes increase the rates of chemical reactions
Enzymes recognize their substrates with high specificity and undergo conformational changes
Enzyme function is influenced by the substrate concentration and by inhibitors
Additional factors influence enzyme function
Overview of Metabolism

How Cellular Enzymatic and Metabolic networks  point to design
https://reasonandscience.catsboard.com/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design

Metabolic pathways in general are found to be ‘optimal’
https://reasonandscience.catsboard.com/t1512-metabolic-pathways-in-general-are-found-to-be-optimal

ATP: The  Energy  Currency for the Cell
https://reasonandscience.catsboard.com/t2137-atp-the-energy-currency-for-the-cell

Where did Glucose come from in a prebiotic world ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world

Glucose and glycogen, and its importance for life
https://reasonandscience.catsboard.com/t2158-glucose-and-its-importance-for-life

The pentose phosphate pathway
https://reasonandscience.catsboard.com/t2172-the-pentose-phosphate-pathway

Catabolic reactions recycle organic building blocks and produce energy intermediates such as ATP
Redox reactions involve the transfer of electrons
Anabolic reactions require an input of energy to make larger molecules

Recycling, and the orchestration of anabolism and catabolism, evidence of natural forces, or design?
https://reasonandscience.catsboard.com/t2696-metabolism-and-catabolism-evidence-of-design

Metabolic pathways are regulated in three general ways
Recycling of organic molecules
Proteins in eukaryotes and archaea are broken down in the proteasome

Proteasome Garbage Grinders, evidence of luck, evolution, or design?
https://reasonandscience.catsboard.com/t1851-proteasome-garbage-grinders

Autophagy recycles the contents of entire organelles

Cellular respiration and fermentation

Overview of cellular respiration
Glycolysis
Glycolysis Is a metabolic pathway that breaks down glucose to pyruvate
Breakdown of Pyruvate

Glycolysis
https://reasonandscience.catsboard.com/t1796-glycolysis

Citric Acid Cycle

The Citric acid cycle, or Krebs (TCA) cycle
https://reasonandscience.catsboard.com/t1464-the-citric-acid-cycle-or-krebs-tca-cycle

Overview of oxidative phosphorylation
The electron transport chain establishes an electrochemical gradient
ATP Synthase makes ATP via chemiosmosis

The irreducibly complex ATP Synthase nanomachine, amazing evidence of design
https://reasonandscience.catsboard.com/t1439-the-irreducibly-complex-atp-synthase-nanomachine-amazing-evidence-of-design

NADH Oxidation makes a large proportion of a cell’s ATP

Nicotinamide adenine dinucleotide (NAD) in origin of life scenarios
https://reasonandscience.catsboard.com/t2708-nicotinamide-adenine-dinucleotide-nad-in-origin-of-life-scenarios

Free-Energy Changes Drive Oxidative Phosphorylation and Other Stages of Glucose Breakdown
A closer look at ATP Synthase
ATP Synthase is a rotary machine that makes ATP as it spins
Connections among carbohydrate, protein, and fat metabolism
Anaerobic respiration and fermentation
Some microorganisms carry out anaerobic respiration
Fermentation is the breakdown of organic molecules without net oxidation

Photosynthesis

Overview of Photosynthesis

Photosynthesis
https://reasonandscience.catsboard.com/t1555-photosynthesis

Photosynthesis powers the biosphere
In plants and algae, photosynthesis occurs in the chloroplast
Photosynthesis occurs in two stages: light reactions and the calvin cycle
Reactions that harness light energy
Light energy is a form of electromagnetic radiation
Pigments absorb light energy

Why the biosynthesis pathway of Chlorophyll must be intelligently designed
https://reasonandscience.catsboard.com/t1546-why-the-biosynthesis-pathway-of-chlorophyll-must-be-intelligently-designed

