Heredity has fundamental physical and functional units {gene}. Johannsen invented the word gene [1909]. Genes are nucleotide sequences at chromosome positions. Genes code for proteins or RNAs {gene product} for regulation, structure, or transport. Genes controlling behavior are not qualitatively different from those governing other cell functions.
Master genes {BMAL1 gene} can control timing. Superchiasmatic nucleus regulates waking and sleeping. Dorsomedial nucleus controls eating cycles.
Genes {CALHM1 gene} can regulate neuron calcium concentration.
Human DNA sequences {human accelerated region} (HAR1) (HAR2) can have rapid mutation compared to chimpanzees. HAR1 codes RNA. HAR2 (HACNS1) regulates wrist and thumb development.
Genes {IRGM gene} can act against bacteria.
Genes {Ku70 gene} can make DNA-repair Ku70 transcription factors.
Worms, insects, and vertebrates have pseudogene-regulated genes {makorin1 gene}.
Gene {MECP2 gene} mutations can cause autism Rett syndrome.
Metal-dependent endopeptidases {metalloproteinase} can break down interstitial type I, II, or III collagen, basement-membrane type IV collagen, or type V collagen. Metalloproteinases {matrilysin} {PUMP-1 gene} can split extracellular matrix. Metalloproteinases {gelatinase A} {gelatinase B} split basement membrane. MMP-1 and MMP-13 split interstitial collagen. Metalloproteinase {stromelysin-3} (MMP-3) splits extracellular matrix.
Plasminogen activators and other serine proteinases activate metalloproteinases. Cells have tissue metalloproteinase inhibitors {TIMP gene}, such as TIMP-1, TIMP-2, TIMP-3, and TIMP-4.
Genes {multidrug resistance 1 gene} {MDR1 gene} can make cell-membrane pumps that can send chemotherapy drugs out tumor cells.
Mice without a gene {Runx1 gene} do not sense heat or cold. Runx1 gene can affect neuropathic pain.
Genes {TRIM5alpha gene} can stop PtERV1 from replicating.
Drosophila genes {Yellow gene} can make black pigment. Without yellow genes, color is yellow.
Genes {AMY1 gene} can make salivary amylase to break down starch. Humans have many copies.
Genes {LCT gene} can make lactase to metabolize lactose.
Protein complexes {lac repressor} can block lactase-gene transcription. Lactose metabolites can bind to lac repressor and cause them to leave DNA, allowing gene transcription.
Genes {CETP gene} can control blood cholesterol-particle size.
Genes {CSE gene} can make enzyme that makes hydrogen-sulfide vasodilator.
Human red-blood-cell surface genes {Duffy gene} can make part of Plasmodium receptor, in brain, spleen, and kidney.
Enzymes {gamma-glutamyl carboxylase} can clot human blood, be in fruit flies, make cone snail venom, and participate in embryonic development. Carboxylase began at least 540 million years ago, when arthropods, mollusks, and chordates diverged, because arthropod, mollusc, and chordate gamma-glutamyl-carboxylase genes have similar introns, which direct protein folding. Therefore, introns began before 540 million years ago.
Transcription factors {hypoxia-inducible factor 1} {HIF-1 gene} can increase after hypoxia and cause increased red-blood-cell mass, blood-vessel growth, and increased ventilation.
Using sugar, proteins {selectin gene} can bind to white blood cells, to allow cells to leave blood and go into tissue.
Genes {tryptophan hydroxylase I gene} can make serotonin for blood.
Gene {AKT gene} products can aid cell suicide.
Gene {BCL-3 gene} products can regulate cell death. Mutated gene causes lymphoma.
Gene {lethal gene} mutations can kill organisms, because gene no longer produces necessary enzyme.
Transcription factors {p53 factor} {p53 protein} can start apoptosis in damaged cells. When p53 gene mutates, gene product causes cancer.
Genes {SEPS1 gene} can break down damaged proteins. Damaged proteins can cause inflammation.
