Week 11 DNA Lab.

Part 1.

 My Personal Chromosome 

I was designated chromosome number 13. 

By going to the website HTTP://www.dnai.org/., I can find my chromosome by going through a few steps

• First, I choose Genome on the top menu. 
• Then, I choose Tour on the top menu. 
• Next, I choose Genome Fishing on the top menu. 
• And now I can find my chromosome # 13 from the drop-down menu at the bottom.

http://www.dnai.org/c/index.html

Now I can view the individual Genomes and find out what role do they play and what genetic information do they carry. 

http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&MAPS=ideogr,ugHs,loc&CHR=13

1) HMGB1 high mobility group box 1 [ Homo sapiens (human) ]

Gene ID: 3146, updated on 4-Nov-2015

Summary

Official Symbol

HMGB1provided by HGNC

Official Full Name

high mobility group box 1provided by HGNC

Primary source

HGNC:HGNC:4983

See related

Ensembl:ENSG00000189403; HPRD:01228; MIM:163905; Vega:OTTHUMG00000016670

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

HMG1; HMG3; HMG-1; SBP-1

Summary

This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription and is involved in the organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation, and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]

In other words: This gene regulates the transcription and organizes the DNA. It plays the role in cellular processes, including inflammation, cell differentiation, and tumor cell migration.

2) RB1 retinoblastoma 1 [ Homo sapiens (human) ]

Gene ID: 5925, updated on 25-Oct-2015

Summary

Official Symbol

RB1provided by HGNC

Official Full Name

retinoblastoma 1provided by HGNC

Primary source

HGNC:HGNC:9884

See related

Ensembl:ENSG00000139687; HPRD:01574; MIM:614041; Vega:OTTHUMG00000016900

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

RB; pRb; OSRC; pp110; p105-Rb; PPP1R130

Summary

The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]

In other words: First tumor suppressor gene found. The chromatin in regions of the chromosomes that are invariably heterochromatic; it contains highly repetitive sequences of DNA that are genetically inactive and serves as a structural element of the chromosome. The active, hypophosphorylated form of the protein binds transcription factor.

3) BRCA2 breast cancer 2, early onset [ Homo sapiens (human) ]

Gene ID: 675, updated on 1-Nov-2015

Summary

Official Symbol

BRCA2provided by HGNC

Official Full Name

breast cancer 2, early onsetprovided by HGNC

Primary source

HGNC:HGNC:1101

See related

Ensembl:ENSG00000139618; HPRD:02554; MIM:600185; Vega:OTTHUMG00000017411

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

FAD; FACD; FAD1; GLM3; BRCC2; FANCD; PNCA2; FANCD1; XRCC11; BROVCA2

Summary

Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, Dec 2008]

In other words: Inherited mutations in this gene increase the risk of developing a breast cancer or ovarian cancer. It involved in a maintenance of genome stability and considered to be a tumor suppressor gene. 

4) POSTN periostin, osteoblast specific factor [ Homo sapiens (human) ]

Gene ID: 10631, updated on 1-Nov-2015

Summary

Official Symbol

POSTNprovided by HGNC

Official Full Name

periostin, osteoblast specific factorprovided by HGNC

Primary source

HGNC:HGNC:16953

See related

Ensembl:ENSG00000133110; HPRD:12295; MIM:608777; Vega:OTTHUMG00000016751

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

PN; OSF2; OSF-2; PDLPOSTN

Summary

This gene encodes a secreted extracellular matrix protein that functions in tissue development and regeneration, including wound healing, and ventricular remodeling following myocardial infarction. The encoded protein binds to integrins to support adhesion and migration of epithelial cells. This protein plays a role in cancer stem cell maintenance and metastasis. Mice lacking this gene exhibit cardiac valve disease, and skeletal and dental defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2015]

In other words: This gene encodes the extracellular protein that functions in the tissue development and regeneration. It supports the cardiac and skeletal muscles, and dental development and maintenance. 

5) TNFSF11 tumor necrosis factor (ligand) superfamily, member 11 [ Homo sapiens (human) ]