Plants contain different types of photosynthetic pigments
Photosystems II and I work together to produce ATP and NADPH
Cyclic electron flow produces only ATP
Molecular features of photosystems
The cytochrome complexes of mitochondria and chloroplasts contain  related proteins
Photosystem II captures light energy and produces O2
Electrons vary in energy as they move from Photosystem II to Photosystem I to NADP+
Synthesizing carbohydrates via the Calvin Cycle
The Calvin Cycle incorporates CO2 into carbohydrate

Cyanobacterias, amazing evidence of design
https://reasonandscience.catsboard.com/t1551-cyanobacteria-amazing-evidence-of-design

Light-harvesting complex
https://reasonandscience.catsboard.com/t1547-light-harvesting-complex-of-photosynthesis

The oxygen-evolving complex (OEC) of photosystem II is irreducibly complex.
https://reasonandscience.catsboard.com/t1583-the-oxygen-evolving-complex-oec-of-photosystem-ii-is-irreducible-complex

The earth's  atmosphere
https://reasonandscience.catsboard.com/t1556-the-earth-s-atmosphere

Light-independent reactions 
https://reasonandscience.catsboard.com/t2164-the-calvin-benson-cycle

Rubisco's amazing evidence of design  
https://reasonandscience.catsboard.com/t1554-the-rubisco-enzymes-amazing-evidence-of-design

Cell Communication

General Features of Cell Communication

Signalling: Main topics on signalling
https://reasonandscience.catsboard.com/t2811-signalling-maintopics-on-signalling

Cells detect and respond to signals from their environment and from other cells

Adaptation of cells to new environments
https://reasonandscience.catsboard.com/t2061p125-my-articles#6174

Cell-to-Cell communication can occur between adjacent cells and between cells that are long distances apart

Cell internet: Cells have their own internet communication channels and cargo delivery service, all in one 
https://reasonandscience.catsboard.com/t2760-cell-internet-cells-have-their-own-internet-communication-channels-and-cargo-delivery-service-all-in-one

Cell Communication and signaling, evidence of design 
http://reasonandscience.heavenforum.org/t2181-cell-communication-and-signaling-evidence-of-design

Cells usually respond to signals via a three-stage process
Cellular receptors and their activation
Receptors undergo conformational changes
Cells contain a variety of cell surface receptors that respond to extracellular signals
Cells also have intracellular receptors activated by signaling molecules that pass through the plasma membrane
Signal transduction and the cellular response
Receptor tyrosine kinases activate signal transduction pathways involving a protein kinase cascade that alters gene transcription
Second messengers such as cyclic AMP are key components of many signal transduction pathways
The main advantages of second messengers are amplification and speed
Apoptosis: Programmed Cell Death
Signal transduction pathways lead to apoptosis

Apoptosis, Cell's essential mechanism of  programmed suicide points to design
https://reasonandscience.catsboard.com/t2193-apoptosis-cell-s-essential-mechanism-of-programmed-suicide-points-to-design

The  essential signaling pathways   for animal development 
http://reasonandscience.heavenforum.org/t2351-the-essential-signaling-pathways-for-animal-development

How Signaling in biology points to design
https://reasonandscience.catsboard.com/t2745-how-signaling-in-biology-points-to-design

How  intracellular Calcium signaling,  gradient and its role as a universal intracellular regulator points to design
https://reasonandscience.catsboard.com/t2448-howintracellular-calcium-signaling-gradient-and-its-role-as-a-universal-intracellular-regulator-points-to-design

How signaling between cells can orient a mitotic spindle 
https://reasonandscience.catsboard.com/t2383-how-signaling-between-cells-can-orient-a-mitotic-spindle

The Hippo signaling pathway in organ size control, tissue regeneration and stem cell self-renewal 
https://reasonandscience.catsboard.com/t2350-the-hippo-signaling-pathway-in-organ-size-control-tissue-regeneration-and-stem-cell-self-renewal

Multicellularity


Extracellular matrix and cell walls

Cell Junctions and the Extracellular Matrix
http://reasonandscience.heavenforum.org/t2187-cell-junctions-and-the-extracellular-matrix