Gene {archipelago gene} (ago gene) (AGO gene) products {ago protein} can regulate cell cycle, cell-differentiation Notch signaling pathway, and Alzheimer's-disease beta-amyloid precursor protein (APP) processing pathway. Ago protein contains F-box domain and seven WD40 repeat motifs. F-boxes and WD40 repeats are typically in ubiquitin-ligase complexes of ubiquitin/proteasome proteolytic pathway.
F-box
F-box domain interacts with proteins {Skp1 protein} of protein complexes {SCF complex}. Organisms have many F-box proteins, with more than 100 in Caenorhabditis elegans roundworm, for example.
WD40
WD40 repeats interact with cyclin E and cyclin F. WD40 repeats have repeating units of 40 amino acids, with tryptophan, with symbol W, and aspartic acid, with symbol D, at defined positions.
LRR repeats
Leucine-rich repeats {LRR repeat} interact with cyclin E.
cyclin E
Ago protein recognizes cyclin E and catalyzes covalent ubiquitin-to-cyclin-E attachment. Ago protein decreases cell proliferation by this mechanism.
In Drosophila cell cycle, regulatory protein {cyclin E} can increase transition from gap-1 phase to S phase, which has DNA synthesis and replication. Cyclin E genes are tumor suppressor genes. Cyclin E problems can cause cancer. Elevated intracellular cyclin E levels increase cell proliferation.
Protein-complex {ubiquitin ligase complex} substrate-recognition components are in proteolytic pathways {ubiquitin/proteasome proteolytic pathway}. Ubiquitination attaches 76-amino-acid peptides {ubiquitin, complex} to proteins. The 26S proteasome then degrades ubiquitin and protein. Ubiquitin/proteasome proteolytic pathway decreases cell-cycle-regulation, cell-proliferation, differentiation, and development proteins.
Ubiquitin/proteasome proteolytic pathway has ubiquitin-activating enzymes {E1 gene}.
Ubiquitin/proteasome proteolytic pathway has ubiquitin-conjugating enzymes {E2 gene}.
Ubiquitin/proteasome proteolytic pathway has ubiquitin ligases {E3 gene}, such as SCF types. Ubiquitin ligase connects cell-cycle protein to ubiquitin and controls protein level.
Receptors {cell-surface receptor} can use hundreds of genes.
peptides
Cell-surface receptors can bind acetylcholine, glutamate, glycine, and gamma-aminobutyric acid and endorphin and enkephalin peptides. Acetylcholine binds to sodium-ion-channel receptor. Glutamate binds to NMDA receptor. Glycine and GABA bind to chloride-ion-channel receptors. Receptor proteins using G proteins can couple to ion-channel proteins. Same-type receptors can have variable binding affinity and transport efficacy.
Alpha-adrenergic and beta-adrenergic cell-surface receptors {adrenergic receptor} can bind epinephrine and similar compounds.
membrane
Amino ends are outside membranes, and carboxyl ends are inside membranes. Seven helices pass through membrane.
functions
Adrenergic receptors can couple to G protein. Adrenergic receptors can activate or inhibit adenylate cyclase to make or decrease cAMP.
functions: phosphates
Adrenergic receptors can activate phospholipase to break down inositol phospholipids in membrane into inositol triphosphate and diacylglycerol. Inositol triphosphate makes calcium vesicles release calcium ions, which bind to calmodulin, which regulates enzymes such as protein kinase. Diacylglycerol activates protein-kinase C proteins. Phosphorylation causes conformational changes that expose active sites and activate protein kinases. Protein phosphatases, such as cytoplasmic CD45 membrane protein, remove phosphates.
Cell-surface receptor proteins {CD4 protein} can bind protein kinase at carboxyl ends inside membranes.
Cell-surface receptors {growth factor receptor} can bind growth factors. Growth factors activate 100 immediate early genes, which then make transcription factors.
structure
Growth-factor receptors pass one helix through membrane. Receptor is outside membrane. Kinase or cyclase is inside membrane.
types
Atrial naturietic peptide has protein kinase and guanylate cyclase. Activin receptor protein has serine-threonine kinase. Phosphoprotein phosphatase has tyrosine phosphatase. Growth factor receptor has tyrosine kinase.
