Oxidative Phosphorylation

Oxidative Phosphorylation is a process where energy is sustained throughout a series of protein complexes that occurs in the inner-membrane of the mitochondria which ends up making ATP. This process is broken down into two parts, oxidation of NADH and FADH2 and Phosphorylation. In the first step, both NADH and FADH3 both experience the process of losing electrons through oxidation. Both NADH and FADH3 will transfer their high energy molecules into two different protein complexes (Protein Complex I and Protein Complex II). The Oxidation of NADH results to a pumping of protons through Protein Complex I. The electrons that were received by Protein Complex I are then given to an electron-carrier called Ubiquinone (Q). On the other hand, FADH3 goes through a similar process that NADH goes through when these two high energy molecules goes through with oxidation. Afterwards, an electrochemical gradient has been created, meaning both sides are different in electrical charge. The protons on the outside of mitochondrial membrane will then push through the ATP synthease. This movement of protons causes ATP synthase to spin, and bind ADP and Pi, producing ATP.

PCR

Polymerase Chain Reaction (PCR) is a laboratory technique used to make millions of copies of a specific region of DNA. This technique can be used for research on a specific gene that may hold a recessive trait or finding the genetic marker in the forensic science field during a crime investigation. Typically, the goal of PCR is to make enough of the target DNA region that it can be analyzed or used in some other way. For instance, DNA amplified by PCR may be sent for sequencing, visualized by gel electrophoresis, or cloned into a plasmid for further experiments. PCR is used in many areas of biology and medicine, including molecular biology research, medical diagnostics, and even some branches of ecology.

Control of Cell Cycle

The Cell Cylce control cycle works just like the control system on a washing machine, and as the cell goes through with DNA replication, mitosis and etc, the process is controlled by a system. There are four stages that the cell cycle is controlled by which are G1, G2, S, and M phase. The control system is effected by either internal or external factors. At each check point, the cell cycle will stop and then proceed to the next cycle when there is a given signal to proceed.

References:

https://www.khanacademy.org/test-prep/mcat/biomolecules/krebs-citric-acid-cycle-and-oxidative-phosphorylation/a/oxidative-phosphorylation-the-major-energy-provider-of-the-cell

https://www.khanacademy.org/science/biology/biotech-dna-technology/dna-sequencing-pcr-electrophoresis/a/polymerase-chain-reaction-pcr

https://www.ncbi.nlm.nih.gov/books/NBK26824/

Cellular Energetics

In photosynthesis, energy enters as a form of light which will then be converted into chemical energy, and carbon dioxide and water are used to store the energy in the form of carbohydrates. The carbohydrate is then taken apart in respiration and the chemical energy is transferred to a different compound called ATP (provides the organelles to do work). In chemosynthesis, energy enters the system in the form of inorganic compounds which have stored energy. The energy is transferred to the bonds of a carbohydrate, meaning that the remaining reactions are the same as a photosynthetic autotroph. On the other hand, heterotrophs take in biochemical energy produced by other organisms, because they can’t use other energy sources.

Electron Transport Chain

The electron transport chain is the final component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Electron transport is a series of redox reactions that resemble a relay race. Electrons are passed rapidly from one component to the next to the endpoint of the chain, where the electrons reduce molecular oxygen, producing water. This requirement for oxygen in the final stages of the chain can be seen in the overall equation for cellular respiration, which requires both glucose and oxygen.

A complex is a structure consisting of a central atom, molecule, or protein weakly connected to surrounding atoms, molecules, or proteins. The electron transport chain is an aggregation of four of these complexes, together with associated mobile electron carriers. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes.

Light Reactions of Photosynthesis

Chloroplast in plants use light energy to convert into sugars that can be used for the cell, which is where photosynthesis occurs. The chloroplast contains an electron transport which contains four threshold that the light photons will go through. The four thresholds are Photosystem II, Cytochrome B6F Complex, Photosystem I, and ATP Synthase. Throughout these four thresholds, a light photon will enter into a chlorophyll molecule in Photosystem II and the resonance energy will move around neighboring chlorophyll molecules that surrounds the reaction center which is embedded in Photosystem II. Two electrons will be released from the reaction center and then transported into Plastoquinone QB which will then be transport over to the Cytochrome B6F Complex. The two electrons will then go through Photosystem I and ATP Synthase in order to create ATP from ADP. Hence, the light reactions of photosynthesis is the transferring of electrons from one threshold into another which will then convert light energy into chemical energy.