Unicellular and multicellular Organisms are best explained through design
https://reasonandscience.catsboard.com/t2010-unicellular-and-multicellular-organisms-are-best-explained-through-design

The extracellular matrix in animals supports and organizes cells and plays a role in cell signalling
Adhesive and structural proteins are major components of the ECM of animals
Animal cells also secrete polysaccharides into the ECM
The cell wall of plants provides strength and resistance to compression
Plant cell walls consist of primary and secondary walls
Cell Junctions
Anchoring jJunctions link animal cells to each other and to the ECM
Cell adhesion molecules (CAMs) form links between cells and to the ECM
Tight junctions prevent the leakage of materials across animal cell layers
Gap Junctions between animal cells provide passageways for intercellular transport
The middle lamella cements adjacent plant cell walls together
Plasmodesmata are channels connecting the cytoplasm of adjacent plant cells
Tissues
Six different cell processes produce tissues and organs
Animals are composed of epithelial, connective, nervous, and muscle tissues
Plants contain dermal, ground, and vascular tissues

Gene Regulation


Overview of Gene Regulation
Bacteria regulate genes in response to changes in their environment
Eukaryotic gene regulation produces different cell types in a single organism
Eukaryotic gene regulation enables multicellular organisms to proceed through developmental stages
Gene regulation occurs at different points in the process from DNA to protein
Regulation of transcription in bacteria
Transcriptional regulation involves regulatory transcription factors and small effector molecules
The lac operon contains genes that encode proteins involved in lactose metabolism
The lac operon is under negative control by a repressor protein
The lac operon is also under positive control by an activator protein
The trp operon is under negative control by a repressor protein
Regulation of transcription in eukaryotes: roles of transcription factors and mediator
Eukaryotic structural genes have a core promoter and regulatory elements
Eukaryotic structural genes have a core promoter and regulatory elements
RNA Polymerase II, General Transcription Factors, and Mediator are needed to transcribe eukaryotic structural genes
Activators and Repressors may influence the function of GTFs or Mediator
Regulation of transcription in eukaryotes: changes in chromatin structure and DNA methylation
Transcription is controlled by changes in chromatin structure
Histone modifications affect gene transcription
Eukaryotic genes Are flanked by nucleosome-free regions
Transcriptional activation involves changes in nucleosome locations, composition, and histone modifications
DNA methylation inhibits gene transcription
Epigenetic Gene Regulation
Different types of molecular changes underlie epigenetic gene regulation
Epigenetic gene regulation may occur as a programmed developmental change
Epigenetic gene regulation may be caused by environmental agents
Regulation of RNA modification and translation in eukaryotes
Alternative splicing of pre-mRNAs increases protein diversity
RNA interference blocks the expression of mRNA
The prevention of iron toxicity in mammals involves the regulation of translation

The Eukaryotic Cell Cycle, Mitosis, and Meiosis

The Eukaryotic Cell Cycle, Mitosis, and Meiosis
The Eukaryotic Cell Cycle

The Cell cycle
https://reasonandscience.catsboard.com/t2109-the-cell-cycle

Cellular reproduction: Mitosis
https://reasonandscience.catsboard.com/t1992-mitosis-and-cell-division

Chromosomes are inherited in sets and occur in homologous pairs
The cell cycle is a series of phases that lead to cell division
The cell cycle is controlled by checkpoint proteins
Mitotic cell division
In preparation for cell division, eukaryotic chromosomes are replicated and compacted to produce pairs called sister chromatids
The mitotic spindle organizes and sorts chromosomes during cell division
The transmission of chromosomes requires a sorting process known as mitosis
Meiosis and sexual reproduction
Bivalent formation and crossing over occur at the beginning of meiosis
Meiosis I separates homologous chromosomes
Meiosis II separates sister chromatids
Mitosis and meiosis differ in a few key steps
Sexually reproducing species produce haploid and diploid cells at different times in their life cycles

