Information

Finding proteins in DNA sequence

Finding proteins in DNA sequence


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

I have to do a task for a university task and I need to understand some things before figuring out how to do it.

The task is the following:

Find matches of known proteins (DNA-PolyI,II,III) to the specific E.Coli DNA, sequence.

I downloaded in FASTA format the protein sequence of DNA-Poly3 DNA-Poly1 of E.coli (strain K-12) and the entire DNA sequence of the E.Coli.

I've studied a bit on-line and using the BioRuby gem and the Ruby programming language I wrote a program that translates DNA to protein sequence. Then I tried to match the known DNA-Poly3 sequence but it did not match. After searching a bit on-line again, I learned about ORF and and the 6 possible reading ways of each frame. The longer, in terms of codons, ORF conformation is chosen but there's no way of telling for sure that the protein was made using this frame.

Then I've read about TATA boxes, but I can't use those since they can be found only in Eukaryotic and Archaea.

So how should I proceed in order to solve this problem: How can I prove that the DNA-Poly3 gets produced by a specific area (gene) in the DNA sequence?

Thanks for your time,

ps. Insights and hints are very much welcomed as this is just the tip of the iceberg for me and I'm very willing to study bioinformatics :-)

EDIT: This is an update for info requested in relevant answer

The files I have used are the following:

➜ Bioinfo ruby dogma.rb ---------------- DNA Length: 4639675 gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome ---------------- DNA Poly-1 sample: 928 gi|16131704|ref|NP_418300.1| fused DNA polymerase I 5'->3' polymerase/3'->5' exonuclease/5'->3' exonuclease [Escherichia coli str. K-12 substr. MG1655]

You can download them here: E.Coli DNA and E.Coli DNA-Poly1.

NOTE: My sample protein is DNA Polymerase I (and not 3).


IMPORTANT EDIT : In your particular case, if you are working with bacterial genes, splicing is not an issue since bacteria do not have introns. I am leaving the information here since it may be useful to someone else. However, I recommend you focus on the UTRs since they are probably what is causing you problems.


There are three things that could be causing you problems. I will briefly touch on each one. I will talk about all genes, bear in mind that bacteria have no introns so any discussion of splicing and/or introns and exons is not directly relevant to your problem.

1. UTRs

Untranslated Regions (UTRs) are sequences at the beginning and end of a gene that are not translated into protein. UTRs are regions that are part of the original genomic sequence, they are also part of the mature mRNA (indeed, UTRs are sometimes modified by splicing events, they are exons not introns) but they do not get translated into protein. To illustrate, have a look at this simplified representation of an mRNA molecule:

Only the green exons will make it into the final protein. Introns are spliced out and UTRs are not translated.

Therefore, if you translate the entire gene, you will not get the correct protein.

2. Reading frames

Genes are read in words of three letters (the codons). The sequence ATGTGTACCTGA has six possible reading frames (three on each strand) which can be read and translated as follows:

  • 5'3' Frame 1

    ATG TGT ACC TGA M C T Stop
  • 5'3' Frame 2

    a TGT GTA CCT ga C V P
  • 5'3' Frame 3

    at GTG TAC CTG a V Y L
  • 3'5' Frame 1

    TCA GGT ACA CAT S G T H
  • 3'5' Frame 2

    t CAG GTA CAC at Q V H
  • 3'5' Frame 3

    tc AGG TAC ACA t R Y T

DNA is double stranded. The sequence of one strand is complementary to that of the other, therefore if you have one strand you can infer the sequence of its complementary one. Genes can be found on either strand, the two are equivalent biologically. However, sequencing projects choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for.

3. Names

I once heard someone say in a conference that

Biologists would rather share a toothbrush than a gene name.

While that might be a little exaggerated, naming conventions vary between research communities and species and databases. So, are you sure that you have downloaded the correct gene? Where did you get it from? How did you identify it? Does the sequence also contain up/downstream regulatory regions, promoters, enhancers and the like? If you post the exact sequence you are attempting to use I can give you more specific help.

For example, the first 20 hits when searching for the E. coliDNA Polymerase 3in ncbi's nucleotide database, are whole genome shotgun sequences. These do not correspond to the gene sequence you are looking for. They are huge pieces of the genome (or even the entire genome) that will contain your gene and many others. Look at the Tools section below for suggestions on extracting your gene from the whole genome.


4. Splicing (irrelevant to bacteria)

Another possible problem is splicing. Lets start with the basics, the process of producing a eukaryotic (bacteria have no introns) protein from a genomic sequence is summarized in the image below (modified slightly from here):

Transcription begins at the transcription start site (TSS) but not all the transcribed sequence is translated into protein. First, the introns are spliced out of the mRNA to produce the mature mRNA (other things like capping and poly-A addition also occur but are not relevant here). So,the mature mRNA contains the exons of the coding gene. This means that a linear translation of the gene's sequence will not correspond to the protein produced. You will need to take splicing into account.

Also, bear in mind that splicing will change the reading frame.

Now, if the sequenceATGTwere spliced at, for example,AT/gt(most splice events cut/join at GT/AG sites) and joined with the sequenceagATTATT, the resulting (spliced) sequence would be (the splicing process will remove thegtfrom the first sequence and theagfrom the second):

ATATTATT

As you can see, the reading frame has now changed. Where before, in the first reading frame, we had the codonATG, the canonical translation initiation codon, we now haveATAwhich codes for isoleucine (I). I hope that is clear, the main point is that splicing can change the reading frame.


5. Tools

OK, that was the background. Now, what you will need to do is use existing programs that model splice sites and can correctly align a protein sequence to genomic DNA. My personal favorites are exonerate and genewise. On a Debian-based Linux distribution, you can install them with this command:

sudo apt-get install exonerate wise

Then, to align the protein to its gene do:

exonerate -m protein2genome -n 1 prot.fa dna.fa > out.txt

or

genewise -pep -pretty -gff -cdna prot.fa dna.fa > out.txt

In my experience exonerate is (much) faster but genewise is a little more accurate. I usually use exonerate if I am dealing with a whole genome and genewise if I only have a few kilobases of sequence. Both are very good and both will be able to align a protein to its genome of origin.

