Sequencing
Thursday, February 3, 2011
Diversity and Evolution Animations
Posted by United JC Union at 2:14 AMAnimations - Evolution
(Peppered Moth Game)
(Interesting overview of evolution)
(Various Animation Links)
(Allopatric Speciation)
(Adapative Radiation)
(Adaptive Radiation)
(Speciation)
Homeostasis and Cell Signalling Animations
Posted by United JC Union at 2:13 AMAnimations - Homeostasis
http://pennhealth.com/health_info/animationplayer/homeostasis.html
http://trc.ucdavis.edu/biosci10v/bis10v/week10/07homeostasis.html
Animations – Cell Signalling
http://entochem.tamu.edu/G-Protein/index.html
http://www.wiley.com/college/pratt/0471393878/student/animations/signal_transduction/index.html
http://www.wiley.com/legacy/college/boyer/0470003790/animations/signal_transduction/signal_transduction.htm
http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/moaction/surface.html
Biological Molecules Animation Links
Posted by United JC Union at 2:11 AM| Topic: Proteins | |
| No. | Web-links |
| 1 | |
| Topic: Enzymes | |
| No. | Web-links |
| 1 | |
| 2 | http://resources.emb.gov.hk/biology/english/virtual_lab/flash/enzyme_lab.html |
| 3 | http://www.stolaf.edu/people/giannini/flashanimat/enzymes/allosteric.swf |
| 4 | |
Common Mistakes & Misconceptions in Biology
Posted by United JC Union at 1:44 AMCommon Mistakes & Misconceptions in Biology
Cell Structure and Cell Membrane
l Cisterna ≠ crista
Cisterna = lumen of RER or Golgi Apparatus
Crista (cristae= plural) = infolding of the inner mitochondrial membrane
| Wrong | Correct |
| Ions are polar….. | Ions are charged hence they cannot pass through the hydrophobic core of the Cell Surface Membrane. |
| Nucleolus contains rRNA | Nucleolus synthesizes rRNA (which forms part of ribosome), but it itself is made of DNA (coiled around histones) |
| Fatty acid/ hydrocarbon tails interact with hydrophobic bonds | Fatty acid/ hydrocarbon tails interact with hydrophobic interactions |
| Ribosomes have one membrane | Ribosomes do not have membranes |
| Facilitated diffusion uses only channel proteins. Active transport uses only carrier proteins. | Facilitated diffusion uses both channel protein and carrier proteins. The carrier protein can change conformation without ATP hydrolysis. Active transport uses only carrier proteins which can change conformation only upon ATP hydrolysis. (Campbell 8th edition pg 135). Once, Cambridge question goes against this rule (see 2006/P2/Q1) but you still have to answer the question based on diagram. |
| Passage of small, hydrophobic molecules through the phospholipid bilayer is called “diffusion” | Passage of small, hydrophobic molecules through the phospholipid bilayer is called “simple diffusion” |
| Exocytosis is the same as active transport | Exocytosis is a type of bulk transport requiring vesicles, while active transport uses carrier proteins. |
Biological Molecules
| Wrong | Correct |
| Cellulose is a protein OR collagen is a polysaccharide | Cellulose is a polysaccharide AND collagen is a (fibrous) protein |
| Collagen is made up of triple helix | Tropocollagen is made up of triple helix. |
| Globular protein is globular in shape | Globular protein is spherical in shape. Use synonyms! |
Enzymes
l Active site can only be used when describing enzymes.
