Bio 1002B Outcomes PDF

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Biology 1002B Outcomes Outcomes: Lecture 1: 1. ● ● ●

Major features of Chlamydomonas? Flagella are used to identify stimuli and allow movement Eye Spot senses light and signals the flagella where to move the organism As a type of green algae, it uses chloroplasts to provide energy to its cellular systems

2. Features of the Chlamydomonas life cycle? ● ● ●

Starts with the products of meiosis Cells are almost indistinguishable when it comes to gender identification (only + and -) Reproduce asexually when the environment is not stressed and sexually when environmental conditions are not ideal

3. What is a mating type? ●

Mating types are similar to genders, plus (+) and (-)

4. What is an Open Reading Frame? ●

A continuous stretch of codons that begins with a start codon (usually AUG) and ends at a stop codon

5. Number of ORFs/genome size for bacteria versus eukaryotes ● ● ●

Synechocystis 1:1085 Chlamydomonas 1: 6256 Arabidopsis 1:4924

6. What is generation time? ●

The average time between two consecutive generations in the lineages of a population.

7. Relationship between photosynthesis and possessing a chloroplast ●

The chloroplast is the site of photosynthesis in eukaryotic cells, and is the site of the Calvin cycle just as the mitochondrion is the site of oxidative phosphorylation.

8. Analysis of 7, 476 Chlamy proteins...what percentage are found in Arabidopsis & humans, in just Arabidopsis, in just humans. ●

Proteins similar to humans are due to similar cellular functions, which is what makes chlamy a model system. Proteins similar to other bacteria are due to the way they reproduce asexually. Proteins similar in all three is because each is from one of the three branches of life and they all come from one similar ancestor in the past.

9. Definition of phototaxis…negative versus positive ●

Chlamy can move towards and away from a light source. Positive phototaxis moves towards light and negative phototaxis moves away from light.

Lecture 2: 1. ● ●

Characteristics of the electromagnetic spectrum travels in the form of a wave at a speed of km/h (the speed of light) and reaches Earth in just over 8 minutes. The electromagnetic spectrum ranges from gamma rays to radio waves; visible light and the wavelengths used for

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photosynthesis occupy only a narrow band of the spectrum. Relationship between wavelength and energy content of a photon. Shorter-wavelength blue light consists of photons of higher energy than red light, which has a longer wavelength and thus photons of lower energy. Definition of photon absorption. When a photon of light hits an object, the photon has three possible fates: it can be reflected off the object, transmitted through the object, or absorbed by the object. To be used as a source of energy or information by an organism, the light must be absorbed Molecular characteristic of pigments that make them able to absorb light. A common feature of all these pigments that is critical for light absorption is the presence of a conjugated system of double/single carbon bonds (shown in red for beta-carotene). Understanding of why biological systems primarily absorb visible wavelengths of the electromagnetic spectrum and not x-rays or radio waves, for example. Shorter wavelengths are absorbed by the ozone layer high in the atmosphere, whereas longer wavelengths are absorbed by water vapour and carbon dioxide in the atmosphere. Second, light contains an ideal amount of energy. Recall that living things are made up of complex molecules held together by often weak bonds such as hydrogen bonds

6. Chlamy life cycle: Why organisms in stressful environments undergo sexual reproduction ●

Stress causes sexual reproduction so that variation creates offspring that will better fit that environment

7. Not all stages of the life cycle gave the same growth rate and the role of the sygospore in helping Chlamy survive. ●

Depending on the environmental conditions, chlamy will take different routes in reproduction to ensure the greatest rate of survival for their offspring

8. Basic organization and functional features of the eyespot. ●

The plasma membrane allow for reflection of the light. Chloroplast membrane is made up of carotenoid granule layers allows for cellular cycles to transpire.

9. Structure and function of channelrhodospin ●

It is a light-gates ion channel with an electrical potential across is (operates by ATP), light depolarizes the membrane because cations can get through (positively charged ions

10. Mechanism by which the signal is transduced from eyespot to flagella. ● ● ● ●

Pigment bound to the photoreceptor sits in the membrane The top is the retinal curve on the absorption spectrum Light is used for information in eye spot and energy in the chloroplast The energy in the photon can cause it to be absorbed and it will excite one electron

11. Basics of generation of an action potential. ●

an action potential occurs when the membrane potential of a specific axon location rapidly rises and falls. This depolarization then causes adjacent locations to similarly depolarize. Action potentials occur in several types of animal cells, called excitable cells, which include neurons, muscle cells, endocrine cells, and in some plant cells.