I will not explain all these options because that is beyond the scope of this site. Have a look at their documentation (which is quite good and clear) and if you still have problems, you could ask a question on our sister site, Bioinformatics Stackexchange

Alternatively, you could link your web application to the ucsc genome browser BLAT service. Click here to see the results when aligning the human DNA-directed RNA polymerase II subunit RPB1 protein.


For what its worth - I have replicated what you are trying to do using a Python script. This is not elegant, but I just wanted to check for you that it is possible, and that there really is a match.

pseudocode is

take the genome sequence

make a reverse complement sequence

for each of the two DNA sequences, for each of three reading frames:

translate the DNA into a single string of amino acids with "*" at stop codons

split the string at "*" characters, call these words

find the first Met residue in each word, the string from that Met to the end of the word is an ORF

if the ORF is >99 (arbitrary cut off) put it in a big list of ORFs

now have a list of all ORFs in all 6 reading frames

search this list for a match to the polI sequence (I actually just looked for the first line in the fasta sequence).

The hit is identical to the entire polI sequence in a CLUSTAL alignment.

Note that this algorithm does not detect any ORFs that cross the breakpoint in the linear sequence representing the circular genome of E coli. Also assumes all initiator codons are ATG/Met but I seem to recall some E.coli initiation codons are GTG/Val


Rather than doing it all from scratch, if you had your own instance of BLAST, you would make a blastable database of your e.coli sequence, and do tblastn, with your putative polymerase protein sequence as the query.

This would find the best matching sequence in the genome, and will work even if there are a fair number of differences between the protein you gave it, and what your DNA sequence actually translates to.


Finding proteins in DNA sequence - Biology

The sequence of a DNA molecule can help us identify an organism when compared to known sequences housed in a database. The sequence can also tell us something about the function of a particular part of the DNA, such as whether it encodes a particular protein. Comparing protein signatures—the expression levels of specific arrays of proteins—between samples is an important method for evaluating cellular responses to a multitude of environmental factors and stresses. Analysis of protein signatures can reveal the identity of an organism or how a cell is responding during disease.

The DNA and proteins of interest are microscopic and typically mixed in with many other molecules including DNA or proteins irrelevant to our interests. Many techniques have been developed to isolate and characterize molecules of interest. These methods were originally developed for research purposes, but in many cases they have been simplified to the point that routine clinical use is possible. For example, many pathogens, such as the bacterium Helicobacter pylori, which causes stomach ulcers, can be detected using protein-based tests. In addition, an increasing number of highly specific and accurate DNA amplification-based identification assays can now detect pathogens such as antibiotic-resistant enteric bacteria, herpes simplex virus, varicella-zoster virus, and many others.


Human reference gene sets

Since the publication of the draft human genome sequence in 2001 [6, 7], a number of human gene reference sets have been created using either computational prediction or manual annotation or a mixture of the two methods. The Ensembl project was initially set up to warehouse and annotate the large amount of unfinished genomic data being produced as part of the public human genome project, as well as to provide browser capacity for both sequences and annotations (Figure 2). Ensembl has expanded and now generates automatic predictions for more than 35 species. The Ensembl gene build process is based on alignments of protein and cDNA sequences to produce a highly accurate gene set with a low rate of false positives [19].

ENSEMBL browser. The ContigView page of the Ensembl browser representing the SPAG4 gene locus on chromosome 20 within the Encode region ENr333. (a) The green transcript represents the CCDS coding region agreed on by the CCDS consortium. (b) The blue transcripts are the Vega transcripts, which are manually annotated by the HAVANA group and are a mixture of coding (solid blues) and noncoding (blue outline) transcripts. (c) Finally, the gold transcript represents the coding transcript on which the HAVANA and Ensembl annotations agree.

Another genome browser supplying sequence and annotation data for a large number of genomes is the University of California, Santa Cruz (UCSC) genome browser database [20]. In April 2007, UCSC released an improved version of their 'Known Gene Set' for the human genome and included putative noncoding RNAs as well as protein-coding genes. Each entry in this set requires the support of a GenBank entry and at least one other line of evidence, except for curated cDNAs, which require no other evidence.

Manual annotation still plays a significant part in annotating high-quality finished genomes. Currently, the National Center for Biotechnology Information (NCBI) reference sequences (RefSeq) collection provides a highly (manually) curated resource of multi-species transcripts, including plant, viral, vertebrate and invertebrate sequences [21, 22]. These are, as their name indicates, transcript-oriented and usually rely on full-length cDNAs for reliable curation, although the dataset also contains predictions using expressed sequence tags (ESTs) and partial cDNAs aligned against genomic sequence using the Gnomon prediction program [23]. Manually reviewed RefSeq nucleotide sequences begin with the reference NM identifier whereas unreviewed predictions have the XM identifier. When a new genome is initially sequenced, researchers usually use the RefSeq data set to identify genes that are missing or identify genomic rearrangements within genes, as RefSeq is used internationally as a standard for genome annotation [21]. RefSeq is a very reliable, but also conservative, gene reference set. Other reference sets usually include RefSeq, but extend it substantially. For instance, the UCSC 'Known Genes' has 10% more protein-coding genes, approximately five times as many putative coding genes and twice as many splice variants as RefSeq.

A different approach to manual gene annotation is to annotate transcripts aligned to the genome and take the genomic sequences as the reference rather than the cDNAs. This is how the HAVANA group at the Wellcome Trust Sanger Institute produces its annotation on vertebrate sequence. Currently, only three vertebrate genomes - human, mouse and zebrafish - are being fully finished and sequenced to a quality that merits manual annotation [24]. The finished genomic sequence is analyzed using a modified Ensembl pipeline [25], and BLAST results of cDNAs/ESTs and proteins, along with various ab initio predictions, can be analyzed manually in the annotation browser tool Otterlace. The advantage of genomic annotation compared with cDNA annotation is that more alternative spliced variants can be predicted, as partial EST evidence and protein evidence can be used, whereas cDNA annotation is limited to availability of full-length transcripts. Moreover, genomic annotation produces a more comprehensive analysis of pseudogenes. One disadvantage, however, is that if a polymorphism occurs in the reference sequence, a coding transcript cannot be annotated, whereas cDNA annotation can select the major haplotypic form and is, therefore, not limited by a reference sequence.