Gene ID: 8600, updated on 1-Nov-2015

Summary

Official Symbol

TNFSF11provided by HGNC

Official Full Name

tumor necrosis factor (ligand) superfamily, member 11provided by HGNC

Primary source

HGNC:HGNC:11926

See related

Ensembl:ENSG00000120659; HPRD:04031; MIM:602642; Vega:OTTHUMG00000016807

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

ODF; OPGL; sOdf; CD254; OPTB2; RANKL; TRANCE; hRANKL2

Summary

This gene encodes a member of the tumor necrosis factor (TNF) cytokine family which is a ligand for osteoprotegerin and functions as a key factor for osteoclast differentiation and activation. This protein was shown to be a dentritic cell survival factor and is involved in the regulation of T cell-dependent immune response. T cell activation was reported to induce expression of this gene and lead to an increase of osteoclastogenesis and bone loss. This protein was shown to activate antiapoptotic kinase AKT/PKB through a signaling complex involving SRC kinase and tumor necrosis factor receptor-associated factor (TRAF) 6, which indicated this protein may have a role in the regulation of cell apoptosis. Targeted disruption of the related gene in mice led to severe osteopetrosis and a lack of osteoclasts. The deficient mice exhibited defects in early differentiation of T and B lymphocytes, and failed to form lobulo-alveolar mammary structures during pregnancy. Two alternatively spliced transcript variants have been found. [provided by RefSeq, Jul 2008]

In other words: Encoded by this gene, the protein have a role in the regulation of cell apoptosis ( apoptosis is a highly regulated and controlled process that confers advantages during an organism's lifecycle. For example, the separation of fingers and toes in a developing human embryo occurs because cells between the digits undergo apoptosis. Apoptosis produces cell fragments called apoptotic bodies that phagocytic cells can engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage.) It also was shown to be a dendritic (branched) cell survival factor and is involved in the regulation of T cell-dependent immune response.

6) CPB2 carboxypeptidase B2 (plasma) [ Homo sapiens (human) ]

Gene ID: 1361, updated on 25-Oct-2015

Summary

Official Symbol

CPB2provided by HGNC

Official Full Name

carboxypeptidase B2 (plasma)provided by HGNC

Primary source

HGNC:HGNC:2300

See related

Ensembl:ENSG00000080618; HPRD:04374; MIM:603101; Vega:OTTHUMG00000016867

Gene type

protein-coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

CPU; PCPB; TAFI

Summary

Carboxypeptidases are enzymes that hydrolyze C-terminal peptide bonds. The carboxypeptidase family includes metallo-, serine, and cysteine carboxypeptidases. According to their substrate specificity, these enzymes are referred to as carboxypeptidase A (cleaving aliphatic residues) or carboxypeptidase B (cleaving basic amino residues). The protein encoded by this gene is activated by trypsin and acts on carboxypeptidase B substrates. After thrombin activation, the mature protein downregulates fibrinolysis. Polymorphisms have been described for this gene and its promoter region. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]

In other words: Plasma carboxypeptidase B2, also known as carboxypeptidase U (CPU) and thrombin-activatable fibrinolysis inhibitor (TAFI), is synthesized by the liver and circulates in plasma as a plasminogen-bound zymogen. When it is activated by the thrombin/thrombomodulin complex, CPB2 exhibits carboxypeptidase B-like activity. CPB2 potently attenuates fibrinolysis by removing the C-terminal fibrin residues that are important for the binding and activation of plasminogenThe CPB2 genotype accounted for approximately 3% of the total variation in diastolic blood pressure, consistent with the expected magnitude of a modest genetic effect in a complex trait such as blood pressure.

7) HTR2A 5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled [ Homo sapiens (human) ]

Gene ID: 3356, updated on 15-Oct-2015

Summary

Official Symbol

HTR2Aprovided by HGNC

Official Full Name

5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupledprovided by HGNC

Primary source

HGNC:HGNC:5293

See related

Ensembl:ENSG00000102468; HPRD:01638; MIM:182135; Vega:OTTHUMG00000016881

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

HTR2; 5-HT2A

Summary

This gene encodes one of the receptors for serotonin, a neurotransmitter with many roles. Mutations in this gene are associated with susceptibility to schizophrenia and obsessive-compulsive disorder, and are also associated with response to the antidepressant citalopram in patients with major depressive disorder (MDD). MDD patients who also have a mutation in intron 2 of this gene show a significantly reduced response to citalopram as this antidepressant downregulates expression of this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

In other words: This gene encodes one of the receptors for serotonin, a neurotransmitter with many roles. Mutations in this gene are associated with susceptibility to schizophrenia and obsessive-compulsive disorder and are also associated with response to the antidepressant citalopram in patients with major depressive disorder (MDD).