Developmental Genetics

Developmental Genetics
Developmental biologists use model organisms to study development
Both animals and plants develop by pattern formation
Pattern formation depends on positional information
Morphogens and Cell-to-Cell contacts convey positional information
Pattern formation occurs in phases that are controlled by transcription factors
Development in Animals
Embryonic development determines the pattern of structures in the adult
Phase 1 Pattern formation: maternal effect genes promote the formation of the body axes
The study of drosophila mutants has identified genes that control the development of segments
Phase 2 pattern formation: segmentation genes act sequentially to divide the drosophila embryo into segments
Phase 3 pattern formation: homeotic genes control the development of segment characteristics
Phase 4 pattern formation: stem cells can divide and differentiate into specialized cell types
Development in Plants
Plant development occurs from meristems that are formed in the embryo
Plant homeotic genes control flower development

Amino Acids 

Amino Acids and peptide bonding
Amino Acids 
What Are the Structures and Properties of Amino Acids?
Amino Acids Are the Building Blocks of Proteins
There Are 20 Common Amino Acids
Synthesis of amino acids on a prebiotic earth
The prebiotic soup hypothesis
Primitive hydrothermal systems
Extraterrestrial input of amino acids
What Are the Optical and Stereochemical Properties of Amino Acids?
Amino Acids Are Chiral Molecules
Homochirality, a unresolved issue
A common step determines the chirality of all amino acids
A common step determines the chirality of all amino acids
The Mechanism of the Aminotransferase (Transamination) Reaction 37
Double-Displacement (Ping-Pong) Reactions Proceed Via Formation of a Covalently Modified Enzyme Intermediate
Aminotransferases Show Double-Displacement Catalytic Mechanisms 
Why are 20 amino acids used to make proteins? Why not more or less ? And why especially the ones that are used amongst hundreds available?
The 20 standard amino acids - as general reasons for choosing side chains, we can now consider the 20 individually.
Transition from prebiotic amino acid synthesis, to biosynthesis pathways in modern cells to synthesize amino acids
The amino acid sequences of polypeptides determine the structure and function of Proteins
The amino acid sequences of polypeptides determine the structure and function of Proteins
Plants and animals require fixed nitrogen
Amino acid synthesis requires solutions to four key biochemical problems
The Nitrogen cycle
Nitrogen acquisition and amino acid metabolism
Which metabolic pathways allow organisms to live on inorganic forms of nitrogen?
Nitrogen fixation
Nitrogen decay (ammonification) 
Nitrification
Denitrification
Nitrate assimilation is the principal pathway for ammonium biosynthesis
Organisms gain access to atmospheric N2 via the pathway of nitrogen fixation
Nitrogen fixation
Overview of the Nitrogenase enzyme complex
The nitrogenase enzyme
Overview of the Nitrogenase enzyme complex
Dinitrogenase reductase - FE Protein subunit
The Nitrogenase MoFe protein subunit 
The Nitrogenase metal clusters 
Nitrogenase Fe Protein [4Fe-4S] cofactor
P-cluster: role in catalysis
FeMo-cofactor ( M-cluster )
The role of MgATP in nitrogenase catalysis 
The Nitrogenase pathway and mechanism
Overview
Docking of the two subunits
Breaking the N2 triple bond: insights into the nitrogenase mechanism 
Electron Transport to Nitrogenase
What Is the Metabolic Fate of Ammonium?
What Is the Metabolic Fate of Ammonium?
Incorporation of Ammonia into Organic Compounds
Glutamate dehydrogenase (GDH)
Glutamine synthetase (GS)
Glutamine Synthetase Is a Central Control Point in Nitrogen Metabolism
A molecular Computer
Communication Between Many Active Sites
Two Doors
What Regulatory Mechanisms Act on coli Glutamine Synthetase?
Glutamine Synthetase Is Allosterically Regulated
Glutamine synthetase (GS), an incredible molecular super-computer which defies naturalistic explanations
Glutamine synthetase (GS), a incredible molecular super-computer which defies naturalistic explanations
A molecular Computer
Communication Between Many Active Sites
How Do Organisms Synthesize Amino Acids?
How Do Organisms Synthesize Amino Acids?
Amino Acid Precursors and Biosynthesis Pathways
What makes an amino acid essential?
Amino acids are made from intermediates of the Citric Acid Cycle and other major pathways
Several classes of reactions play special roles in the biosynthesis of amino acids and nucleotides
Pyridoxal phosphate (PLP) - Vitamin B6
BIOSYNTHESIS OF VITAMIN B6
Tetrahydrofolate ( THF  H4 folate ) and Vitamin B12 
One-carbon Metabolism: Basic Concepts
Folate
The folate biosynthesis pathway
The folate biosynthesis pathway
The proteins used in the folate biosynthesis pathway
GTP cyclohydrolase I
Dihydroneopterin aldolase
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
Dihydropteroate synthase
Dihydrofolate synthetase/folylpolyglutamate synthetase
Dihydrofolate reductase
S-adenosylmethionine (adoMet or SAM)
S-adenosylmethionine (adoMet or SAM) synthesis
Cheating of secular science papers, claiming of evolutionary mechanisms in place prior to life fully setup and self-replication.