Calvin Cycle

The Calvin Cycle is divided into three main stages: carbon fixation, reduction, and regeneration. Carbon Fixation is where organisms convert inorganic mater into organic mater. The cycle starts off with CO2, start subscript, 2, end subscript molecule combines with a five-carbon acceptor  called ribulose-1,5-bisphosphate (RuBP). This step makes a six-carbon compound that divides into two molecules of a three-carbon compound, 3-phosphoglyceric acid (3-PGA). This reaction is catalyzed by the enzyme RuBP carboxylase/oxygenase, or rubisco. Reduction, the second stage, ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3-phosphate (G3P). This stage is considered a reduction because NADPH donates electrons to a three-carbon intermediate to make G3P. In the regeneration process of the starting molecule, a few G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor.

References:

http://www2.sluh.org/bioweb/apbio/apclassoutlines/ol_cellular_energetics.htm

https://www.khanacademy.org/science/biology/photosynthesis-in-plants/the-calvin-cycle-reactions/a/calvin-cycle

https://www.boundless.com/biology/textbooks/boundless-biology-textbook/cellular-respiration-7/oxidative-phosphorylation-76/electron-transport-chain-362-11588/

Darwin’s natural selection is a theory where environmental factors play a larger role for each generation of a species that has started off with a plethora of heredital variation. By the time Darwinism was booming in the late 19th century, Mendel had further investigated these variations of heredity and had already gave solutions for Darwin on his idea on natural selection. As a result some of Mendel’s variations on heredity have refuted and/or supported the idea of natural selection. Darwin at the time had believed in blending inheritance which was a contradictory theory against natural selection which was a huge issue by the early 19th century. Some of Darwin’s contemporaries needed answers to this phenomenon. The problem with blending inheritance is that rare variants, such as black bunnies will have no opportunity to increase in rate of production even if they survive and reproduce more compared to white bunnies. The black bunnies will gradually disappear over time. By the mid 19th century, Mendel had found the solution to the issue, it is not traits that are transmitted by inheritance, instead it is genes that are transmitted.

References:

Mendel, Darwin, and Evolution. (n.d.) Retrieved April 12, 2017 from:

http://www.scientus.org/Mendel-Darwin.html

Not all genetic traits abide strictly by the laws discovered by Mendel, instead some variations from Mendelian genetics have branched out into four categories. These four types of variation are incomplete dominance, codominance, polygenic inheritance, and sex linked traits/sex influenced. Incomplete dominance is a condition when during the heterozygous condition, the dominant allele does not completely overpower the recessive allele. As a result, will give a blending of the traits. For example, a white bunny and a black bunny produces a gray bunny. Codominance is a condition when during the heterozygous condition, the dominant allele does not completely overpower the recessive allele so both traits are seen at the same time. For instance, a white bunny and a black bunny produce a bunny with both white and black patches. Polygenic Inheritance is when many genes interact together to produce one trait that contains many phenotypes. For example, hair color is controlled by three sets of genes all working together to create various hair color and same the same concept goes for skin as well. Sex linked/sex influenced traits are controlled by a gene located only on the X chromosome. For example, colorblindness is a recessive trait that occur to more males than female because males contain one less X chromosome compared to that of females.

These variations of mendelian genetics are fundamental for everyday lives such as for breeding purposes, personalized medication research, along with enhancing genetic information for curing cancer or viral infections.

References:

www.greensburgsalem.org/cms/lib4/…/108/Variations_to_Mendelian_Genetics.ppt

Evolution is the process where modern organisms have originated from ancient ancestors. Evolution is responsible for both the remarkable similarities we see across all life and the amazing diversity of that life, but how does this all work? Fundamental to the process is genetic variation where selective forces can act in order for evolution to occur. This section examines the mechanisms of evolution, and there are seven factors mechanisms that play into evolution. The first is descent and the genetic differences that are heritable and passed on to the following generation. The second is mutation, migration, genetic drift and natural selection as mechanisms of change. The third is the importance of genetic variation. The fourth is the random nature of genetic drift and the effects of the reduction within genetic variation. The fifth is how variation, differential reproduction, and heredity result in evolution by natural selection. Lastly, is the difference in species can effect each other’s evolution through coevolution (where two or more species can effect each other’s evolution).

