Chapter 4: Helpful Hints
This video is a song/rap about cells and their organelles. The video is set to the song "Empire State of Mind" by Jay Z, so the song goes to a popular tune that is easy to remember. There are lots of diagrams, pictures, and labels so one can identify the parts while hearing/singing about them. Lastly, the video shows both eukaryotic and prokaryotic cells, so one can identify the cell types and structures in both types.
So this video is about endosymbiosis. Endosymbiosis is how it is believed that mitochondria and chloroplasts ended up in cells. This video has clay figures clearly labeled to represent the large and small cells involved. It also has words describing what is happening during endosymbiosis. Last but certainly not least, it has "You've Got a Friend in Me" playing in the background which relates to the video and is also such a great song!
Human Plasma Proteome
This article talks about how the human plasma proteome holds a world of answers involving disease diagnosis and therapeutic monitoring. The plasma proteome is not the only proteome being studied, but it has the largest and deepest version of the human proteome. The plasma proteome not only included plasma proteins, but also included tissue proteins and multiple distinct immunoglobin sequences.
Before, standard proteomic technology only allowed for scientists to study 289 plasma proteins. However, new technologies are guaranteeing twice the amount of proteins to be studies in the near future. Research suggests that among these numerous plasma proteins are indicators of many human diseases. However, very few proteins are used in routine clinical diagnosis, and the rate of introduction of new protein test approved by the FDA has declined in the past ten years to one new protein per year.
This article talks about the importance of protein folding and a few of the diseases that occur because of improper protein folding or a cell's protein quality control not being as strong.. Protein synthesis is essential for life, but it's not the only step. In order for proteins to function properly, they need to fold in the correct manner. One simple error in folding can lead to a completely inactive protein.
An example of this would be Huntington's Disease. Huntington's Disease (HD) is a dominantly inherited autosomal neurodegenerative disorder. It is characterized by the progressive development of mood disturbances, behavioral changes, involuntary choreiform movements, and cognitive impairments. Onset usually occurs in adulthood, and HD usually lasts 15-20 years before ending a person's life in a premature death.
What cause HD is the expansion of an unstable CAG repeat which encode glutamines close to the 5'-end of the gene for the huntingtin protein. The length of the CAG determines the phenotype of HD. The protein huntingin is found predominantly in the cytoplasm. It's function is not yet fully understood yet, but may involve cytoskeletal function or vesicle recycling. It has also been proposed that the gene may be transported to the nucleus and serve a role in the regulation of gene transcription, but this is not yet certain. The toxicity of huntingin may be caused by mutant full-length proteins or cleaved proteins. The Huntington gene is expressed in all cells but only affects a subset of neurons.
Tay-Sachs disease is a terminal disease of the nervous system. It was first identified in 1881. Tay-Sachs disease occurs because of problems with lysosomes. Lysosomes are organelles in cells which essentially process waste. They are kind of like the garbage men of the cell! I came up with that analogy all by myself! Clever, I know.
This article explains how a person with Tay-Sachs has mutated genes that result in the production of enzymes less effective in breaking down gangliosides. These enzymes are found in lysosomes. Gangliosides are fatty cell products. Since these enzymes are less effective, gangliosides build up in the lysosomes and eventually overload the cell. This build up causes damage to nerve cells.
This mess up on a cellular level results in terrible outcomes for people with Tay-Sachs disease. This article talks about symptoms of the disease include deafness, blindness, decreased muscle tone, loss of motor skills, loss of muscle function/paralysis, and many others. Tay-Sachs is an inherited genetic disease. The child must receive the gene from both parents in order to be affected by it, otherwise the child will just be a carrier. This is why nerve damage caused by the disease often begins when the child is still in the womb. Symptoms usually start popping up when the child is 3 to 6 months old. Unfortunately, most people with Tay-Sachs disease don't live past 4 or 5 years old.
This blog will be based off of the virtual lectures on proteins and nucleic acids.
Proteins
Proteins are quintessential in our survival. They have so many functions in a cell, and thus in our lives. Proteins are used for support, as enzymes (speeding up biological reactions), membrane transport, and producing cellular movements. Amazingly, proteins functions don't stop there! Proteins are also regulators, receptors, hormones, antibodies, venom and toxins, and for storage. Proteins do so many things that allow us to live.