What Is the Metabolic Fate of Ammonium?
https://reasonandscience.catsboard.com/t2590p25-origins-what-cause-explains-best-our-existence-and-why#5934

Proteins, the complex nanomachines of the Cell

Five factors are critical for protein folding and stability
The Defining Concept of Biochemistry Is “Molecular Recognition Through Structural Complementarity”
Proteins contain functional domains within their structures
Cellular Proteins are primarily responsible for the characteristics of living cells and an organism’s traits
The impossible task to synthesize proteins on a prebiotic earth without external direction
Proteins: how they provide striking evidence of design
Few of the many  possible polypeptide chains will be useful to Cells
Amino Acids Used by Life Are Finely Tuned to Explore "Chemistry Space"
Problems with Making Mutation the Basis for Macroevolution
Peptide bonding of amino acids to form proteins and its origins
The amino acid sequences of polypeptides determine the structure and function of Proteins
Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains
Peptidyl transferase catalyzes peptide-bond synthesis
Structure of the Active Site of the Peptidyl Transferase Center (PTC)
The Mechanism of Peptide Bond Formation
The formation of a peptide bond is followed by the GTP-driven a translocation of tRNAs and mRNA
Mystery of Life's Origin 
Amino Acids Are Added to the C-terminal End of a Growing Polypeptide Chain
Peptide Bond Formation: RNA's Big Bang
The Emergence of Information-Rich Biopolymers
Forces Stabilizing Proteins - essential for their correct folding
Evolution of the correct protein foldings
Chaperones
Chaperones
Molecular chaperones help guide the folding of most proteins
The Hsp70 family
Evolution of Hsp70 proteins
GroEL/ES Chaperonins
The GroEL/ES Chaperonin forms closed chambers in which proteins fold 
ATP binding and hydrolysis drive the conformational changes in GroEL/ES 
Protein "dressing room" has electronic walls 
What Chaperone Proteins Know 
Cells utilize several types of chaperones
Exposed Hydrophobic Regions Provide Critical Signals for Protein Quality Control
Chaperone-assisted protein folding 
Chaperone machines for protein folding, unfolding and disaggregation
Chaperone machines for protein folding, unfolding and disaggregation  1
Hsp70 chaperones: Cellular functions and molecular mechanism 
Biochemists trap a chaperone machine in action 6
How chaperones emerged based on naturalistic explanations:
Hsp90 chaperones
The interdependent and irreducible structures required to make proteins
Gene Regulation