In 2006, the groups mentioned above (NCBI (RefSeq), UCSC, the Wellcome Trust Sanger Institute (HAVANA) and Ensembl) identified a need to collaborate and produce a consensus gene set for the human reference genome as there was still no official agreement between the different databases on the human protein-coding genes. Referred to as the Consensus Coding Sequence Set (CCDS) [26], it currently contains only those coding transcripts that are equivalent in each database's gene build from start codon to stop codon. The latest human CCDS release (May 2008) contains 20,151 consensus coding sequences representing 17,052 genes. For the first time, this provides researchers with a consistent reliable gene set that has been derived independently from a combination of manual and automated annotation by three groups (Ensembl, NCBI and HAVANA) and quality checked at the UCSC. The protein-coding genes that differ between the gene sets of the different groups and cannot be merged automatically will be re-examined manually and either rejected or added to the consensus set if they get a unanimous vote from the groups at NCBI, UCSC and HAVANA.

Complementary to the CCDS project is the GENCODE project [27]. The GENCODE consortium [28] was initially formed to identify and map all protein-coding genes within the regions selected in the framework of the ENCODE project [29, 30], representing 1% of human genome sequence. This was achieved by a combination of initial manual annotation by HAVANA, computational predictions and experimental validation, and the consequent refinement of the annotation on the basis of these experimental results. The project has been funded in 2008 to annotate the whole reference human genome sequence and experimentally verify a number of putative loci. The scaled-up annotation includes identification of pseudogenes and noncoding loci supported by transcript evidence. The initial manual annotation is compared with automated predictions to highlight inconsistencies based on comparative analysis or new transcript data. It is expected that, upon completion in 2011, this gene set will become the standard human gene reference set.


Finding Genes in DNA with a Hidden Markov Model

This study describes a new Hidden Markov Model (HMM) system for segmenting uncharacterized genomic DNA sequences into exons, introns, and intergenic regions. Separate HMM modules were designed and trained for specific regions of DNA: exons, introns, intergenic regions, and splice sites. The models were then tied together to form a biologically feasible topology. The integrated HMM was trained further on a set of eukaryotic DNA sequences and tested by using it to segment a separate set of sequences. The resulting HMM system which is called VEIL (Viterbi Exon-Intron Locator), obtains an overall accuracy on test data of 92% of total bases correctly labelled, with a correlation coefficient of 0.73. Using the more stringent test of exact exon prediction, VEIL correctly located both ends of 53% of the coding exons, and 49% of the exons it predicts are exactly correct. These results compare favorably to the best previous results for gene structure prediction and demonstrate the benefits of using HMMs for this problem.


Figure (PageIndex<8>): The central dogma: Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic information inscribed on a strand of messenger RNA and use this information to string amino acids together into a protein.
  1. Relate protein synthesis and its two major phases to the central dogma of molecular biology.
  2. Identify the steps of transcription, and summarize what happens during each step.
  3. Explain how mRNA is processed before it leaves the nucleus.
  4. Describe what happens during the translation phase of protein synthesis.
  5. What additional processes may a polypeptide chain undergo after it is synthesized?
  6. Where does transcription take place in eukaryotes?
  7. Where does translation take place?
  8. Which type of RNA (mRNA, rRNA, or tRNA) best fits each of the statements below? Choose only one type for each.
    1. Contains the codons
    2. Contains the anticodons
    3. Makes up the ribosome, along with proteins
    1. What is the complementary sequence on the other DNA strand?
    2. What is the complementary sequence in the mRNA? What is this sequence called?
    3. @hat is the resulting sequence in the tRNA? What is this sequence called? What do you notice about this sequence compared to the original DNA triplet on the template strand?
    1. DNA
    2. mRNA
    3. tRNA
    4. Both A and B

    FUTURE DIRECTIONS

    To increase the sensitivity of MEME searches, we will add an option in the web server to let the user upload a background sequence model to MEME. We hope to add algorithms for removing low-complexity regions (SEG and DUST) and repeated elements (RepeatMasker) in the MEME website as a convenience to users. These services will also be exposed as web services and are integrated using workflow tools developed by using NBCR.

    We have also planned to add buttons to the MEME output to allow TFBS motifs to be used in searching for cis -regulatory modules via algorithms such as MCAST ( 15 ). MCAST will be configured to be able to search the same DNA databases as MAST. In conjunction with this, we will add databases of upstream sequences for many additional organisms to the MAST/MCAST websites to facilitate the analysis of TFBS motifs discovered by using MEME.

    NBCR has developed a set of tools built on top of the open source software that allows bioinformatics applications to be deployed as Web Services easily (S. Krishnan, B. Stearn, K. Bhatia, W. W. Li and P. Arzberger, manuscript submitted) and leverage the Cyberinfrastructure components transparently ( 14 ). A prototype has been deployed using MEME as a scientific driver ( 16 ) that offers a user with a dynamic pool of distributed compute resource, workflow management console and a friendly user interface. This portal will be deployed to the production web server in the future.

    Sample MEME output.This portion of an MEME HTML output form shows a protein motif that MEME has discovered in the input sequences. The sites identified as belonging to the motif are indicated, and above them is the ‘consensus’ of the motif and a color-coded bar graph showing the conservation of each position in the motif. Some of the hyperlinked buttons that allow the motif to be viewed and analyzed in other ways can be seen at the bottom of the screen shot.

    Sample MEME output.This portion of an MEME HTML output form shows a protein motif that MEME has discovered in the input sequences. The sites identified as belonging to the motif are indicated, and above them is the ‘consensus’ of the motif and a color-coded bar graph showing the conservation of each position in the motif. Some of the hyperlinked buttons that allow the motif to be viewed and analyzed in other ways can be seen at the bottom of the screen shot.