Cell-surface receptors {hormone binding receptor} can bind hormones. Hormone-binding receptors affect G proteins inside cell membranes. G proteins use GTP to activate adenylate cyclase and make cAMP. cAMP affects protein kinase A, which then phosphorylates transcription factors, such as CRE-binding protein, that bind to cAMP response elements (CRE).
Muscle-synapse cell-surface receptors {nicotinic cholinergic receptor} can bind acetylcholine. Nicotinic receptors have membrane alpha-helix pores. Acetylcholine binds to two alpha helices. Four genes make protein receptors. Gene alleles have different mRNA splicings, making many slightly different nicotinic cholinergic receptors.
Cell-surface receptors {steroid receptor} can bind steroids. Steroids can cross membranes and bind to steroid-receptor proteins inside cells, allowing them to move to cell nucleus.
Cell-surface receptors can bind hormones and affect GTP-binding proteins {G protein} inside cell membranes. Activated G protein catalyzes its return to unactivated state, thus timing rate of G-protein processes. Immediate-early genes activated in learning use cAMP signal paths.
cyclic AMP
G protein uses GTP to activate adenylate cyclase and make cAMP. cAMP affects protein kinase A, which then phosphorylates CRE-binding protein, which binds to cAMP response elements (CRE).
senses
Olfactory sensors use G-protein transduction.
structure
G protein is similar to proteins for cross-membrane signaling, protein synthesis, cell molecule transport, and cross-membrane transport.
Steroid-receptor proteins bind to regulatory-region 15-base sequences {hormone-response element}, for activation or repression.
Chemicals {ionophore} can artificially raise cell calcium concentration.
Serine proteinases {plasminogen activator} can have cell-surface receptors. Urokinase plasminogen activator (uPA) can activate matrix metalloproteinases. Plasminogen-activator inhibitors counteract tissue plasminogen activator (tPA).
Retina rod-cell proteins {rhodopsin}| can absorb light and bind GTP to transducin, which activates phosphodiesterase, which breaks down cGMP, which closes cGMP-dependent ion channels and so causes hyperpolarization. Rhodopsin is similar to adrenergic receptor. Opsin proteins are similar to rhodopsin, because both use 11-cis-retinal as chromophore. Absorption maximum differs for opsins and rhodopsin.
GTP-binding proteins {transducin} can transduce signals in eye.
ATR protein, matrilins, integrins, and other cell-surface protein-interaction proteins have extra-cellular domains {von Willebrand factor type A}.
Genes {development genes} can control development. Serotonin affects early embryo development, and mother supplies it before fetus can make it.
Genes {histone deacetylase 4 gene} (HDAC4) can regulate muscle and bone development and maintain rod and bipolar cells.
Genes {early-response gene} {immediate early gene} can respond first to stimulation and then trigger later changes.
Homeobox and other genes {master control gene} can start gene-expression chains.
Stickleback-fish gene {Pitx1 gene} products can affect pelvic fin and other structures.
Gene {Notch gene} products can activate signaling pathways and regulate whether neural precursors become neurons or glia. Enzymes cleave Notch and APP transmembrane proteins in membrane plane {regulated intramembrane proteolysis}, to liberate cytosolic fragments, which enter cell nucleus to control gene transcription. Regulated intramembrane proteolysis is similar from bacteria to humans.
Gene {Bmi-1 gene} products can activate signaling pathways.
Gene {Wnt gene} products can activate signaling pathways.
