Information

W2017_Lecture_24_reading - Biology

W2017_Lecture_24_reading - Biology


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.

Mutations

Errors occurring during DNA replication are not the only way by which mutations can arise in DNA. Induced mutations are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. Spontaneous mutations occur without any exposure to any environmental agent; they are a result of spontaneous biochemical reactions taking place within the cell.

Mutations may have a wide range of effects. Some mutations are not expressed; these are known as silent mutations. Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types, either transitions or transversions. Transition substitution refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. Transversion substitution refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a nucleotide, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is known as translocation.

As we will visit later, when a mutation occurs in a protein coding region it may have several effects. Transition or transversion mutants may lead to no change in the protein sequence (known as silent mutations), change the amino acid sequence (known as missense mutations), or create what is known as a stop codon (known as a nonsense mutation). Insertions and deletions in protein coding sequences lead to what are known as frameshift mutations. Missense mutations that lead to conservative changes results in the substitution of similar but not identical amino acids. For example, the acidic amino acid glutamate being substituted for the acidic amino acid aspartate would be considered conservative. In general we do not expect these types of missense mutations to be as severe as a non-conservative amino acid change; such as a glutamate substituted for a valine. Drawing from our understanding of functional group chemistry we can correctly infer that this type of substitution may lead to severe functional consequences, depending upon location of the mutation.

Note: Vocabulary Watch

Note that the preceding paragraph had a lot of potentially new vocabulary - it would be a good idea to learn these terms.

Mutations can lead to changes in the protein sequence encoded by the DNA.

Suggested discussion

Based on your understanding of protein structure, which regions of a protein would you think are more sensitive to substitutions, even conserved amino acid substitutions? Why?

Suggested discussion

A insertion mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?

Mutations: Some nomenclature and considerations

Mutation

Etymologically speaking, the term mutation simply means a change or alteration. In genetics, a mutation is a change in the genetic material - DNA sequence - of an organism. By extension, a mutant is the organism in which a mutation has occurred. But what is the change compared to? The answer to this question, is that it depends. The comparison can be made with the direct progenitor (cell or organism) or to patterns seen in a population of the organism in question. It mostly depends on the specific context of the discussion. Since genetic studies often look at a population (or key subpopulations) of individuals we begin by describing the term "wild-type".

Wild Type vs Mutant

What do we mean by "wild type"? Since the definition can depend on context, this concept is not entirely straightforward. Here are a few examples of definitions you may run into:

Possible meanings of "wild-type"

  1. An organism having an appearance that is characteristic of the species in a natural breeding population (i.e. a cheetah's spots and tear-like dark streaks that extend from the eyes to the mouth).
  2. The form or forms of a gene most commonly occurring in nature in a given species.
  3. A phenotype, genotype, or gene that predominates in a natural population of organisms or strain of organisms in contrast to that of natural or laboratory mutant forms.
  4. The normal, as opposed to the mutant, gene or allele.

The common thread to all of the definitions listed above is based on the "norm" for a set of characteristics with respect to a specific trait compared to the overall population. In the "Pre-DNA sequencing Age" species were classified based on common phenotypes (what they looked like, where they lived, how they behaved, etc.). A "norm" was established for the species in question. For example, Crows display a common set of characteristics, they are large, black birds that live in specific regions, eat certain types of food and behave in a certain characteristic way. If we see one, we know its a crow based on these characteristics. If we saw one with a white head, we would think that either it is a different bird (not a crow) or a mutant, a crow that has some alteration from the norm or wild type.

In this class we take what is common about those varying definitions and adopt the idea that "wild type" is simply a reference standard against which we can compare members of a population.

Suggested discussion

If you were assigning wild type traits to describe a dog, what would they be? What is the difference between a mutant trait and variation of a trait in a population of dogs? Is there a wild type for a dog that we could use as a standard? How would we begin to think about this concept with respect to dogs?

Mutations can lead to changes in the protein sequence encoded by the DNA that then impact the outward appearance of the organism.
Source:http://blogs.brandeis.edu/flyonthewa...y-in-the-life/

Mutations are simply changes from the "wild type", reference or parental sequence for an organism. While the term "mutation" has colloquially negative connotations we must remember that change is neither inherently "bad". Indeed, mutations (changes in sequences) should not primarily be thought of as "bad" or "good", but rather simply as changes and a source of genetic and phenotypic diversity on which evolution by natural selection can occur. Natural selection ultimately determines the long-term fate of mutations. If the mutation confers a selective advantage to the organism, the mutation will be selected and may eventually become very common in the population. Conversely, if the mutation is deleterious, natural selection will ensure that the mutation will be lost from the population. If the mutation is neutral, that is it neither provides a selective advantage or disadvantage, then it may persist in the population. Different forms of a gene, including those associated with "wild type" and respective mutants, in a population are termed alleles.