    LOGO of protein motif. LOGOS are a visualization tool for motifs. The height of a letter indicates its relative frequency at the given position ( x -axis) in the motif.

    LOGO of protein motif. LOGOS are a visualization tool for motifs. The height of a letter indicates its relative frequency at the given position ( x -axis) in the motif.

    Usage of MEME at the NBCR web server. The plot shows the number of different users submitting jobs to the NBCR MEME web server each month since December 2000. Usage figures for March 2006 include up to March 20 only.

    Usage of MEME at the NBCR web server. The plot shows the number of different users submitting jobs to the NBCR MEME web server each month since December 2000. Usage figures for March 2006 include up to March 20 only.


    Investigation Dna Proteins And Mutations Answers

    Gene And Chromosome Mutation Worksheet Reference Pgs In Modern Biology Textbook Pdf Free Download. The dna that makes up the gene that encodes a protein sometimes has mistakes, called mutations, which cause defects in proteins. Dna, proteins, and mutations below are two partial sequences of dna bases (shown for only one strand of dna) sequence 1 is from a human and sequence 2 is from a cow. Terms in this set (11) yes because combinations of codons can have the same amino acid. Dna is a polymer that lies within the nucleus of all cells. Could two humans have some differences in their dna sequences for insulin, yet still make the exact same insulin proteins?

    Dna mutations occur when there are changes in the nucleotide sequence that makes up a strand of dna. Investigation dna proteins and mutations answers. Copying errors when dna replicates or is transcribed into rna can cause changes in the sequence of bases which makes up the genetic code. Dna mutation simulation answer key : Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning.

    Hs Ls3 1 The Wonder Of Science from images.squarespace-cdn.com Investigation dna proteins and mutations answers / solved: A molecule of dna consists of two chains that are wrapped during translation, mrna is converted to protein. Changes in the dna code are called mutation and they can cause a protein to not function properly. Learn vocabulary, terms and more with flashcards, games and other study tools. A mutation is a change in a dna sequence brought about either by a mistake made when the dna is certain types of mutations are silent and have no effect, but others affect protein production in a variety short answers : Investigation dna proteins and mutations answers investigation regulatory switches of the pitx1 gene in stickleback fish biology libretexts a molecule of dna consists of two chains that are wrapped around from media. Dna mutations occur when there are changes in the nucleotide sequence that makes up a strand of dna. View copy of elaborate a_ dna, proteins, and mutations.pdf from bio 101 at highland high school.

    Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning.

    Terms in this set (11) yes because combinations of codons can have the same amino acid. Which type of mutation results in shortening of a dna strand? A single change in the dna of the hemoglobin gene will cause sickle cell anemia. Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning. Copying errors when dna replicates or is transcribed into rna can cause changes in the sequence of bases which makes up the genetic code. The full name for dna, the full name for rna, substance that causes mutations, the four nitrogen bases of rna. Dna (deoxyribonucleic acid) is the information storage system of the body. Point mutations that occur in dna sequences encoding proteins are either silent, missense or nonsense. Investigation dna proteins and mutations answer key. Dna, proteins, and sickle cell sickle cell is disease where person has abnormally synthesis: Investigation dna proteins and mutations answers. Dna mutation lab activity, dna mutations activity for middle school, dna mutations quiz flashcards, dna mutation notation, dna mutation test mutations and genetic variability 1 what is occurring in the from dna mutations practice worksheet answers , source: Mutations mutations the genes encoded in your dna result …

    Dna, proteins, and sickle cell sickle cell is disease where person has abnormally synthesis: Investigation dna proteins and mutations answers / solved: Part a in both humans and cows, this dna sequence is part of a set of A mutation, which may arise during replication and/or recombination, is a permanent change in the nucleotide sequence of dna. Different forms of the same gene are called alleles.

    Turning Science Into Lifesaving Care Aacr Cancer Progress Report from cancerprogressreport.aacr.org Dna, proteins, and students must fill in blanks to answer the question. A single change in the dna of the hemoglobin gene will cause sickle cell anemia. Spontaneous mutagenesis is generally a random process. Different alleles produce variations in inherited characterisitics (traits). Investigation dna proteins and mutations, a mutation is a change that occurs in our dna sequence, either due to mistakes when the dna is copied or as the result of environmental factors such as uv light and mutations contribute to genetic variation within species. View copy of elaborate a_ dna, proteins, and mutations.pdf from bio 101 at highland high school. Protein synthesis answers dna replication and protein synthesis answers 1. Dna, proteins, and sickle cell sickle cell is disease where person has abnormally synthesis:

    Investigation dna proteins and mutations the biology corner answer key.

    Answer each of the following using complete sentences. Investigation dna proteins and mutations answers. Below are two partial sequences of dna bases (shown for only one strand of dna) sequence 1 is from a human and sequence 2 is from a cow. Copying errors when dna replicates or is transcribed into rna can. The worksheet asks students to review terms and label an image showing trna mrna codons amino acids and ribosomes. Dna (deoxyribonucleic acid) is the information storage system of the body. Part a in both humans and cows, this dna sequence is part of a set of Spontaneous mutagenesis is generally a random process. A molecule of dna consists of two chains that are wrapped during translation, mrna is converted to protein. 13 multiple choice rna and protein synthesis chapter test a write the letter that best answers the. A sequence of dna specifying the sequence of amino acids of a particular protein involved in the expression of a trait. The full name for dna, the full name for rna, substance that causes mutations, the four nitrogen bases of rna. A single change in the dna of the hemoglobin gene will cause sickle cell anemia.

    Dna mutation lab activity, dna mutations activity for middle school, dna mutations quiz flashcards, dna mutation notation, dna mutation test mutations and genetic variability 1 what is occurring in the from dna mutations practice worksheet answers , source: Copying errors when dna replicates or is transcribed into rna can. Different forms of the same gene are called alleles. Alternatively, of course, you could well get a code for a different amino acid or even a stop codon. Dna is a polymer that lies within the nucleus of all cells.