8) F10 coagulation factor X [ Homo sapiens (human) ]

Gene ID: 2159, updated on 4-Nov-2015

Summary

Official Symbol

F10provided by HGNC

Official Full Name

coagulation factor Xprovided by HGNC

Primary source

HGNC:HGNC:3528

See related

Ensembl:ENSG00000126218; HPRD:01966; MIM:613872; Vega:OTTHUMG00000017374

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

FX; FXA

Summary

This gene encodes the vitamin K-dependent coagulation factor X of the blood coagulation cascade. This factor undergoes multiple processing steps before its pre-proprotein is converted to a mature two-chain form by the excision of the tripeptide RKR. Two chains of the factor are held together by 1 or more disulfide bonds; the light chain contains 2 EGF-like domains while the heavy chain contains the catalytic domain which is structurally homologous to those of the other hemostatic serine proteases. The mature factor is activated by the cleavage of the activation peptide by factor IXa (in the intrinsic pathway), or by factor VIIa (in the extrinsic pathway). The activated factor then converts prothrombin to thrombin in the presence of factor Va, Ca+2, and phospholipid during blood clotting. Mutations of this gene result in factor X deficiency, a hemorrhagic condition of variable severity. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing to generate mature polypeptides. [provided by RefSeq, Aug 2015]

In other words: This gene encodes the vitamin K-dependent coagulation factor X of the blood. Mutations in this gene result in factor X deficiency, a hemorrhagic condition of variable severity.

9) CDX2 caudal type homeobox 2 [ Homo sapiens (human) ]

Gene ID: 1045, updated on 15-Oct-2015

Summary

Official Symbol

CDX2provided by HGNC

Official Full Name

caudal type homeobox 2provided by HGNC

Primary source

HGNC:HGNC:1806

See related

HPRD:02622; MIM:600297

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

CDX3; CDX-3; CDX2/AS

Summary

This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded protein is a major regulator of intestine-specific genes involved in cell growth an differentiation. This protein also plays a role in early embryonic development of the intestinal tract. Aberrant expression of this gene is associated with intestinal inflammation and tumorigenesis. [provided by RefSeq, Jan 2012]

In other words: This encoded protein is a major regulator of intestine-specific genes involved in cell growth and differentiation it also plays a role in an early embryonic development of the intestinal tract.

10) FLT1 fms-related tyrosine kinase 1 [ Homo sapiens (human) ]

Gene ID: 2321, updated on 25-Oct-2015

Summary

Official Symbol

FLT1provided by HGNC

Official Full Name

fms-related tyrosine kinase 1provided by HGNC

Primary source

HGNC:HGNC:3763

See related

Ensembl:ENSG00000102755; HPRD:01297; MIM:165070; Vega:OTTHUMG00000016648

Gene type

protein coding

RefSeq status

REVIEWED

Organism

Homo sapiens

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo

Also known as

FLT; FLT-1; VEGFR1; VEGFR-1

Summary

This gene encodes a member of the vascular endothelial growth factor receptor (VEGFR) family. VEGFR family members are receptor tyrosine kinases (RTKs) which contain an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and a tyrosine kinase (TK) domain within the cytoplasmic domain. This protein binds to VEGFR-A, VEGFR-B and placental growth factor and plays an important role in angiogenesis and vasculogenesis. Expression of this receptor is found in vascular endothelial cells, placental trophoblast cells and peripheral blood monocytes. Multiple transcript variants encoding different isoforms have been found for this gene. Isoforms include a full-length transmembrane receptor isoform and shortened, soluble isoforms. The soluble isoforms are associated with the onset of pre-eclampsia.[provided by RefSeq, May 2009]

In other words: This gene encodes a member of the vascular endothelial growth factor receptor. It is found in vascular endothelial cells, placental trophoblast cells, and peripheral blood monocytes. This protein binds to VEGFR-A, VEGFR-B, and placental growth factor and plays an important role in angiogenesis (the development of the new blood cells) and vasculogenesis (is the term used for the formation of new blood vessels when there are no pre-existing ones.)

.

Part 2. 

Genetic Blueprints. 

 I will begin this part by logging into the website:

https://aelp.smartsparrow.com/learn/open/adcudyn4

I have completed the lesson up to the level 17, (from where I shall continue when the glitch is resolved and corrected.)

Update: The glitch has been fixed, and the lab proceeded to explain the formation and structure of the DNA molecule.  

Following the lesson through the visual graphics, like an illustration of the dead and alive mice made the learning fun and comprehencible. The introduction to the discovery of the double helix form of the DNA and example of the bonding of the bases makes this lab a useful learning tool. 

Aside of the glitch that was discovered by one of the classmates; the lesson seems to be structured and preceded on smoothley.  I would like to have these kind of lessons in the future.

The only dislike I have about this lesson, I don't get to see my score at the end.

Works cited:

Wikipedia. Wikimedia Foundation. Web. 5 Nov. 2015.

 Web. 5 Nov. 2015. 

"DNA Interactive: Discovering the DNA Structure and beyond." DNA Interactive: Discovering the DNA Structure and beyond. Web. 5 Nov. 2015.

Https://aelp.smartsparrow.com/v/open/adcudyn4. Web. 5 Nov. 2015