Proteins are able to do so many things because they are built differently. The structure of a protein determines its function. There are four levels of protein structure. These four structures are the primary structure, secondary structure, tertiary structure, and quaternary structure.
Primary Structure: The primary structure of a protein is the sequence of amino acids that characterizes a specific protein. The amino acids are joined together by dehydration synthesis. The bonds are commonly referred to as peptide bonds. There are about 20 amino acids. The sequence of these amino acids in a polypeptide is what determines its function. Of these amino acids some are acidic, some are basic, some are polar, and some are non polar.
Secondary Structure:The secondary structure occurs when amino acids interact with one another. They bend/twist and form hydrogen bonds with one another. Certain secondary structure have distinctive shapes and have been named alpha-helix and beta-strands. Secondary structures are stabilized by the presence of hydrogen bonds. Tertiary Structure: The tertiary structure is the overall three-dimensional shape of a protein. As each secondary structure takes hold, the protein takes a globular shape. In an aqueous (polar) environment, the folding into a compact, globular structure would be to "hide" the hydrophobic amino acids by putting them in the interior, and exposing the hydrophilic heads to the exterior aqueous environment. In the tertiary structure, the R-groups are what stabilize the structure. Proteins can denature, or lose their structure and function. Proteins are function when folded, so when they are denatured, they become unfolded and inactive. Denaturation can be caused by an increase in heat, change in pH levels, and/or the addition of salt. Quaternary Structure: Quaternary structures occurs when two or more proteins join together. This forms a larger, more complex protein. Proteins exist all throughout our cells and bodies. Their many structures and functions keep us going and alive everyday.
Nucleic Acids
Nucleic acids are long polymers of nucleotide building blocks. The two types of nucleic acids are DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid). DNA stores our hereditary information, which includes all of the information for our cells to function properly. RNA is used in various forms to assemble proteins. Nucleotides are made up of a five-carbon sugar, a nitrogenous base, and three phosphate groups. In a DNA nucleotide, the 2' carbon only has Hydrogen (Hence the deoxy), while RNA has a hydroxyl (hydrogen and oxygen) at it's 2' carbon. A nucleoside only consists of the sugar and nitrogen base. A nucleoside with one phosphate group is referred to as nucleoside monophosphate. It is referred to as a nucleoside diphosphate and nucleoside triphosphate with 2 and 3 phosphates, respectively.
There are 4 nucleotides used to construct DNA and 4 nucleotides used to construct RNA. DNA consists of the nucleotides adenine (A), thymine (T), cytosine (C), and guanine (G). RNA consists of the nucleotides adenine (A), uracil (U), cytosine (C), and guanine (G). What varies in nucleotides is the nitrogenous base. The two categories of nucleotides are pyrimidines and purines. Pyrimidines only have one ring and purines have two rings.
The double-helical structure in DNA is caused by the formation of hydrogen bonds. Phosphodiester bonds are covalent bonds found specifically in nucleic acids. The phosphodiester bonds are what link the two, antiparallel strands together. One nucleotide is linked to the next nucleotide by dehydration synthesis. In DNA, A links with T, and C links with G. In RNA, A links with U, and C links with G. DNA has opposite ends. One end is 5' and the other is 3', based off of which sugar is on what end. As previously stated, DNA is antiparallel. This is because one strand runs in the 5' to 3' direction, while the other runs in the 3' to 5' direction. There are major differences between RNA and DNA. RNA is usually found in one strand rather than in a double-helix like DNA, and has a ribose sugar rather than a deoxyribose sugar. In RNA, uracil replaces thymine, which is found in DNA. Lastly, RNA is synthesized from a DNA template.
Helpful Hints!
Alright so this video is a song about DNA set to the tune of (You Drive Me) Crazy by Britney Spears. The only downside is you can't hear anyone singing, but the lyrics are there for you to follow. I guess it's like a karaoke thing... I wasn't going to include it as a helpful hint, but the lyrics actually fit into the song and make you memorize some DNA facts in fun, creative ways!