Consequences of Mutations

For an individual, the consequence of mutations may mean little or it may mean life or death. Some deleterious mutations are null or knock-out mutations which result in a loss of function of the gene product. These mutations can arise by a deletion of the either the entire gene, a portion of the gene, or by a point mutation in a critical region of the gene that renders the gene product non-functional. These types of mutations are also referred to as loss-of-function mutations. Alternatively, mutations may lead to a modification of an existing function (i.e. the mutation may change the catalytic efficiency of an enzyme, a change in substrate specificity, or a change in structure). In rare cases a mutation may create a new or enhanced function for a gene product; this is often referred to as a gain-of-function mutation. Lastly, mutations may occur in non-coding regions of DNA. These mutations can have a variety of outcomes including altered regulation of gene expression, changes in replication rates or structural properties of DNA and other non-protein associated factors.

Suggested discussion

In the discussion above what types of scenarios would allow such a gain-of-function mutant the ability to out compete a wild type individual within the population? How do you think mutations relate to evolution?

Mutations and cancer

Mutations can affect either somatic cells or germ cells. Sometimes mutations occur in DNA repair genes, in effect compromising the cell's ability to fix other mutations that may arise. If, as a result of mutations in DNA repair genes, many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. Cancers, including forms of pancreatic cancer, colon cancer, and colorectal cancer have been associated with mutations like these in DNA repair genes. If, by contrast, a mutation in DNA repair occurs in germ cells (sex cells), the mutation will be passed on to the next generation, as in the case of diseases like hemophilia and xeroderma pigmentosa. In the case of xeroderma pigmentoas individuals with compromised DNA repair processes become very sensitive to UV radiation. In severe cases these individuals may get severe sun burns with just minutes of exposure to the sun. Nearly half of all children with this condition develop their first skin cancers by age 10.

Consequences of errors in replication, transcription and translation

Something key to think about:

Cells have evolved a variety of ways to make sure DNA errors are both detected and corrected, rom proof reading by the various DNA-dependent DNA polymerases, to more complex repair systems. Why did so many different mechanisms evolve to repair errors in DNA? By contrast, similar proof-reading mechanisms did NOT evolve for errors in transcription or translation. Why might this be? What would be the consequences of an error in transcription? Would such an error effect the offspring? Would it be lethal to the cell? What about translation? Ask the same questions about the process of translation. What would happen if the wrong amino acid was accidentally put into the growing polypeptide during the translation of a protein? Contrast this with DNA replication.

Mutations as instruments of change

Mutations are how populations can adapt to changing environmental pressures.

Mutations are randomly created in the genome of every organism, and this in turn creates genetic diversity and a plethora of different alleles per gene per organism in every population on the planet. If mutations did not occur, and chromosomes were replicated and transmitted with 100% fidelity, how would cells and organisms adapt? Whether mutations are retained by evolution in a population depends largely on whether the mutation provides selective advantage, poses some selective cost or is at the very least, not harmful. Indeed, mutations that appear neutral may persist in the population for many generations and only be meaningful when a population is challenged with a new environmental challenge. At this point the apparently previously neutral mutations may provide a selective advantage.

Example: Antibiotic resistance

The bacterium E. coli is sensitive to an antibiotic called streptomycin, which inhibits protein synthesis by binding to the ribosome. The ribosomal protein L12 can be mutated such that streptomycin no longer binds to the ribosome and inhibits protein synthesis. Wild type and L12 mutants grow equally well and the mutation appears to be neutral in the absence of the antibiotic. In the presence of the antibiotic wild type cells die and L12 mutants survive. This example shows how genetic diversity is important for the population to survive. If mutations did not randomly occur, when the population is challenged by an environmental event, such as the exposure to streptomycin, the entire population would die. For most populations this becomes a numbers game. If the mutation rate is 10-6 then a population of 107 cells would have 10 mutants; a population of 108 would have 100 mutants, etc.