References:

Mechanisms: the process of evolution. (n.d.) Retrieved from April 12, 2017 from:

http://evolution.berkeley.edu/evolibrary/article/evo_14

Natural selection is one of the basic mechanisms of evolution, along with mutation, migration, and genetic drift. Darwin’s grand idea of evolution by natural selection is simple but often misunderstood. To find out how it works, imagine a population of beetles where some are brown and some are green which gives variation in traits. However, since the environment can’t support an infinite population growth, not all individuals get to produce for the next generation. Since green beetles are mistaken to look like plants, more herbivore predators have been feeding on green beetles more often than brown beetles. Meaning that green beetles will survive to produce less offspring compared to the brown beetles; hence, there is differential reproduction. As a result, the surviving brown beetles produce more brown beetle offspring because this trait has a genetic basis and there is heredity involved over time. After multitudes of generations of each offspring, the beetle population will consist of only brown beetles because this trait had more chances of survival in an area where more predators would feed off of more green beetles than brown. Therefore, the saying ‘survival of the fittest’ is best fit for heredity that has been effected/not effected by environmental factors over time.

References:

Natural Selection. (n.d) Retrieved From April 12, 2017 from:

http://evolution.berkeley.edu/evolibrary/article/evo_25

During the 1860’s, Austrian monk Gregor Mendel had introduced a new theory of inheritance based off of his experimental work with pea plants. At the time most of society believed that inheritance was due to a blending of parental “essences” such as mixing blue and yellow paint to create green paint. Mendel instead believed that heredity is the result of discrete units of inheritance, and every single unit (or gene) was independent in its actions in an individual’s genome.  According to this Mendelian concept, inheritance of a trait depends on the passing-on of these units.  For any given trait, an individual inherits one gene from each parent so that the individual has a pairing of two genes. We now understand the alternate forms of these units as ‘alleles’.  If the two alleles that form the pair for a trait are identical, then the individual is said to be homozygous and if the two genes are different, then the individual is heterozygous for the trait.

Reference:

Genetics Generation, 2015. Mendelian Genetics.

Mendelian Genetics

The term “Redox”, is an abbreviated term for reduction and oxidation reactions, where reduction is the gaining of electrons and oxidation is the losing of electrons within a reaction. Biological reactions such as cellular respiration and photosynthesis are the best examples of Redox reactions. For example, in cellular respiration, redox reactions occur when glucose is oxidized (losing electrons) to become carbon dioxide, and oxygen is reduced (gaining electrons) to become water.

In a Redox reaction, there are four aspects to observe; the oxidizing agent (gains e− during reaction and is therefore reduced during reaction), the reducing agent (loses e− during reaction and is therefore oxidized during reaction), oxidized form (form of molecule lacking (it’s all relative) an e−), and reduced form (form of the molecule having an additional (again, relative) e−).

There are three ways to represent a redox reaction; these are shown below with a representative biological redox reaction:

(1) Overall reaction:

acetaldehyde + NADH + H+ → ethanol + NAD+

(2) Electron-transfer diagram:

 Acetaldehyde          e-                NAD+

             ↓                     ←                     ↓

      ethanol                               NADH + H+

(3) Half-reactions

 Acetaldehyde + 2 H+ + 2e− → Ethanol

    +

                                         NADH → NAD+ + H+ + 2e– 

____________________________________________

 Acetaldehyde + NADH + H+ → Ethanol + NAD

In the reaction shown above:

NADH is oxidized to NAD+

acetaldehyde is reduced to ethanol

acetaldehyde is the oxidizing agent

NADH is the reducing agent

NADH and ethanol are the reduced forms

NAD+ and acetaldehyde are the oxidized forms

References:

https://ocw.mit.edu/courses/biology/7-014-introductory-biology-spring-2005/readings/l17_redox_handou.pdf

Picture: https://goo.gl/images/71eLjf

Gel electrophoresis is a technique used to cut and separate DNA fragments due to their size. This technique is vital for modern personalized medication, because this technique can also detect recessive traits of autosomal recessive diseases(genetic diseases). Gel electrophoresis has also been used to detect the identity of a person that carries a recessive trait such as colorblindness or having blue eyes.