    Http Ecdoe Co Za Documents Learners Self Study Guides Life Sciences Gr12 Pdf from Different forms of the same gene are called alleles. Copying errors when dna replicates or is transcribed into rna can cause changes in the sequence of bases which makes up the genetic code. The full name for dna, the full name for rna, substance that causes mutations, the four nitrogen bases of rna. Dna, proteins, and sickle cell sickle cell is disease where person has abnormally synthesis: Genetic mutations worksheet answer key dna mutations practice. A mutation is a change in a dna sequence brought about either by a mistake made when the dna is certain types of mutations are silent and have no effect, but others affect protein production in a variety short answers : Dna, proteins, and students must fill in blanks to answer the question. Protein synthesis answers dna replication and protein synthesis answers 1.

    Dna mutations range from missense errors occur when the mutated dna can still code for an amino acid, but not the correct amino acid.

    A mutation is a change in a dna sequence brought about either by a mistake made when the dna is certain types of mutations are silent and have no effect, but others affect protein production in a variety short answers : Investigation dna proteins and mutations answers : 14—how can a cell fix potential dna mutations? Dna (deoxyribonucleic acid) is the information storage system of the body. Investigation dna proteins and mutations answers : Mutations mutations the genes encoded in your dna result … Dna mutations occur when there are changes in the nucleotide sequence that makes up a strand of dna. Below are two partial sequences of dna bases (shown for only one strand of dna) sequence 1 is from a human and sequence 2 is from a cow. Changes in the dna code are called mutation and they can cause a protein to not function properly. A sequence of dna specifying the sequence of amino acids of a particular protein involved in the expression of a trait. Investigation dna proteins and mutations the biology corner answer key. Learn about dna mutation and find out how human dna. Dna, proteins, and sickle cell sickle cell is disease where person has abnormally synthesis:

    Source: d20ohkaloyme4g.cloudfront.net

    Genetic mutations worksheet answer key dna mutations practice. Alternatively, of course, you could well get a code for a different amino acid or even a stop codon. Different forms of the same gene are called alleles. In both humans and cows, this sequence is part of a set of instructions for controlling a bodily function. A mutation is a change in a dna sequence brought about either by a mistake made when the dna is certain types of mutations are silent and have no effect, but others affect protein production in a variety short answers :

    Source: images.squarespace-cdn.com

    Terms in this set (11) yes because combinations of codons can have the same amino acid. Investigation dna proteins and mutations answers. Investigation dna proteins and mutations, a mutation is a change that occurs in our dna sequence, either due to mistakes when the dna is copied or as the result of environmental factors such as uv light and mutations contribute to genetic variation within species. Dna mutations range from missense errors occur when the mutated dna can still code for an amino acid, but not the correct amino acid. Below are two partial sequences of dna bases (shown for only one strand of dna) sequence 1 is from a human and sequence 2 is from a cow.

    Source: els-jbs-prod-cdn.jbs.elsevierhealth.com

    Investigation dna proteins and mutations answer key. Protein synthesis answers dna replication and protein synthesis answers 1. Investigation dna proteins and mutations the biology corner answer key. Terms in this set (11) yes because combinations of codons can have the same amino acid. Dna mutation simulation answer key :

    Source: s3-us-west-2.amazonaws.com

    Dna (deoxyribonucleic acid) is the information storage system of the body. Copying errors when dna replicates or is transcribed into rna can. Dna is a polymer that lies within the nucleus of all cells. Investigation dna proteins and mutations answers investigation regulatory switches of the pitx1 gene in stickleback fish biology libretexts a molecule of dna consists of two chains that are wrapped around from media. Point mutations that occur in dna sequences encoding proteins are either silent, missense or nonsense.

    Point mutations that occur in dna sequences encoding proteins are either silent, missense or nonsense. Copying errors when dna replicates or is transcribed into rna can. Could two humans have some differences in their dna sequences for insulin, yet still make the exact same insulin. Learn about dna mutation and find out how human dna. Investigation dna proteins and mutations answers.

    Investigation dna proteins and mutations answers : Could two humans have some differences in their dna sequences for insulin, yet still make the exact same insulin. Point mutations that occur in dna sequences encoding proteins are either silent, missense or nonsense. Dna, proteins, and mutations below are two partial sequences of dna bases. Dna is a polymer that lies within the nucleus of all cells.

    A molecule of dna consists of two chains that are wrapped during translation, mrna is converted to protein. Investigation dna proteins and mutations answers : Copying errors when dna replicates or is transcribed into rna can. Different forms of the same gene are called alleles. A mutation is a change in a dna sequence brought about either by a mistake made when the dna is certain types of mutations are silent and have no effect, but others affect protein production in a variety short answers :

    Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning. Changes in the dna code are called mutation and they can cause a protein to not function properly. Investigation dna proteins and mutations answers / solved: A molecule of dna consists of two chains that are wrapped during translation, mrna is converted to protein. A mutation is a change in a dna sequence brought about either by a mistake made when the dna is certain types of mutations are silent and have no effect, but others affect protein production in a variety short answers :

    Dna, proteins, and mutations below are two partial sequences of dna bases (shown for only one strand of dna) sequence 1 is from a human and sequence 2 is from a cow. Alternatively, of course, you could well get a code for a different amino acid or even a stop codon. Dna, proteins, and sickle cell sickle cell is disease where person has abnormally synthesis: Dna is a polymer that lies within the nucleus of all cells. The worksheet asks students to review terms and label an image showing trna mrna codons amino acids and ribosomes.

    Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning.

    Dna mutation lab activity, dna mutations activity for middle school, dna mutations quiz flashcards, dna mutation notation, dna mutation test mutations and genetic variability 1 what is occurring in the from dna mutations practice worksheet answers , source:

    Source: ecdn.teacherspayteachers.com

    A sequence of dna specifying the sequence of amino acids of a particular protein involved in the expression of a trait.

    A molecule of dna consists of two chains that are wrapped during translation, mrna is converted to protein.