For other proteins eg. Receptors, pumps, transcription factors, use allosteric sites / binding sites.
l Failure to name the types of bonds affected when subjected to denaturation agents/ factors. E.g. Candidates must mention hydrogen/ionic bonds when high temperature is applied, ionic bonds when pH is changed or heavy metals added, hydrophobic interactions when organic solvents added and disulphide bonds when a reducing agent is added.
l Denaturation has two meanings:
- For proteins: disruption of tertiary structure, causing the protein to lose its 3D conformation
- For DNA : breaking of hydrogen bonds between complementary base pairs causing the two DNA strands to separate
Cell and Nuclear Division
l Chromatids separate to become chromosomes
Chromatids are no longer called chromatids after they separate from the centromere
| Wrong | Correct |
| Chromosomes are pulled to opposite ends of the cells by spindle fibres | Chromosomes are pulled to opposite poles of the cells by spindle fibres |
| Centromere split | Centromere divide |
| Chromosome replicate | DNA replicate (so each chromosome is now seen comprising of two sister chromatids) |
| Mitosis has no homologous chromosomes | Homologous chromosomes are already in cells irregardless of whether they are undergoing cell and nuclear division. All humans have 23 pairs of homologous chromosomes. |
| Diploid number = amount of DNA | Diploid number is the total number of chromosomes. DNA amount is twice in a chromosome with 2 sister chromatids compared to a chromosome that does not have sister chromatids. |
| DNA replication occurs in the interphase between meiosis I and II | DNA replication occurs once only in the interphase before meiosis I |
| Organism is sterile because gametes have odd number of chromosomes | Organism is sterile because the organism itself have odd number of chromosomes and/or have even number of chromosomes that do not occur in homologous pairs |
DNA and Genomics
l Unzip ≠ unwind
Unzip = breaking of hydrogen bonds between complementary base pairs to separate the two DNA strands.
Unwind = untwisting of the DNA double helix
l
|
1 DNA strand = 1 polynucleotide chain l 1 DNA molecule is made up of 2 DNA strands
l The triplet of 3 bases that forms the genetic code is known as
Base triplet in DNA
Codon in mRNA (some textbooks refer codon to DNA too, but we’ll keep to mRNA for now)
Anticodon in tRNA
| Wrong | Correct |
| Non-coding genes | Non-coding sequences/ regions Genes are already defined as coding DNA |
| In leading strand, DNA is synthesized in the 5’ to 3’ direction, while in lagging strand, DNA is synthesized in the 3’ to 5’ direction | DNA polymerase III synthesizes DNA daughter strands in 5’ to 3’ direction only. Leading strand is formed due to replication towards replication fork, while the lagging strand is formed due to replication away from replication fork. |
Control of Eukaryotic and Prokaryotic Genome
| Wrong | Correct |
| Control elements are proteins/ transcription factors are DNA | Control elements (promoter, silence and enhancer) are non-coding DNA sequences. Transcription factors (which are proteins) bind to control elements to regulate transcription. |
| Prokaryotes have control elements | Eukaryotes have control elements, while prokaryotes have regulatory sequences (like operator) and regulatory genes (like lacI gene). |
| Bacteria divides by mitosis | Bacteria divides by binary fission. |
Energetics
| Wrong | Correct |
| One of the electron carriers in the electron transport chain is a proton pump. | The electron carriers in the electron transport chain are coupled to proton pumps. |
| Electrochemical gradient is the same as concentration gradient | Electrochemical gradient includes concentration gradient AND electric potential gradient (so be careful how you use the term!) |
| When Cl- ions enter the neurone, it leads to repolarization. | When Cl- ions enter the neurone, it leads to hyperpoloarization. |
| Light dependent reactions occur in the presence of light while light independent reaction occurs in the dark | Light dependent reactions occur in the presence of light while light independent reaction can occur in the presence and absence of light. |
Genetic Basis of Variation
| Wrong | Correct |
| The two genes are linked so closely together that crossing over does not happen. | The two genes are linked so closely together that crossing over to separate the two genes does not happen. |
Diversity and Evolution
| Wrong | Correct |
| Traits are passed on to the next generation | Genes/alleles are passed on to the next generation |
| Organisms mutate to adapt to the environment | Mutations are random, they cause variation within populations |