Uncorrected errors in DNA replication lead to mutation. In this example, an uncorrected error was passed onto a bacterial daughter cell. This error is in a gene that encodes for part of the ribosome. The mutation results in a different final 3D structure of the ribosome protein. While the wildtype ribosome can bind to streptomycin (an antibiotic that will kill the bacterial cell by inhibiting the ribosome function) the mutant ribosome cannot bind to streptomycin. This bacteria is now resistant to streptomycin.
Source: Bis2A Team original image

Suggested discussion

Based on our example, if you were to grow up a culture of E. coli to population density of 109 cells/ml; would you expect the entire population to be identical? How many mutants would you expect to see in 1 ml of culture?

An example: Lactate dehydrogenase

Lactate Dehydrogenase (LDH), the enzyme that catalyzes the reduction of pyruvate into lactic acid in fermentation, while virtually every organism has this activity, the corresponding enzyme and therefore gene differs immensely between humans and bacteria. The proteins are clearly related, they perform the same basic function but have a variety of differences, from substrate binding affinities and reaction rates to optimal salt and pH requirements. Each of these attributes have been evolutionarily tuned for each specific organism through multiple rounds of mutation and selection.

Suggested discussion

We can use comparative DNA sequence analysis to generate hypotheses about the evolutionary relationships between three or more organisms. One way to accomplish this is to compare the DNA or protein sequences of proteins found in each of the organisms we wish to compare. Let us, for example, imagine that we were to compare the sequences of LDH from three different organisms, Organism A, Organism B and Organism C. If we compare the LDH protein sequence from Organism A to that from Organism B we find a single amino acid difference. If we now look at Organism C, we find 2 amino acid differences between its LDH protein and the one in Organism A and one amino acid difference when the enzyme from Organism C is compared to the one in Organism B. Both organisms B and C share a common change compared to organism A.

Schematic depicting the primary structures of LDH proteins from Organism A, Organism B, and Organism C. The letters in the center of the proteins line diagram represent amino acids at a unique position and the proposed differences in each sequence. The N and C termini are also noted H2N and COOH, respectively.
Attribution: Marc T. Facciotti (original work)

Question: Is Organism C more closely related to Organism A or B? The simplest explanation is that Organism A is the earliest form, a mutation occurred giving rise to Organism B. Over time a second mutation arose in the B lineage to give rise to the enzyme found in Organism C. This is the simplest explanation, however we can not rule out other possibilities. Can you think of other ways the different forms of the LDH enzyme arose these three organisms?

GLOSSARY

induced mutation:

mutation that results from exposure to chemicals or environmental agents

mutation:

variation in the nucleotide sequence of a genome

mismatch repair:

type of repair mechanism in which mismatched bases are removed after replication

nucleotide excision repair:

type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed

proofreading:

function of DNA pol in which it reads the newly added base before adding the next one

point mutation:

mutation that affects a single base

silent mutation:

mutation that is not expressed

spontaneous mutation:

mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent

transition substitution:

when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine

transversion substitution:

when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine


Fourth Graders' Cognitive Processes and Learning Strategies for Reading Illustrated Biology Texts: Eye Movement Measurements

Previous research suggests that multiple representations can improve science reading comprehension. This facilitation effect is premised on the observation that readers can efficiently integrate information in text and diagram formats however, this effect in young readers is still contested. Using eye-tracking technology and sequential analysis, this study investigated students' reading strategies and comprehension of illustrated biology texts in relation to adult readers' performance. The target population was fourth-grade students with high reading ability, and the control group was university students. All participants read a biology article from an elementary school science textbook containing two illustrations, one representational and one decorative. After the reading task, participants answered questions on recognition, textual, and illustration items. Unsurprisingly, the university students outperformed the younger students on all tests however, more interestingly, eye movement patterns differed across the two groups. The adult readers demonstrated bidirectional reading pathways for both text and illustrations, whereas the fourth graders' eye fixations only went back and forth within paragraphs in the text and between the illustrations, but made fewer references to both text and illustration. This suggests that regardless of their high reading ability, fourth-grade students' visual literacy is not mature enough to perceive connections between corresponding features of different representations crucial to reading comprehension. Despite differences in cognitive processes between adult readers and young readers, high-ability young readers still have certain capabilities in reading comprehension. The results of sequential analysis showed that they looked back to previous paragraphs frequently, indicating that they were monitoring their comprehension.