    Investigation dna proteins and mutations answers / investigation dna proteins and mutations docx name investigation dna proteins and mutations below are two partial sequences of dna bases shown for course hero / different alleles produce variations in inherited characterisitics (traits).

    Could two humans have some differences in their dna sequences for insulin, yet still make the exact same insulin proteins?

    Could two humans have some differences in their dna sequences for insulin, yet still make the exact same insulin.

    Could two humans have some differences in their dna sequences for insulin, yet still make the exact same insulin proteins?

    Terms in this set (11) yes because combinations of codons can have the same amino acid.

    Investigation dna proteins and mutations, a mutation is a change that occurs in our dna sequence, either due to mistakes when the dna is copied or as the result of environmental factors such as uv light and mutations contribute to genetic variation within species.

    Investigation dna proteins and mutations the biology corner answer key.

    Different forms of the same gene are called alleles.

    Mutations mutations the genes encoded in your dna result in the production of proteins that this pdf book contain genetic mutations pogil answers information.

    Copying errors when dna replicates or is transcribed into rna can.

    Point mutations that occur in dna sequences encoding proteins are either silent, missense or nonsense.

    Source: media.springernature.com

    Spontaneous mutagenesis is generally a random process.

    Dna, proteins, and mutations below are two partial sequences of dna bases (shown for only one strand of dna) sequence 1 is from a human and sequence 2 is from a cow.

    Source: media.springernature.com

    Investigation dna proteins and mutations answer key.

    Point mutations that occur in dna sequences encoding proteins are either silent, missense or nonsense.

    Source: upload.wikimedia.org

    A mutation, which may arise during replication and/or recombination, is a permanent change in the nucleotide sequence of dna.

    Terms in this set (11) yes because combinations of codons can have the same amino acid.

    Investigation dna proteins and mutations answers.

    Investigation dna proteins and mutations answers :

    Investigation dna proteins and mutations answers.

    Dna mutations occur when there are changes in the nucleotide sequence that makes up a strand of dna.


    Learning Goals

    Activity specific goals:

    After completing this activity, all students will be able to

    • load generic text files into MATLAB and search them for specific strings.
    • utilize pre-built MATLAB tools such as fastaread for faster import of specifically formatted text.
    • evaluate the efficiency and scaling of algorithms by benchmarking and tracking execution time.
    • retrieve data from online databases such as NCBI.
    • Compare MATLAB based algorithm implementation and algorithms in other languages.
    • Consider scaling of execution time and storage needs for big data.
    • Apply string searches to contemporary problems in molecular biology research.

    Scientific computing and problem solving goals:

    After completing this activity, students will be able to

    • access data stored in online databases or from files provided from them.
    • generate plots with multiple panels to best
    • synthesize pre-built tools with additional MATLAB code to solve specific problems.
    • reuse code snippets and single-purpose functions.
    • quickly develop code by taking a complex problem and breaking it down into smaller pieces
    • appreciate that skillsets necessary for success in modern scientific computing require both domain specific knowledge and algorithm development

    Domain specific goals (Molecular Biology/Bioinformatics):

    • DNA and proteins primary structure can be represented by an ordered series of letters. The language of DNA only requires 4 and proteins roughly 20 letters.
    • Bacterial genomes have a length of a few million basepairs. To uniquely define a location in the genome, one must use a sequence of roughly 10-15 base pairs. For example, this is relevant for designing site specific oligonucleotides for genome amplification or genome editing.
    • Enzymes are proteins that can catalyze specific reactions and are often a few hundred amino acid residues long, roughly the length of a sentence. To achieve this chemistry, they often have specific residues in an active site that are required for this function. Other residues (letters) in the sentence are not as highly conserved between closely related organisms. These active site residues can sometimes be found by looking for conservation in a multiple sequence alignment across proteins from different organisms.
    • Immune cells make antibodies with unique protein sequences by mixing and matching sequences from V, D, and J sites. This makes sequence matching difficult because the template is split and rejoined in different ways, creating a vast repertoire of antibodies from a relatively small starting pool of DNA sequences.
    • Big data will continue to be an issue for molecular biology in the post-genomic era. In RNAseq experiments, the mRNA of a sample is matched back to genome of the organism to provide a quantitative measure of the number of transcripts a certain gene has. While the final data (counts per gene) may only be a few megabytes in size, the text search algorithms need to be able to handle inputs of hundreds of gigabytes of data for each sample. Additionally, these data need to allow mismatches as the reference genome or individual read may be incomplete or incorrect.

    14.2 DNA Structure and Sequencing

    In this section, you will explore the following questions:

    • What is the molecular structure of DNA?
    • What is the Sanger method of DNA sequencing? What is an application of DNA sequencing?
    • What are the similarities and differences between eukaryotic and prokaryotic DNA?

    Connection for AP ® Courses

    The currently accepted model of the structure of DNA was proposed in 1953 by Watson and Crick, who made their model after seeing a photograph of DNA that Franklin had taken using X-ray crystallography. The photo showed the molecule’s double-helix shape and dimensions. The two strands that make up the double helix are complementary and anti-parallel in nature. That is, one strand runs in the 5' to 3' direction, whereas the complementary strand runs in the 3' to 5' direction. (The significance of directionality will be important when we explore how DNA copies itself.) DNA is a polymer of nucleotides that consists of deoxyribose sugar, a phosphate group, and one of four nitrogenous bases—A, T, C, and G—with a purine always pairing with a pyrimidine (as Chargaff found). The genetic “language” of DNA is found in sequences of the nucleotides. During cell division each daughter cell receives a copy of DNA in a process called replication. In the years since the discovery of the structure of DNA, many technologies, including DNA sequencing, have been developed that enable us to better understand DNA and its role in our genomes.

    Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A Learning Objective merges required content with one or more of the seven science practices.

    Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
    Enduring Understanding 3.A Heritable information provides for continuity of life.
    Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
    Science Practice 6.5 The student can evaluate alternative scientific explanations.
    Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA to support the claim that DNA is the primary source of heritable information.
    Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
    Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question.
    Learning Objective 3.2 The student is able to justify the selection of data from historical investigations that support the claim that DNA is the source of heritable information.
    Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
    Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models.
    Learning Objective 3.5 The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies.