Homeodomain binding proteins have one helix in DNA major groove and another helix across DNA that contacts other proteins. Fruitfly homeotic genes {homeobox gene} control head, jaws, teeth, thorax, and abdomen development and contain 180-base control regions {homeobox} that have helix-turn-helix {homeodomain} sequences, which are in many development genes. Regulatory region has 200,000 bases total.
retinoic acid
Extracellular-fluid retinoic acid controls homeotic-gene expression by binding to cell receptors and builds spinal cord, hindbrain, eye, and limbs. Low concentrations start gene expression at forebrain, and then higher concentrations start gene expression in sequence down to tail.
hormone
Thyroid hormone has similar receptors and controls gene expression.
Human Hox gene and other homeobox development genes {homeotic gene} can have sequences {homeotic series} along chromosomes. First gene is for mouth/nose, and last gene is for tail. Earliest homeobox genes were 1, 2/3, 4, 5, 6/7/8, and 9/10/11/12/13, in sequence. Fruit flies have 1, 2/3, 4, 5, 6, 7, 8, and 9/10/11/12/13. Fruit flies have non-homeobox region of DNA between 6 and 7. Chordates have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 13. Vertebrates have chordate-set variants on four different chromosomes.
Mammal genes {BF gene} can control gut, liver, and lungs. BF genes are similar to forkhead genes. BF-1 enlarges nasal retina and dorsal forebrain and is where neurons start dividing {germinal zone} before migrating. BF-2 enlarges ventral forebrain and temporal retina.
Mammal Emx-1 and Emx-2 genes {Emx gene} enlarge cerebrum, including corpus callosum. Fruitfly genes {empty spiracles gene} are similar.
Fruitfly genes {engrailed gene} can have homeoboxes but not be in homeotic gene sequence for body development. In most vertebrates, En-1 and En-2 genes, similar to engrailed gene, control midbrain and cerebellum growth.
Fruitfly genes {forkhead gene} can develop gut beginning and end.
Vertebrate genes {Hox gene} can be similar to fruitfly homeobox genes. If Hox genes are missing, symptoms are similar to DiGeorge congenital disease. Hox-b1, Hox-b2, Hox-b3, Hox-b4, and Hox-b5 genes enlarge hindbrain from third rhombomere down.
Genes {Lim-1 gene} can enlarge forebrain, midbrain, cerebellum, and first two or three hindbrain rhombomeres.
Genes {Otx gene} can affect brain development. Otx2 protein is for head development in embryo. After birth, it signals eye coordination.
Genes {Pax6 gene} can affect halteres balancing-wing development. Pax genes also affect eye and brain development.
Fruitfly genes {tailless gene} can develop gut beginning and end. Tailless gene enlarges forebrain, retina, and olfaction receptors.
At fertilization, genes {maternal-effect gene} from mother can code for transcription factors that establish front-to-back and top-to-bottom embryo polarity: bicoid protein, nanos protein, and dorsal gene protein transcription factor.
Proteins {bicoid protein transcription factor}, at only one pole, can make top-to-bottom gradient across embryo {morphogen, bicoid}. Nanos is at one pole, and bicoid is at other pole.
Proteins {nanos protein transcription factor}, at only one pole, can make top-to-bottom gradient across embryo. Nanos is at one pole, and bicoid is at other pole.
Maternal-effect follicle-cell genes can code for transcription factors {dorsal gene protein transcription factor} that establish front-to-back embryo polarity. Factor is similar to rel protein and NF-kappaB. Factor concentrates in cell nucleus ventrally, and cytoplasm dorsally, in all embryo cells. Cactus gene and Toll gene can partition dorsal-gene-protein transcription factor to these cell locations.
After first cell divisions, genes {gap gene} {hunchback gene} {hunchback-maternal gene} {knirps gene} {Kruppel gene} can code zinc-finger transcription factors that make bands along embryo and body regions by working with maternal-effect genes and by repressing each other. Gap genes also regulate genes expressed later. Transcription-factor binding sites are high-affinity or low-affinity, so transcription-factor concentration affects which genes transcribe and how much, leading to gradients and bands. In small regions, same chemicals cause different effects.