Chinese

Spanish

Trabajos de investigación anteriores sugieren que representaciones múltiples pueden mejorar la comprensión de lecturas científicas. Este efecto facilitador se basa en la observación que los lectores pueden eficazmente integrar información que aparece en textos y diagramas sin embargo, todavía no hay consenso sobre dicho efecto en lectores jóvenes. Usando la tecnología del rastreo ocular y el análisis secuencial, este estudio investigó las estrategias de lectura y la comprensión de textos de biología ilustrados usados por estudiantes en relación al rendimiento de lectores adultos. La población estudiada fueron estudiantes de cuarto grado con buena habilidad lectora, y el grupo de control eran estudiantes universitarios. Todos los participantes leyeron un artículo de biología de un texto de ciencias de escuela primaria que incluía dos ilustraciones, una representacional y otra decorativa. Después de la lectura, los participantes contestaron preguntas de reconocimiento, textuales, y sobre las ilustraciones. Como era de esperarse, los estudiantes universitarios salieron mejor en todos las pruebas que los estudiantes jóvenes, sin embargo, interesantemente, el patrón de movimiento ocular era diferente en los dos grupos. Los lectores adultos mostraron caminos de lectura bidireccionales tanto con el texto como con las ilustraciones, mientras que los ojos de los estudiantes de cuarto grado sólo iban de un párrafo a otro en el texto y entre las ilustraciones, pero iban menos entre el texto y las ilustraciones. Esto sugiere que, a pesar de su buena habilidad lectora, la competencia visual de los estudiantes de cuarto grado no es lo suficientemente madura para que ellos se den cuenta de las conexiones entre los aspectos de diferentes representaciones que son importantes para la comprensión lectora. A pesar de las diferencias en los procesos cognitivos entre lectores adultos y jóvenes, los lectores jóvenes de gran habilidad aún tienen ciertas capacidades en cuanto a la comprensión lectora. Los resultados del análisis secuencial mostraron que volvían a párrafos anteriores con frecuencia, indicando que estaban monitoreando su comprensión.

Arabic

تشير الأبحاث السابقة أن تمثيلات متعددة يمكن لها أن تحسن قراءة وفهم المواضيع العلمية. هذا التأثير متعلق على الملاحظة أنه يمكن للقراء دمج المعلومات في النصوص والرسموم التخطيطية بسهولة؛ ولكن، لا يزال هذا التأثير مختلف عليه في القراء عند الصغار. باستخدام تقنية تتبع حركة العين والتحليل المتسلسل، بحثت هذه الدراسة استراتيجيات القراءة وفهم نصوص علم الأحياء المصورة بالمقارنة مع أداء القراء الكبار. كانت المجموعة المستهدفة طلاب الصف الرابع ذوات القدرة المرتفعة على القراءة، وكانت المجموعة المقارنة من طلبة الجامعات. قراء جميع المشاركين نص أحياء من كتاب العلوم في مدارس الابتدائية يحتوي على رسمين توضيحيين، أحدهما يوضح النص والأخر للزغرفة فقط. بعد القراءة، أجاب المشاركون على أسئلة وحول التعرف على البنود النصية، والتوضيحة. مما لا يثير الدهشة، أن طلبة الجامعة تفوقوا على الطلاب الصغار في جميع الاختبارات. ولكن، مما أثار الاهتمام أكثر ، هو اختلاف أنماط حركة العين في المجموعتين. القراء الكبار مارسوا قراءة ثنائية الاتجاه لكل من النصوص والرسوم التوضيحية ، في حين أن حركة العين عند طلاب الصف الرابع تنقلت فقط ذهابا وإيابا ضمن فقرات النصوص وبين الرسوم التوضيحية، ولكن الحركة كانت أقل بين النصوص وبين الرسومات التوضيح. وهذا يشير إلى أنه بغض النظر على قدرة طلاب الصف الرابع العالية للقراءة، لا يزال الإستيعاب البصري ليس ناضج بما فيه الكفاية لإدراك أهمية الربط بين الصوص والرسوم التوضيحية المقابلة لها و التي هية الضرورية للفهم. على الرغم من الاختلافات في الوسائل المعرفية بين القراء الكبار والقراء الصغار، القراء الصغار ذو القدرة العالية لا تزال لديها قدرات معينة في القراءة والفهم. وأظهرت نتائج التحليل المتسلسل أن الطلاب كانوا تيظرون إلى الفقرات السابقة في كثير من الأحيان، مما يشير إلى أنهم كانوا يراقبو فهمهم.