    Teacher Support

    Franklin’s X-ray diffraction pictures helped lead to the discovery of the structure of DNA, but Watson and Crick did not mention Franklin in their seminal 1953 paper, which can be found here. This paper includes annotations that help place the work in historical context. Students might be interested to learn how Watson and Crick discovered the structure of DNA. Details can be found at this PBS website. If possible, find a copy of the announcement of the discovery as it appeared in The New York Times. The wording is interesting and the significance of the discovery is understated.

    The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
    [APLO 3.3][APLO 3.5][APLO 3.13]

    The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group (Figure 14.5). The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T).

    The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines are smaller in size they have a single six-membered ring structure. The carbon atoms of the five-carbon sugar are numbered 1', 2', 3', 4', and 5' (1' is read as “one prime”). The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar of one nucleotide and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide, thereby forming a 5'-3' phosphodiester bond.

    In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin's data because Crick had also studied X-ray diffraction (Figure 14.6). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.

    Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature that is, the 3' end of one strand faces the 5' end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (Figure 14.7).

    Science Practice Connection for AP® Courses

    Activity

    Read Watson and Crick’s original Nature article, “Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid,” How did Watson and Crick’s model build on the findings of Rosalind Franklin? How did their model of DNA build on the findings of Hershey and Chase, and others, showing that DNA can encode and pass information on to the next generation?

    Think About It

    Watson and Crick’s work determined the structure of DNA. However, it was still relatively unknown how DNA encoded information into genes. Select one modern form of biotechnology and research its basic methods online. Examples include gene sequencing, DNA fingerprinting, PCR (polymerase chain reaction), genetically-modified food, etc. Briefly describe your chosen technology, and what benefits it provides us. Then describe how Watson and Crick’s findings were vital to the development of your chosen technology.

    Teacher Support

    The activity is an application of Learning Objective 3.1 and Science Practice 6.5 because students are analyzing Watson and Crick’s model of DNA relative to the findings of other DNA researchers who determined that DNA is the molecule of heredity. The activity is also an application of Learning Objective 3.2 and Science Practice 4.1 because students are analyzing the historic published results of Watson and Crick and selecting evidence that Watson and Crick used to create their model of DNA and further show that DNA is the molecule of heredity.

    Possible answer:

    The Think About It question is an application of Learning Objective 3.5 and Science Practice 6.4 because students are researching the methods by which humans can manipulate heritable information and describing how those methods were based on the scientific theories and models of Watson and Crick.

    Possible answer:

    DNA Sequencing Techniques

    Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheap, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today (Figure 14.8).

    Link to Learning

    Visit this site to watch a video explaining the DNA sequence reading technique that resulted from Sanger’s work.

    1. Sanger’s method can be used to sequence more than one strand at a time which is less time consuming. Challenges of Sanger’s method includes its decreased accuracy to sequence DNA strands.
    2. Sanger’s method is a reliable and accurate way of sequencing DNA strands. However, only one strand at a time can be sequenced at a time. Also, it can look for one base only at a time which can be time consuming.
    3. Sanger’s method is highly inexpensive and less accurate. However, it is not readily adaptable to commercial kits.
    4. Sanger’s method is less time consuming and highly accurate. However, it is more expensive than other methods available for sequencing.

    The method is known as the dideoxy chain termination method. The sequencing method is based on the use of chain terminators, the dideoxynucleotides (ddNTPs). The dideoxynucleotides, or ddNTPSs, differ from the deoxynucleotides by the lack of a free 3' OH group on the five-carbon sugar. If a ddNTP is added to a growing a DNA strand, the chain is not extended any further because the free 3' OH group needed to add another nucleotide is not available. By using a predetermined ratio of deoxynucleotides to dideoxynucleotides, it is possible to generate DNA fragments of different sizes.

    The DNA sample to be sequenced is denatured or separated into two strands by heating it to high temperatures. The DNA is divided into four tubes in which a primer, DNA polymerase, and all four nucleotides (A, T, G, and C) are added. In addition to each of the four tubes, limited quantities of one of the four dideoxynucleotides are added to each tube respectively. The tubes are labeled as A, T, G, and C according to the ddNTP added. For detection purposes, each of the four dideoxynucleotides carries a different fluorescent label. Chain elongation continues until a fluorescent dideoxy nucleotide is incorporated, after which no further elongation takes place. After the reaction is over, electrophoresis is performed. Even a difference in length of a single base can be detected. The sequence is read from a laser scanner. For his work on DNA sequencing, Sanger received a Nobel Prize in chemistry in 1980.

    Link to Learning

    Sanger’s genome sequencing has led to a race to sequence human genomes at a rapid speed and low cost, often referred to as the $1000 in one day sequence. Learn more by selecting the Sequencing at Speed animation here.

    1. Faster genetic sequencing will help in quick analysis of the genetic makeup of bacteria that can cause diseases in humans for better and more efficient treatments. Also, sequencing of a cancerous cell’s DNA can provide better ways to treat or prevent cancer.
    2. Fast DNA sequencing can help us quickly analyze the genetic information of existing only bacteria (not new strains) only that cause disease in humans, which may lead to more efficient treatments.
    3. Fast DNA sequencing can help doctors to treat and diagnose diseases which are not rare in populations.
    4. Faster genetic sequencing can be used to treat and prevent a few types of cancers and thus increase the life expectancy of patients suffering from the diseases.

    Gel electrophoresis is a technique used to separate DNA fragments of different sizes. Usually the gel is made of a chemical called agarose. Agarose powder is added to a buffer and heated. After cooling, the gel solution is poured into a casting tray. Once the gel has solidified, the DNA is loaded on the gel and electric current is applied. The DNA has a net negative charge and moves from the negative electrode toward the positive electrode. The electric current is applied for sufficient time to let the DNA separate according to size the smallest fragments will be farthest from the well (where the DNA was loaded), and the heavier molecular weight fragments will be closest to the well. Once the DNA is separated, the gel is stained with a DNA-specific dye for viewing it (Figure 14.9).