12. Mechanism of photoisomerization of retinal and its consequences ● ● ●

Photon absorption can bring energy to change orientation from trans to cis Protein Conformation Retinal transformation opens and closes the light gate ion channel

13. Key similarities and differences between function of channelrhodopsin in the eyespot and rhodopsin in the human eye. ●

Both use cis and trans retinal areas to absorb and transfer light, then use an action potential to move ions across the membrane

14. Correct interpretation of the term homology. ●

the existence of shared ancestry between a pair of structures, or genes, in different taxa.

15. Distinction between photochemistry as it occurs in eyes and eyespots compared to how it occurs within a photosystem in photosynthesis. ● ●

Photosynthetic pigments, such as chlorophyll a, chlorophyll b, and carotenoids, are light-harvesting molecules found in the thylakoid membranes of chloroplasts. In the eye, rods and cones process light to show images and send stimuli to the brain

16. Basic understanding of optogenetics: what is it, why is it useful, and the basics of what one does to a neutron to make ontogenetic experiments possible. ●

is a biological technique that involves the use of light to control cells in living tissue, typically neurons, that have been genetically modified to express light-sensitive ion channels. It is a neuromodulation method that uses a combination of techniques from optics and genetics to control and monitor the activities of individual neurons in living tissue—even within freely-moving animals—and to precisely measure these manipulation effects in real-time

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Purpose of Northern analysis ● The northern blot, or RNA blot, is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample. Rationale for all the steps: gel electrophoresis, transfer to membrane, hybridization ● Gel electrophoresis separates the DNA fragments by their size in order to analyze them ● Transfer to a membrane is a rapid, alkaline transfer method that increases blot sensitivity by efficiently moving RNA, especially larger transcripts, onto the membrane. This step only takes 2 hours and can trim an almost entire day off the standard procedure, which generally requires overnight transfer. Importance of the probe being "labelled" and single stranded. ● It has been designed to have a sequence that is complementary to a particular RNA sequence in the sample; this allows the probe to hybridize, or bind, to a specific RNA fragment on the membrane Basics of the movement of information from DNA to RNA to Proteins ● During the process of transcription, the information stored in a gene's DNA is transferred to a similar molecule called RNA (ribonucleic acid) in the cell nucleus. Both RNA and DNA are made up of a chain of nucleotide bases, but they have slightly different chemical properties. The type of RNA that contains the information for making a protein is called messenger RNA (mRNA) because it carries the information, or message, from the DNA out of the nucleus into the cytoplasm.Translation, the second step in getting from a gene to a protein, takes place in the cytoplasm. The mRNA interacts with a specialized complex called a ribosome, which "reads" the sequence of mRNA bases. Each sequence of three bases, called a codon, usually codes for one particular amino acid. (Amino acids are the building blocks of proteins.) A type of RNA called transfer RNA (tRNA) assembles the protein, one amino acid at a time. Protein assembly continues until the ribosome encounters a “stop” codon (a sequence of three bases that does not code for an amino acid).The flow of information from DNA to RNA to proteins is one of the fundamental principles of molecular biology. It is so important that it is sometimes called the “central dogma.” Comparison between genomics, transcriptomics, proteomics. Advantages of each. ● Genomics: looking a gene sequence as a whole, easier to do due to technology ● Transcriptomics: looking at transcription of DNA and RNA, middle ground on difficulty ● Proteomics: looks at all the individual proteins, looks closer at phenotype and behaviour of cells Different types of RNA: mRNA, tRNA and rRNA ● mRNA: a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. ● tRNA: a type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein. tRNAs function at specific sites in the ribosome during translation, which is a process that synthesizes a protein from an mRNA molecule. ● rRNA: he RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight, or 3/5 of ribosome mass. Aspects of gene expression: transcription, translation, mRNA and protein breakdown (decay) ● transcription: a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase ● translation: messenger RNA (mRNA) is decoded in a ribosome to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell. The