This video is extremely informative. The structure of DNA is explained in detail, yet is still understandable. The DNA is examined all the way down to atomic level, but it does not over-complicate the subject. If one had a few questions/uncertainties about DNA, or wanted a quick refresher, this would be a great video to watch!
Article
This article, talks about how there's increasing evidence showing that cancer cells. acquire "stem-like" epigenetic and signaling characteristics during the tumorigenic process. This includes global DNA hypo-methylation, gene-specific DNA hyper-methylation, and small RNA deregulation. In both stem cells and in differentiated cells, RNA has been shown to be an epigenentic regulator. Piwi-interacting RNAs (piRNAs), maintains genome integrity by epigenetically silencing transposons by DNA methylation. The human Piwi ortholog (a protein), Hiwi, has been found to be expressed in many human cancers. Unfortunately, there has not been much investigation about the role Piwi and piRNAs might play in contributing to the "stem-like" epigenetic state of a cancer.
This article explains the negative effects of a drug called Thalidomide. Thalidomide was an anti nausea drug given to pregnant women in the late 1950s and early 1960s to help deal with morning sickness. Unfortunately, Thalidomide caused the babies to develop a variety of horrible birth defects. Some of these birth defects included shortened arms and legs, ear deformities, and malformations in the digestive system. Luckily, the drug was pulled off of the market in 1961. Thalidomide has been brought back onto the market again to treat things like various cancers and leprosy.
How Thalidomide exactly works to cause all of these birth effects is still unknown. Scientists were able to establish that although the drug reaches all areas of the body via the bloodstream, one of its main targets is the brain. Thalidomide's second main targets are blood vessels. It appeared that the drug prevented proper limb growth by preventing angiogenesis, which is new blood vessel growth. Lastly Thalidomide reduces inflammation.
2.1 Atoms
Biology is the study of life. In order to truly understand biology, one must understand basic chemistry, which is the study of matter. This is because matter is anything that contains mass and shape. Life-forms contain mass and shape, and therefore are composed of matter. The smallest functional unit of matter is the atom. Atoms cannot be broken down into smaller substances by ordinary chemical or physical means. However, atoms are made up of subatomic particles. When two atoms bond together a molecule is formed.
Each specific type of atom is called an element. The subatomic particles that compose atoms are protons, neutrons, and electrons. Protons carry a positive charge, neutrons carry no charge, and electrons carry no charge. Protons and neutrons are found in the middle of the atom in the atomic nucleus. Electrons are found in orbitals around an atom's nucleus. Orbitals occupy energy shells or energy levels. Energy is the capacity to do work. Different energy shells may contain one or more orbitals. Most atoms have outer shells that are not filled. This outer shell is known as the valence shell.
Each element has a unique number of protons. This is what distinguishes one element from another. The number of protons an atom has is its atomic number. For example, carbon has 6 protons, and therefore its atomic number is 6. Atoms are quite small, but they still have mass. The atomic mass scale shows an atom's mass relative to the mass of other atoms. Atomic mass is measured in daltons or atomic mass units (amu). A mole of any substance contains the same number of particles as there are atoms in 12g of carbon. (I was going to include information about Avogadro's number but it confused me so...) Elements can exist in many forms. When the number of neutrons differ in an atom, it is called an isotope. Unstable isotopes are called radioisotopes. The mass of all living organisms is largely composed of oxygen, carbon, hydrogen, and nitrogen. These four elements make up about 95% of a living organism.
2.2 Chemical Bonds and Molecules
When two or more atoms bond together, a molecule is formed. A compound is a molecule of two or more elements. Electronegativity is the measure of an atoms ability to attract electrons in a bond with other atoms. One type of bond is a covalent bond. In a covalent bond, atoms share a pair of electrons. Covalent bonds are the strongest types of bonds. In a polar covalent bond, atoms with different electronegativities bond causing a difference in electric charge for the atoms. In a nonpolar covalent bond, atoms with similar electronegativities bond, causing no difference in charge for the atoms. Ionic bonds are the next strongest strongest bond. In ionic bonds, one or more atoms completely give up electrons to other atoms. A hydrogen bond is the weakest bond. In a hydrogen bond, a hydrogen atom from a polar molecule is attracted to an electronegative atom.