So how does this work? DNA is a double helical staircase made up of nucleic acids, and phosphate groups are contained within the nucleic acids. Those phosphate groups are negatively charged and are attracted to positively charged poles. The gel box is a box that is negatively charged on the top portions of the box and more positively charged closer to the bottom of the box and there is a power source connected to both ends. Hence, the system creates an electrical circuit which creates a steady flow of the electrical current traveling from the negative pole,through the agarose gel (the surrounding gel that make up the gel box), and to the positive pole. In this system, there are small indention columns called “walls”, the walls function as a placeholder for the DNA samples. The DNA samples are converted into loading dye called bromophenol-blue. These samples are then injected into the walls with a micro pipette, then the power source is turned on in order to run the current of the system. After the DNA fragments have separated and traveled downwards, away from the negatively charged pole and toward the positively charged pole, the fragments are then observed under UV light with a max range from 300nm to 360nm.

So what is the result from the procedure? When the box is observed under UV light, each sample has been cut into small bands underneath each of the walls. The bands that are closer to the walls are considered to be the large-range bands since the phosphate group from the nucleic acid of that particular DNA sample was attracted to the negatively charged pole itself. The larger bands are considered to carry the dominant traits contained within the DNA. On the other hand, the bands that have traveled further toward the positively charged pole are called short-range bands, and these bands are considered to contain the recessive traits contained within the DNA. In conclusion, gel electrophoresis is vital for research of genetic identification for patients with genetic diseases.

The person who wrote this did this in Lab.

Reference:

https://drive.google.com/drive/folders/0B5yZh40dXqFzNEo2NThOLWhrMXM

Shaina Song

What is a Macromolecule?

A macromolecule is a molecule that consists of large biological polymers, and the polymers are made up of smaller molecular subunits called monomers. Their functions are to store energy and/or be used for structure. There are four main classes of macromolecules which are lipids, carbohydrates, proteins, and nucleic acids.

Carbohydrates

Carbohydrates are one of the major macromolecules that are essential for the building blocks of life. They are often called “sugars” and are found in essential everyday needs such as fruits, vitamins, antioxidants, minerals, and more. Carbohydrates, also called saccharides, are molecular compounds made from three elements: carbon, hydrogen and oxygen.  They can function as a source of energy for the body, building blocks for polysaccharides and components of other molecules such as DNA, RNA and ATP. There are three main types of carbohydrates which are Monosaccharides, Disaccharides, and Polysaccharides.

Monosaccharides, known as simple sugars, are the simplest carbohydrates and are also the building blocks from much larger carbohydrates. These simple sugars have a molecular formula (CH2O)n, where n can be 3,5 or 6. The number of carbons within a monosaccharide are classified as trioses (n=3), pentoses (n=5), and hexoses (n=6). If the monosaccharide contains an aldehyde it is called an aldoses. However, if the monosaccharide contains a ketone then it is called a ketoses.

Disaccharides are products of two monosaccharides that’s been reacted. Most sugars are found to be disaccharides rather than monosaccharides. There are three types of disaccharides which are sucrose, lactose, and maltose which were all formed from a specific monosaccharide. Disaccharides tend to be soluble in water, but they are too large to enter through the cell membrane by diffusion.

Polysaccharides are made up of monosaccharides that have been chained together and each building block structure is called a monomer. The properties of a polysaccharide molecule depend on its length, additional side chain units, folding of the chain, and whether the chain is straight or coiled.

Nucleic Acids

Nucleic acids are one of the four major macromolecules that are essential for the building blocks of life. These molecules are called information molecules because they are large molecules that can carry information in the sequence of nucleotides that make them up. This molecular information in is much like the information carried by the letter in an alphabet, but in the case of nucleic acids, the information is in chemical form. The nucleic acid, DNA (deoxyribonucleic acid), is the genetic material in all organisms. It is transmitted from parents to offspring, and it contains the information needed to specify amino acid sequence of all the proteins synthesized in an organism. The nucleic acid, RNA (ribonucleic acid), has multiple functions; it is a key player in protein synthesis and the regulation of gene expression.

Works Cited

“Background on Carbohydrates and Sugars” International Food Information Council Foundation, n.d.Web. 26 Feb. 2017. < http://www.foodinsight.org/Background_on_Carbohydrates_Sugars>

“Carbohydrates” Royal Society of Chemistry, n.d.Web.26 Feb.2017 < http://www.rsc.org/Education/Teachers/Resources/cfb/carbohydrates.htm>

“Macromolecules” Olemiss University, n.d.Web. 26 Feb. 2017 < http://www.olemiss.edu/courses/bisc102/macromol.html>

“Nucleic Acids Encode Genetic Information in Their Nucleotide Sequence” Biology How Life Works,n.d.Web.26 Feb.2017 < https://reg.macmillanhighered.com/Account/Unauthenticated?>