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ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome. ● Protein Decay: Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Low pH or high temperatures can also cause proteolysis non-enzymatically. Importance of correct folding for protein function ● Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure. Folding begins to occur even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure Regulatory importance for why mRNA degrades relatively rapidly. ● The greater the stability of an mRNA the more protein may be produced from that mRNA. The limited lifetime of mRNA enables a cell to alter protein synthesis rapidly in response to its changing needs Identify intact versus degraded total RNA ● Gel electrophoresis separates RNA by size in order to identify which pieces are degrading and which are still intact Distinction between constitutive, induced and repressed gene expression, and the process that can account for a change in transcript abundance.. ● Consecutive Gene Expression: the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. Consecutive expression is defined by genes continuing to express in a healthy and successful way, despite mutations and errors ● Induced Gene Expression: In molecular biology, an inducer is a molecule that regulates gene expression. An inducer can bind to protein repressors or activators. Inducers function by disabling repressors. The gene is expressed because an inducer binds to the repressor. The binding of the inducer to the repressor prevents the repressor from binding to the operator. RNA polymerase can then begin to transcribe operon genes. Inducers also function by binding to activators. Activators generally bind poorly to activator DNA sequences unless an inducer is present. Activator binds to an inducer and the complex binds to the activation sequence and activates target gene. Removing the inducer stops transcription Factors that act at the level of transcription that alter transcript abundance. ● Control is at the level of the promoter (RNA polymerase), so it is not transcribed ● Dependent on errors, environmental conditions, etc. Factors that act that the level of mRNA stability that alter transcript abundance. ● Change in environmental conditions leads to increase in proteins and stability in mRNA What is needed to measure the half-life on a particular transcript (mRNA). ● Mixing actinomycin to a mixture with nRNA blocks further transcription, therefore mRNA decays and gel electrophoresis is used to look at specific genes, change in temperature can affect how quickly the mRNA decays How is mRNA half-life calculated. ● The mRNA is isolated at different time periods in order to distinguish the amount of decay over time Rough idea of the median half-life of a mammalian mRNA, protein. ● mRNA: 9 hours ● Protein: 46 hours Rough idea of the median number of molecules of transcript of a particular mammalian gene and the number of molecules of protein for a protein-coding gene. ● mRNA: 17 ● Protein: 16,000 Understanding of how genes influence biochemical pathways (e.g. retinal, hormone biosynthesis ● Depending on the environmental conditions, different genes will be expressed in order to keep the cells alive Concept of post-translational modification. ● Cofactor + Apoprotein = Functional Protien ● Needs retinal and opsin to come together to make the functional molecule or it wont work [1]

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GlsA gene from Volvox versus Chlamydomonas. Function, sequence similarity, evolutionary history ● GlsA in Volvox is necessary for asymmetrical division, in chlamy it has no known function. They are very similar in genetic sequence, which makes it less likely that they evolved independently Basics of NCBI and databases...what are they for, what kind of questions can be addressed ● By inputing either a gene sequence or protein sequence, the algorithm will show all organisms with a similar sequence Reasons why one does sequence alignments. ● Compared to other researchers’ work and other DNA sequences Differences between global versus local (advantages of each). ● Global searches for large sections of high similarity which allows for homology ● Local looks for any small sections of similarity to get more results How does BLAST work....basics ● People upload their sequences into the algorithm, then the system searches for matches and then puts them all side by side Basics of a BLAST report...what does it show you, how is the data organized ● It shows any similar sequences in any organism and it is organized side by side so that you can see all similarities Distinction between the BLAST score and the E-value…. ● E value is based on homology, BLAST score is just the number of matches Relationship between E-value and likelihood of homology ● If the E value is less than 0.000001, they organisms are homologous

Lecture 5:

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Synonymous vs nonsynonymous mutations ● Synonymous Substitutions do not alter amino acid sequences of a protein ● Nonsynonymous Substitutions alters the amino acid sequence of a protein, typically cause biological change in an organism 2. Characteristics of the neutral theory of molecular evolution ● The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level 3. Relationship between frequency of amino acid substitutions in given proteins vs. time since common ancestor ● Proportional 4. Relative rates of accumulation of synonymous vs. non-synonymous mutations: why the difference? ● Both types of mutations are expected to arise at the same rate. However, synonymous substitutions do not change the amino acid sequence of a protein and generally have no phenotypic effect. They are therefore not subject to natural selection and are expected to accumulate freely 5. Variables that affect the rate of evolution of a particular protein ● Time of divergence, environment, mutations, how much a difference would affect the function of the protein 6. Deduce time of divergence given number of amino acid changes in particular protein 7. Why two proteins with very similar sequences would not occur by convergent evolution ● Sequence similarity does not always mean similarity in function ● May have evolved at different times in different organisms 8. Difference between Contingency and Convergence in understanding evolutionary change ● Contingency - each step in evolution is dependent on all the steps before it. ● Convergence....the evolutionary routes are many, but the destinations are limited. 9. Evolution of channelrhodopsin vs rhodopsin ● They have no similarity ● They have different sequences and functions, evolved separately 10. Basics of the two kinds of opsin ● Channelrhodopsin: function as light-gated ion channels, sensory photoreceptors that control phototaxis in algae ● Rhodopsin: light-sensitive receptor involved in visual phototransduction. Found in rods of retina and is a G-protein-coupled receptor 11. Characteristics of ruminant organisms that enable them to extract energy from cellulose ● Lysozymes are proteins the allow animals to eat grass, leaves, etc. and extract energy from them 12. Role of lysozyme in digestive physiology of ruminants, langur monkeys and ho...