Transcription is the first step in gene expression and initiates the central dogma of molecular biology. Transcription is the process in which DNA sequences are transcribed to make RNA molecules over 3 steps; initiation, elongation, and termination. The process is initiated by RNA polymerase binding to a promotor; a specified sequence of DNA nucleotides. Once bound to a promotor RNA polymerase separates the two DNA strands. Once the two strands of DNA are separated elongation occurs, one strand acts as a template for RNA polymerase to build complimentary RNA nucleotides one base at a time. As RNA polymerase reads the DNA template, forming the RNA molecule, the chain grows from 5’ to 3’. RNA polymerase will continue transcribing until it reaches a specific group of nucleotides forming a terminator, this causes the entire process to end and is known as termination. The RNA molecule is then processed to make messenger RNA or mRNA, this molecule will go on to be translated into a protein.

References:

https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/stages-of-transcription

​In the early 1900’s the scientific field of molecular biology was a complete mystery to scientists, the name molecular biology wasn’t even coined until the year 1938 by Warren Weaver. Scientists at the time had no explanation for how genetic information dictated the formation of proteins in a biological system or even which biological molecule contained the genetic information. Francis Crick and James Watson were two scientists who were fixated on answering these questions. By the year 1953, they discovered that genetic information was encoded by DNA in a double helical structure. Shortly after, in 1957 they presented the relationship between DNA, RNA, and proteins called “the central dogma of molecular biology”. This explained how genetic information in the form of nucleotide sequences in DNA are transcribed into RNA to be later be translated into functional proteins. This discovery was a major breakthrough in molecular biology and allowed the field to progress heavily.

References:

http://sandwalk.blogspot.com/2007/01/central-dogma-of-molecular-biology.html

The plasma membrane encasing cells is selectively permeable, it controls which substances enter and exit the cell through many processes. These processes can be active or passive requiring a “fuel” such as ATP or can occur without any assistance. One means of transporting molecules across the membrane is by using the electrochemical gradients formed by the plasma membrane. An electrochemical gradient is formed when the charge and chemical concentration is different within and out of the cell. This allows the cell membrane to piggy back much needed molecules on ions such as Potassium or Sodium into and out of the cell. Using this gradient is a passive process which means no energy is required but if a molecule wants to move against the gradient energy is required. In this active process, ATP is consumed to move the molecules against the gradient. The electrochemical gradients allow cells to regulate the transport of molecules efficiently and accurately, this is just one of the means of transport a cell membrane uses to maintain normal processes.

References:

https://www.boundless.com/biology/textbooks/boundless-biology-textbook/structure-and-function-of-plasma-membranes-5/active-transport-66/electrochemical-gradient-336-11473/

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

Leeza-Marie Williams

Membrane as a dynamic structure:

The general structure of all biological membranes consists of noncovalent bonds that hold lipid and protein molecules together. The dynamic structure of cell membranes enables molecules to move within the membrane. A cluster of lipid molecules packed together forms a lipid bilayer which functions as an impermeable barrier to water soluble or hydrophilic molecules. Protein molecules are responsible for most of the functions within the membrane. Because of protein molecules, specific molecules can travel across and catalyzing membrane associated reactions like ATP synthesis are mediated. Protein molecules also serve as a means of providing structure towards connecting the cytoskeleton through the lipid bilayer to the extracellular matrix or to an adjacent cell. Some protein molecules act as receptors in detecting and transducing chemical signals in the cell’s environment.

Function of membrane proteins:

              Each membrane contains a set of membrane proteins that enables the membrane to carry out specific activities. Proteins are bound to different locations such as the membrane surface or the domains of one or both sides of the membrane. Proteins that are bound to the extracellular membrane are involved in cell to cell signaling and interactions. Proteins that are bound within the membrane form channels and pores to allow for the movement of molecules across the membrane.

              There are two general categories of membrane proteins based on the behavior of membrane-protein interactions: integral (intrinsic) and peripheral (extrinsic). Through embedding in the phospholipid bilayer, integral proteins contain hydrophobic residues that interact with fatty acyl groups located within membrane phospholipids which allows the protein to bind to the membrane. Since most integral proteins take up most of the space within the phospholipid bilayer, they are called transmembrane proteins. These transmembrane proteins consist of membrane spanning domains called α helices or multiple β strands. Some integral proteins have covalently bonded fatty acids that are anchored to a portion of the membrane however the polypeptide chain does not enter the phospholipid bilayer.

              Peripheral membrane proteins which are also known as extrinsic proteins are indirectly bound to the membrane via interactions with lipid polar head groups or with integral membrane proteins. Therefore, extrinsic proteins do not interact with the hydrophobic core of the phospholipid bilayer. Peripheral membrane proteins located in the region where the cytosol and the plasma membrane meet contain the protein kinase C which plays a role in signal transduction by moving to and from the cytosol and the cytosolic face of the plasma membrane. Other proteins are found on the outer surface of the plasma membrane.

Phospholipid bilayers:

              Phospholipids are the most abundant type of lipids which consists of a hydrophilic, polar head group and two hydrophobic, fatty acid tails that vary in length from between 14 to 24 carbon atoms. One tail contains unsaturated or cis- bonds while the other tail is saturated. Double bonds create kinks in the tail which alters the length of the tail. Since phospholipids contain a polar and a nonpolar end, there are amphipathic. Because of their amphipathic structure, when placed into water, phospholipids spontaneously arrange themselves where the hydrophilic end faces the water and the hydrophobic end is tucked into the lipid bilayer in the shape of micelles or bilayers. Micelles occur when all of the fatty acid tails face one another and form a spherical shape while bilayers occur when all of the fatty acid tails face one another and form a raft-like shape.