Nucleosomes function and design
https://reasonandscience.catsboard.com/t2051-nucleosomes-function-and-design

Chromosome condensation and compaction is nothing short than awe-inspiring, amazing evidence of setup by a supreme intelligence.  
https://reasonandscience.catsboard.com/t2086-chromosome-condensation-amazing-evidence-of-design

Eukaryotic genes Are flanked by nucleosome-free regions
Transcriptional activation involves changes in nucleosome locations, composition, and histone modifications
Different types of molecular changes underlie epigenetic gene regulation
Epigenetic gene regulation may occur as a programmed developmental change
Epigenetic gene regulation may be caused by environmental agents
Regulation of RNA modification and translation in eukaryotes
Alternative splicing of pre-mRNAs increases protein diversity
RNA interference blocks the expression of mRNA
The prevention of iron toxicity in mammals involves the regulation of translation



Last edited by Admin on Fri 29 May 2020 - 13:30; edited 4 times in total

https://reasonandscience.catsboard.com

Otangelo


Admin
The gene regulatory network

Control of Gene Expression and gene regulatory networks  point to intelligent design
https://reasonandscience.catsboard.com/t2194-control-of-gene-expression-and-gene-regulatory-networks-point-to-intelligent-design

Gene Regulatory Networks Controlling Body Plan Development  
https://reasonandscience.catsboard.com/t2318-gene-regulatory-networks-controlling-body-plan-development

A walk through the epigenetic landscape which regulates Gene expression points to the requirement of intelligent setup and design
https://reasonandscience.catsboard.com/t2061p125-my-articles#6169

Activation
Repression
Dynamic exchange of enzymatic activities in coregulatory complexes
Signal-dependent activator/coactivator cycles and epigenetic control
Chromatin modifications as signals for dynamic transcriptional modulation
Ordered Recruitment: Gene-Specific Mechanism of Transcription Activation

Nucleosomes function and design
https://reasonandscience.catsboard.com/t2051-nucleosomes-function-and-design#3509

Regulation of transcription in eukaryotes: changes in chromatin structure and DNA methylation
Regulation of transcription in eukaryotes: changes in chromatin structure and DNA methylation
Transcription is controlled by changes in chromatin structure
Histones

Post-transcriptional modifications (PTMs) of histones affect gene transcription
https://reasonandscience.catsboard.com/t2727-post-transcriptional-modifications-ptms-of-histones-affect-gene-transcription#6179

Combinatorial readout of and cross-talk between PTMs

What defines body structures and architecture?

An overview of the various mechanisms that define body shape and form
The genetic toolkit
Field-specific selector genes
Compartment selector genes
What is a compartment boundary?
Why are boundaries important?
Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation
Combinatorial gene regulation by modulation of relative pulse timing
Sets of morphogenetic markers on the cell surface can be written in the form of a matrix
Transcriptional Regulation by Trithorax-Group Proteins
Epigenetic Gene Regulation
Homeobox and Hox Genes
Homeotic genes
Homeobox Genes and the Vertebrate Body Plan
The Homeotic Selector Genes
Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell


Transcription factors (TF)
https://reasonandscience.catsboard.com/t2738-transcription-factors-tf

The DNA methylation code and language
https://reasonandscience.catsboard.com/t2725-the-dna-methylation-code-and-language#6177

Chromatin remodeling
https://reasonandscience.catsboard.com/t2726-chromatin-remodeling#6178

The modification of histones is dynamic, and the corresponding enzymes include

The DNA methylation code and language
https://reasonandscience.catsboard.com/t2725-the-dna-methylation-code-and-language#6177

Chromatin remodeling
https://reasonandscience.catsboard.com/t2726-chromatin-remodeling#6178

What defines body structures and architecture?
Homeobox and Hox Genes
Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell

Transcription factors (TF)
https://reasonandscience.catsboard.com/t2738-transcription-factors-tf

The make and maintenance of specialized Cell types

https://reasonandscience.catsboard.com

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