| Mutations occur at a constant rate in neutral theory | Neutral mutations have been observed/ found to occur at a constant rate in certain DNA sequences or genes |
| Only silent mutation is involved in neutral theory | Neutral theory involves silent mutation and any mutation that results in a phenotype which is selectively neutral. |
Applications
| Wrong | Correct |
| Gene therapy is a technique for introducing healthy/ therapeutic gene | …..introducing normal allele/gene |
| Package the normal allele into liposomes/ virus | Package the DNA containing the normal allele/gene into liposomes/ virus |
| Deletion of a codon results in phenylalanine not to be produced/ gene lacking the amino acid | Deletion of a codon results in phenylalanine not to be coded/ protein lacking the amino acid |
| Insertional inactivation can be used to distinguish recombinant plasmids from reannealed plasmids | Insertional inactivation can be used to distinguish bacteria containing recombinant plasmids from bacteria containing reannealed plasmids. |
| In plant cloning, clones have same genes/ genetically similar to the same parent | In plant cloning, clones are genetically identical to the same parent |
| Stem cells repair damaged cells | Stem cells replace damaged cells Stem cells repair damaged organs |
| In autoradiography, expose the nitrocellulose membrane to X-ray | In autoradiography, place a piece of X-ray film over the nitrocellulose membrane, which will reveal the bands |
| Southern Blotting includes gel electrophoresis | Southern Blotting is carried out AFTER gel electrophoresis. |
l When describing gel electrophoresis, write “ direct current was applied”
l In nucleic aid hybridization: if radioactive probe is used, autoradiography is used to visualise the DNA bands on X-ray film
l In gel electrophoresis: If ethidium bromide is use, UV light is used to visualise the bands on the gel
l DNA ligase forms phosphodiester bonds
l Restriction enzymes breaks/cleave phosphodiester bonds. Always write, restriction enzyme cuts (not cleave, degrade, break down) DNA at restriction sites
l Ligation = formation of phosphodiester bonds between nucleotides
l Annealing = formation of hydrogen bonds between complementary base pairs
l Southern Blotting simply means putting the gel into an alkali so the alkali can denature the DNA into single-strands. Place a nitrocellulose/ nylon membrane over the gel under heavy weight so that the single-stranded DNA can bind to the membrane after travelling by capillary action.
l Nucleic acid hybridization simply means complementatary base pairing through hydrogen bonds between single-stranded, radioactive and specific probe and single-stranded DNA.
l Autoradiography simply means placing a piece of photographic or X-ray film over the nitrocellulose membrane, which will reveal the bands.
l How to use “RFLP” term? This can be used in e.g. ….perform RFLP analysis…/… if RFLP band fragment is seen…/… RFLP locus is located so close to disease allele…
Independent Assortment of Chromosomes
Posted by United JC Union at 1:42 AMSynapsis
Crossing-over
Chiasmata
Bivalents
THREE Sources of Variation
Crossing Over at Prophase I
Crossing Over at Prophase I
Independent Assortment at Metaphase I
Independent Assortment at Metaphase I
Possible combinations = 2n, n = haploid number.
Humans: n = 23.
Possible combinations = 223 = 8.4 million!
Independent Assortment is also known as Mendel’s Second Law
Random Fertilization
Each Gamete
One out of about 8.4 million (223) possible chromosome combinations due to independent assortment.
2 gametes fuse
Zygote with any of about 70 trillion (223 X 223) diploid combinations!!
Mendel’s First Law
Law of Segregation
A somatic cell carries two alleles at any one locus.
Alleles of a gene pair segregate during anaphase I of meiosis
Half of the gametes carry one allele of a gene pair; the other half carry the other allele.
Summary of meiosis and mitosis
Assignment
Explain the need for the production of genetically identical cells & fine control of replication
Since the functions of mitosis are to produce new cells for growth, repair of body tissues, and asexual reproduction,
essential that the cells are identical so that the daughter cells would continue to code for essential proteins that can function properly
How to Get Seedless Watermelon?
Double the diploid number (2n) in a normal watermelon plant by the use of the chemical colchicine to tetraploid (4n).
Colchicine’s function?
Tetraploid’s gamete = 2n
Normal watermelon’s gamete = n
Fuse the tetraploid’s gamete (2n) with normal water melon’s gamete (n)
Why is triploid watermelon sterile?
During meiosis the normal pairing of chromosomes cannot properly take place since one set will have no homologous set to pair with
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