After gap-gene expression, genes {segmentation gene} can code for transcription factors that segment body, pair segments, and make segment polarity. Segmentation genes work with gap-gene products, and interact with each other using autofeedback, to sharpen segment boundaries. Segmentation genes include pair-rule genes, such as fushi tarazu gene, even-skipped gene, hairy gene, runt gene, and eve gene.
Segmentation genes {pair-rule gene} {eve gene} {even-skipped gene} {fushi tarazu gene} {hairy gene} {runt gene} can be about splitting body regions. In small regions, same chemicals cause different effects.
Genes {segment polarity gene} can be about front and back. In small regions, same chemicals can cause different effects.
Genes {FTO gene} can have alleles related to obesity.
Gene {NCoR gene} products can regulate fat-metabolism genes.
Hypothalamus proteins {PTP1B gene} can affect leptin signaling inside cells.
Hypothalamus proteins {SOC3 gene} can block leptin receptors.
Gene products {ERK factor} can be for cell growth.
Gene products {MEK factor} can be for cell growth.
Genes {NEGR1 gene} can affect hypothalamus neuron growth.
Transcription factors {NF-kappaB} can be for cell growth and cytokine production.
Mice genes {p16INK4a gene} can regulate cell growth and regeneration. With age, protein increases, and cells regenerate less.
Transcription factors {RSK factor} can be for cell growth.
Gene {SOS gene} products can be for cell growth.
Fox-01, Fox03, and Fox04 transcription factors {fox factor} {Fox gene} are for glucose metabolism and cell defense.
Gene products {orai 1 protein} can be in T-cell calcium-ion channels.
Proteins {siglec proteins} can prevent immune-system cells from activation.
Genes {intoxication genes} can affect intoxication.
Genes {ADH2 gene} can prevent alcoholism in some East Asians by affecting alcohol metabolism.
Genes {ALDH2 gene} can prevent alcoholism in some East Asians by affecting alcohol metabolism.
Alcohol affects fruitfly genes {cheap date gene}.
Genes {CHRM2 gene} can affect alcohol use.
Genes {DRD2 gene} can relate to alcoholism.
Genes {GABRA2 gene} can affect alcohol use.
C. elegans genes {slo-1 gene} can code for neuron, muscle-cell, and gland-cell BK potassium-ion-channel proteins. Alcohol affects BK-channel.
Genes {ATP1A2 gene} can code for membrane sodium-pump and potassium-pump proteins.
Genes {CACNA1A gene} can code for P/Q calcium-channel protein.
Gene {SCN1A gene} codes for sodium-channel proteins.
Transcription factors {MyoD gene} can be for muscle development and repair.
Genes {POP3 gene} can build striated muscle. POP2 and POP3 are also in plants.
Immediate-early genes {cFos gene} can make proteins that are neuronal activation markers.
Trimer proteins {clathrin triskelion} {clathrin gene} can have tetrahedron shapes at corners of presynaptic-nerve-ending icosahedral neurotransmitter-release structures.
Genes {Dscam gene} can guide axon growth.
Genes {Eph gene} can build brain topographic maps.
Notch, split enhancer, big brain, mastermind, and neuralized genes {neurogenic gene} can make cell-adhesion, signal-transduction, membrane-channel, and transcription-factor cell-to-cell signal proteins, to develop cells and inhibit nearby cells.
After making neurons, genes {neurotrophic gene} can code for secreted proteins {neurotrophic factor} that keep neurons alive, differentiate neurons, and make neurotransmitters, such as nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), CNTF, and NT-3. Other genes code for neurotrophic-factor receptor proteins.
After head and tail develop, daughterless and achaete-scute genes {proneural gene} can code for helix-loop-helix transcription factors that make neural precursor cells to start brain development. da enhances achaete-scute, and emc inhibits it.
Vertebrate genes {reelin gene} can affect axon branching and synapse creation.
Genes {Robo gene} can affect axon travel between hemispheres.
Cut and other genes {selector gene} can code for homeobox transcription factors that make neuron types.