A free radical is a molecule containing an atom with a single, unpaired electron in its outer shell. When one or more substances are changed into other substance a chemical reaction has occurred. Reactants are what go into the chemical reaction and products are what are produced.
2.3 Properties of Water
Water is known as the universal solvent. A solute is a substance dissolved in a liquid and a solvent is the liquid the solutes dissolve into. When solutes dissolve in water, a solution is formed. Solutions containing water are known as aqueous solutions. Molecules that dissolve in water are said to be hydrophylic (like salt), while substances that do not dissolve in water are said to be be hydrophobic (like oil). Hydrophilic substances are polar, hydrophobic substances are nonpolar, and molecules containing both polar and nonpolar regions are known as amphipathic.
Water exists in three states. When water boils it goes into the gaseous state of water vapor. When water goes into water vapor at normal temperatures, it is known as evaporation. When water is in it's regular state it is a liquid. When water goes below the freezing point, it is becomes ice which is a solid.
Hydrolysis reactions is when long chains of molecules are broken apart by water molecules. Dehydration synthesis is when water is removed from separate chains of molecules and thus joins them together. Cohesion is the phenomenon of water molecules sticking together. Adhesion is the phenomenon of water molecules sticking to surfaces that are electrically neutral. Surface tension is the measure of the attraction between molecules at the surface of a liquid.
The H+ concentration of a solution is what determines its pH. Pure water has a neutral pH of 7. A solution with a pH lower than 7 is said to be acidic, and a solution with a pH higher than 7 is said to be alkaline or basic. A buffer is made up of a weak acid and its related base. Buffers help to to neutralize solutions.
Helpful Hints!
Now this video is kind of old school but it's still helpful! I found this video helpful because it starts out with a nice explanation and then shows experiments and other displays to put a visual to cohesion, adhesion, and surface tension. It also, makes a clear difference between cohesion and adhesion which I often confused for one another. Lastly, the video shows how cohesion, adhesion, and surface tension are all working together.
Alright now this video is a claymation about electronegativity! This would constitute as being sooo fetch! So I like this video because it tells you all of the different atoms before each scene starts so you know what you're looking at. It also gives different scenarios involving electronegativity. Lastly, the song in the background is nice and calming. One can enjoy it and still enjoy the video because it definitely somewhat relates to electronegativity. So basically, this claymation helps to electronegativity in simpler terms.
Article
In this article, the morphology of gelatin with three different substances was discussed. Tizanidine hydrochloride, Gatifloxacin and Fluconazole were entrapped and then released from gelatin nanoparticles. The particles were prepared by nanoprecipitation. Water and ethanol were used as a solvent and a nonsolvent, respectively. The 80% of loaded Tizanidine hydrochloride was released after about 15 hours. The 20% of loaded Gatifloxacin was released more rapidly than the loaded Tizanidine hydrochloride and generally sustained slow release during the remaining period of its release experiment. This study relates to chapter 2 because it is about soluts, solvents, and solutions.
Scientists have long believed that the moon was 4.6 billion years old. However, Lars Borg of the Lawrence Livermore National Lab says that the moon is actually 4.4 billion years old. That makes the moon 200 million years younger than we previously thought it was! Astronauts John Young and Charles Duke of Apollo 16 in April 1972 brought back the oldest piece of moon that we have. Based on the decay of chemical isotopes of the piece of the moon, that oldest piece of moon that scientists believe we have is 4.56 billion years old and two other Apollo samples have been dated at 4.47 billion years. Borg and his colleagues believe this is impossible. Borg feels that either the moon is younger than past studies suggest or everyone's been wrong about how the moon formed. The most common theory about how the moon formed is that the early solar system was so hot, with so many space rocks crashing into each other, that the moon had lots of molten rock which cooled once debris cleared. Other scientists, like Erik Asphaug of the University of California have their doubts about Borg's theory. NASA is staying agnostic on the matter.
This article shows how isotopes are always being used in science. This use of isotopes was to determine how old the piece of moon was. In the article Borg does not dispute the age of the rocks that were tested by isotopes. He uses the age given and his knowledge of the solar system to say that either the moon is younger than we think or that it did not form in the way we believe it did. This article shows how the thoughts and beliefs in science are always changing and how the same method, like dating using isotopes can be used to prove or disprove a belief.