Russian

Ранее проведенные исследования свидетельствуют о том, что разнообразие в формах подачи материала улучшает понимание текстов научной тематики: читатели успешно объединяют информацию из текста и сопроводительных графиков и иллюстраций. Однако работает ли это для читателей младшего возраста? Используя технологию, отслеживающую движение глаз, и последовательный анализ, ученые сравнили стратегии чтения школьников и взрослых читателей и понимание ими иллюстрированных текстов по биологии. Целевой группой исследования были ученики четвертого класса с хорошими навыками чтения и понимания прочитанного, в контрольную группу входили студенты университета. Обеим группам был предложен параграф из школьного учебника биологии, содержащий две иллюстрации: содержательную и декоративную. После чтения все участники исследования отвечали на вопросы по содержанию текста и иллюстраций. Неудивительно, что студенты университета выполнили задания лучше, чем школьники однако интересно, насколько отличались движения глаз у целевой и контрольной групп. Внимание взрослых читателей было двунаправленно: на текст и на иллюстрации, тогда как четвероклассники переводили взгляд от абзаца к абзацу и от иллюстрации к иллюстрации, но гораздо реже устанавливали визуальные связи между текстом и иллюстрациями. Это свидетельствует о том, что даже при высокой способности к чтению, визуальная грамотность студентов четвертого класса не сформирована в достаточной степени, чтобы почувствовать соответствие между определенными моментами текста и иллюстративным материалом, что крайне важно для понимания прочитанного. Тем не менее, несмотря на различия в познавательных процессах между взрослыми и юными читателями, последние также стремятся понять прочитанное. Результаты последовательного анализа показали, что дети часто возвращались к уже прочитанным абзацам, что означает, что они контролируют свое понимание текста.

French

Des recherches précédentes suggèrent que disposer de représentations multiples peut améliorer la compréhension de textes scientifiques. Cet effet de facilitation repose sur l'observation que les lecteurs peuvent intégrer efficacement une information présentée sous forme de textes et de diagrammes. Cependant cet effet est contesté quand il s'agit de jeunes lecteurs. En utilisant une technologie basée sur le suivi du mouvement des yeux et l'analyse séquentielle, cette étude examine les stratégies de lecture des élèves et leur compréhension de textes de biologie illustrés, en relation avec la façon de faire de lecteurs adultes. La population cible est constituée d’élèves de 4e année ayant un bon niveau de lecture et d’étudiants d'université. Tous les participants lisent un article de biologie provenant d'un manuel d’école élémentaire et contenant deux illustrations, dont l'une est d'ordre représentatif et l'autre d'ordre décoratif. Après la lecture, les participants répondent à des questions de reconnaissance, et à des items sur le texte et les illustrations. Comme on pouvait s'y attendre, les étudiants d'université réussissent mieux que les plus jeunes à tous les tests, cependant, et c'est plus intéressant, la structure des mouvements oculaires n'est pas la même pour les deux groupes. Les lecteurs adultes présentent des itinéraires de lecture bidirectionnels aussi bien pour le texte que pour les illustrations, tandis que la fixation des yeux des élèves de 4e année indique qu'ils vont en avant et en arrière à l'intérieur des paragraphes du texte et d'une illustration à l'autre, mais se réfèrent moins souvent en même temps au texte et aux illustrations. Ceci signifie que, malgré leur bon niveau de lecture, la littératie visuelle des élèves de 4e année n'est pas assez mature pour faire des relations entre les traits correspondants de représentations différentes qui sont cruciales pour la compréhension. En dépit des différences des processus cognitifs entre adultes et jeunes lecteurs, de jeunes lecteurs ayant un bon niveau ont cependant certaines compétences de comprehension de la lecture. Les analyses de lecture séquentielle montrent qu'ils reviennent souvent à des praragraphes précédents, ce qui signifie qu'ils savent piloter leur compréhension.



Comments:

  1. Ullock

    I congratulate, what necessary words ..., excellent thought

  2. Medredydd

    the dumbest divorce

  3. Phrixus

    Of course. It was with me too.

  4. Anh Dung

    Thanks so much for the information, now I know.

  5. Archibaldo

    How interesting that sounds



Write a message