Chromosome-7 genes {Forkhead box P2 gene} {FOXP2 gene} can have a mutation [-100000] associated with speech and language problems. Neanderthals also have this allele.
Fruitfly genes {Fru gene} can affect courtship rituals.
Amygdala proteins {stathmin} can affect fear.
Genes {ASPM gene} can help control brain size.
Genes {MCPH1 gene} can help control brain size.
Genes {CDK5RAP2 gene} can help control brain size.
Genes {CENPJ gene} can help control brain size.
One base change in a recessive gene {hothead gene} can cause fused petals, but Arabidopsis thaliana mustard plant can revert to wild type.
Plants have POP2 and POP3 genes {POP gene}.
Genes {terminator gene} can make proteins {ribosome inhibitor protein} that kill seeds.
Nuclear genes {cytochrome b gene} can make mitochondrial respiratory-chain proteins.
cybS
Nuclear genes {cybS gene} {SDHD gene, cytochrome} can make small cytochrome-b subunits. cybS protein is in mitochondria protein complexes {mitochondrial complex II} {succinate-ubiquinone oxidoreductase}, which are in electron transport chains.
Perhaps, cybS genes are tumor suppressor genes, because they are typically not in bladder, breast, cervix, stomach, lung, and ovary cancers or in melanomas. Perhaps, cybS protein is in carotid-body oxygen-sensing system. Without cybS protein, chronic hypoxic stimulation causes cell proliferation. Solid tumors are typically hypoxic compared to normal tissues.
Regulators {PGC-1alpha regulator} {PGC gene} can develop muscles by controlling respiration.
Nuclear genes {SDHD gene, mitochondria} can make mitochondrial respiratory chain proteins, which are small cytochrome-b subunits.
Genes {RNA gene} can make rRNA, tRNA, microRNA, RNA-protein enzyme complexes such as RMRP, and riboswitches.
In bacteria, long RNAs {riboswitch} have aptamer ends that bind to other molecules to act as sensors and other ends {expression platform, riboswitch} that change structurally, by making and unmaking hairpins, to affect protein translation or RNA transcription.
Protein complexes {TRAP complex} can bind tryptophan mRNA and inhibit tryptophan-gene transcription and mRNA translation.
X-chromosome genes {DAX gene} can tend to suppress SRY gene {sex-chromosome drive}. Y-chromosome is too small to reduce such suppression.
Maleness or femaleness genes {sexually antagonistic gene} cluster together and do not work in other sex. Maleness or femaleness genes are in different chromosomes in birds and mammals.
Y-chromosome genes {Sry gene} can control testes development and so testosterone production. Sry gene starts masculinization. Human SRY differs greatly from ape SRY, but has had few mutations.
Nematodes transcription-factor ELT-3, ELT-5, and ELT-6 genes {ELT gene} are active in youth. ELT genes are more active in old age. ELT genes are similar to human GATA transcription factors.
Human transcription-factor genes {GATA gene} can be active in youth. Nematode ELT genes are similar to GATA transcription factors.
Transcription-factor genes {c-myc gene} can restore pluripotency to cells.
Transcription-factor genes {Klf4 gene} can restore pluripotency to cells.
Transcription-factor genes {Oct4 gene} can restore pluripotency to cells.
Transcription-factor genes {Sox2 gene} can restore pluripotency to cells.
Individuals have ancestors {pedigree} {family tree} {geneaology}|.
Children or grandchildren can breed with parents {back cross}|.
In isolated populations, genetically similar individuals can breed {inbreeding, population}|. Continual inbreeding can result in species varieties in which all individuals are essentially genetically identical. 10% gene flow prevents too much inbreeding and keeps human populations from differentiating into new species.
Geographic isolation {isolating mechanism}, ecology, and genetic factors can increase interbreeding.
First filial generation {F1 generation} is children of parents.
Second filial generation {F2 generation} {grandchildren} is children of children.
Parental generation can have children {filial generation}, grandchildren, and so on.
Males and females {parental generation} can start reproductive lines.
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Date Modified: 2022.0225