    Evolution Connection

    Neanderthal Genome: How Are We Related?

    The first draft sequence of the Neanderthal genome was recently published by Richard E. Green et al. in 2010. 1 Neanderthals are the closest ancestors of present-day humans. They were known to have lived in Europe and Western Asia before they disappeared from fossil records approximately 30,000 years ago. Green’s team studied almost 40,000-year-old fossil remains that were selected from sites across the world. Extremely sophisticated means of sample preparation and DNA sequencing were employed because of the fragile nature of the bones and heavy microbial contamination. In their study, the scientists were able to sequence some four billion base pairs. The Neanderthal sequence was compared with that of present-day humans from across the world. After comparing the sequences, the researchers found that the Neanderthal genome had 2 to 3 percent greater similarity to people living outside Africa than to people in Africa. While current theories have suggested that all present-day humans can be traced to a small ancestral population in Africa, the data from the Neanderthal genome may contradict this view. Green and his colleagues also discovered DNA segments among people in Europe and Asia that are more similar to Neanderthal sequences than to other contemporary human sequences. Another interesting observation was that Neanderthals are as closely related to people from Papua New Guinea as to those from China or France. This is surprising because Neanderthal fossil remains have been located only in Europe and West Asia. Most likely, genetic exchange took place between Neanderthals and modern humans as modern humans emerged out of Africa, before the divergence of Europeans, East Asians, and Papua New Guineans.

    Several genes seem to have undergone changes from Neanderthals during the evolution of present-day humans. These genes are involved in cranial structure, metabolism, skin morphology, and cognitive development. One of the genes that is of particular interest is RUNX2, which is different in modern day humans and Neanderthals. This gene is responsible for the prominent frontal bone, bell-shaped rib cage, and dental differences seen in Neanderthals. It is speculated that an evolutionary change in RUNX2 was important in the origin of modern-day humans, and this affected the cranium and the upper body.

    1. Early humans emerged from Africa, then spread out to populate different parts of the globe. An isolated population of these early humans interbred with Neanderthals.
    2. Early humans interbred with Neanderthals, emerged from Africa, then spread out to populate different parts of the globe.
    3. Early humans emerged from Africa, interbred with Neanderthals, then spread out to populate different parts of the globe.
    4. Early humans did not interbreed with Neanderthals, but we have many genetic similarities because we share a common ancestor.

    Link to Learning

    Watch Svante Pääbo’s talk explaining the Neanderthal genome research at the 2011 annual TED (Technology, Entertainment, Design) conference.

    1. It has been suggested that all humans most likely descended from Africa. This is supported by the research that genetic variance in Africa was also found in the rest of the world.
    2. The theory that humans descended from Africa was supported by the research that most of the human genomes tested outside of Africa had close ties to the genomes of people in Africa but a genetic variance in Africa was not found in the rest of the world.
    3. Humans have most likely descended from Africa. This research is supported by the fact that all the human genomes tested outside of Africa had close ties to the genomes of people in Africa. Also, there is a genetic variance in Africa that was not found in the rest of the world.
    4. The transition to modern humans occurred within Africa which was sudden. Thus, human genomes tested outside of Africa had close ties to the genomes of people in Africa.

    DNA Packaging in Cells

    When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features (Figure 14.10). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid.

    Visual Connection

    1. Compartmentalization in eukaryotic cells enables the building of more complex proteins and RNA products. In prokaryotes, the advantage is that RNA and protein synthesis occurs much more quickly because it occurs in a single compartment.
    2. Compartmentalization in prokaryotic cells enables the building of more complex proteins and RNA products. In eukaryotes, the advantage is that RNA and protein synthesis occurs much more quickly because they occur in a single compartment.
    3. Compartmentalization in eukaryotic cells enables the building of simpler proteins and RNA products. In prokaryotes, the advantage is only simpler proteins and RNA products because complex ones are not needed.
    4. Compartmentalization in eukaryotic cells enables the building of more complex proteins and RNA products. In prokaryotes, the advantage is that RNA and protein synthesis takes more time because it occurs in a single compartment.

    The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.

    Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure 14.11). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins.

    In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.

    Footnotes

    As an Amazon Associate we earn from qualifying purchases.

    Want to cite, share, or modify this book? This book is Creative Commons Attribution License 4.0 and you must attribute OpenStax.

      If you are redistributing all or part of this book in a print format, then you must include on every physical page the following attribution:

    • Use the information below to generate a citation. We recommend using a citation tool such as this one.
      • Authors: Julianne Zedalis, John Eggebrecht
      • Publisher/website: OpenStax
      • Book title: Biology for AP® Courses
      • Publication date: Mar 8, 2018
      • Location: Houston, Texas
      • Book URL: https://openstax.org/books/biology-ap-courses/pages/1-introduction
      • Section URL: https://openstax.org/books/biology-ap-courses/pages/14-2-dna-structure-and-sequencing

      © Jan 12, 2021 OpenStax. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution License 4.0 license. The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.


      Step-by-Step Algorithm for the K-mers problem

      The following is a simple procedure for solving the above problem:-

      • Create list L of all K-mers in the original string
      • For every K-mer X in the original string
        • Consider every K-mer Y in the original string
          • Count the number of mismatches m between X and Y
          • If m <= d, then increase score of X by 1

          Computational Efficiency: If the original length of the string is L, then the algorithm does about L 2 K calculations. Note that L can sometimes be quite large, say 10s of millions or even billions (human DNA has comprises of about 3-4 billion nucleic acids).

          Correctness: The above algorithm works only if the K-mer appears correctly (without any mismatches) at-least once in the DNA sequence. Although this is not necessary, in practice this is usually the case. This is the case for many algorithms in bioinformatics, whereby an algorithm is not proved to give optimal results all the time, but in practice, it works quite well.


          Watch the video: From DNA to protein - 3D (November 2022).