The amphipathic and shape of the phospholipid as well as temperature determines the fluidity of a lipid bilayer. A shorter fatty acid chain length reduces the tendency of hydrocarbon tails which means the hydrocarbon to interact whereby the formation of kinks occurs due to cis- double bonds. Therefore, at lower temperatures the membrane remains fluid. Some organisms like bacteria and yeasts maintain their fatty acid structures when the temperature fluctuates. In reference to a decrease in temperature, these organisms increase the synthesis of cis-double bonds to avoid a decrease in bilayer fluidity. Since the lipid bilayer is not 100% fat, cholesterol also impacts the fluidity of the membrane by immobilizing regions of hydrocarbon chains that are closer to the hydrophilic end of the phospholipid. Therefore, an increase in cholesterol results in a decrease in fluidity of the phospholipid.

Passive transport:

              Passive transport is the most basic form of transporting molecules in and out of the cell by using a process called diffusion. Diffusion is the random movement of molecules across a membrane. Since passive transport does not require the expenditure of energy by the cell, substances diffuse from an area of high concentration to an area of low concentration across the membrane. Diffusion results in the net movement of molecules from one region to the other in presence of a concentration gradient. Small molecules like oxygen and carbon dioxide move easily across the plasma membrane through the process of diffusion. Hydrophobic substances such as triacylglycerols do not encounter problems when trying to diffuse in and out of a membrane. However, some hydrophilic molecules cannot move passively from regions of higher concentration to regions of lower concentration. Therefore, these molecules must protein transporters through the process of facilitated diffusion. The difference between facilitated diffusion and simple diffusion is that diffusion only uses the lipid bilayer to move molecules while facilitated diffusion uses a membrane transporter and bypasses the lipid bilayer.

              There are two types of membrane transporters: a channel and a carrier. Channel membrane transporters allow molecules of a specific shape and charge to pass through an opening similar to a tunnel. Gated membrane channels require a chemical or an electrical signal in order to respond and allow molecules in and out of the membrane. Carrier membrane transporters bind to specific molecules and then transports them across the membrane. When molecules bind to the carrier membrane, a conformational change occurs in the membrane protein whereby it is determined if a molecule can be transported across the lipid bilayer. One membrane carrier is open to movement of molecules on one side of the cell and the other membrane carrier located on the opposite side performs a similar function.

              Water molecules also are allowed to pass through by using simple diffusion the lipid bilayer because of their small size and because of aquaporins which are protein channels specifically geared towards transporting water molecules through facilitated diffusion. Solvents like water that move across a selectively permeable membrane from an area of higher water concentration to an area of lower water concentration do so through the process of osmosis. Movement of water occurs due to a force such as gravity or pressure on a cell wall.

Active transport:

              In instances where molecules cannot diffuse through the membrane from regions of low concentration to regions of high concentration, the cell must expend energy in the form of ATP in order to move these molecules through the process called active transport. Naturally, glucose moves from inside of the cell to outside of the cell, therefore the cell must use active transport in order to bring in more glucose molecules from outside of the membrane. Substances are transported in and out of the cell using proteins that are embedded in the cell membrane act as pumps in moving substances against the concentration gradient. For example, as in the case of the sodium-potassium pump, the sodium concentration inside of the cell is lower than outside of the cell, however, the potassium concentration inside of the cell is higher than outside of the cell. Both sodium and potassium must use primary active transport in order to move against the concentration gradient. Primary active transport directly uses a source of chemical energy to move molecules against the concentration gradient. Sodium is pumped out of the cell while potassium is pumped into the cell. Since the protein that is used to move sodium and potassium in opposite directions, the protein transporter is referred to as an antiporter. Likewise, protein transporters that move two molecules in the same direction are called symporters or co transporters.

              Through the process of secondary active transport, an electrochemical gradient is used to move molecules against the concentration gradient without the use of ATP, a chemical source of energy. The electrochemical gradient is formed when there is an increase in the concentration of small ions on one side of the membrane. The build up of potential energy can be used to move molecules across the membrane against the concentration gradient. When protons are moved across the membrane, a difference in charge occurs which causes the formation of an electrical gradient. The protons move from regions of common positive charge to regions of opposite or negative charge. An electrochemical gradient, as its name suggests, forms when a gradient has both charged and chemical aspects.

              To summarize, the difference between primary active transport and secondary active transport is that primary active transport uses chemical energy of ATP to move molecules while secondary active transport uses the build up of potential energy in order to power an electrochemical gradient that enables for the movement of molecules.

Bulk transport:

              When macromolecules like proteins or polysaccharides are moved across the plasma membrane in a process called bulk transport occurs. Bulk transportation has two forms, that both require the expenditure of ATP: exocytosis and endocytosis. During exocytosis, secretory vesicles formed by the Golgi apparatus are used to excrete molecules out of the cell by fusing to the unneeded molecules and transporting them to the plasma membrane. Once at the plasma membrane, the molecules are released into the extracellular space. Endocytosis is the process in which molecules outside of the cell are encapsulated by vesicle made out of a plasma membrane that folds inwards. Using specialized proteins, the pocket then pulls apart from the membrane and forms a vesicle in the cell.

The three types of endocytosis are as followed: phagocytosis, pinocytosis, and receptor-mediated endocytosis. Nicknamed “cellular eating,” phagocytosis involves having the cell membrane pocket the macromolecule to form a phagosome, a food vacuole. Pinocytosis is nicknamed “cellular drinking” because the cell plasma membrane engulfs small amounts of extracellular fluid. Receptor-mediated endocytosis occurs when receptors proteins located on the cell’s surface cluster in coated pits which are regions of the plasma membrane capture specific target molecules that otherwise would not be captured via phagocytosis nor pinocytosis.

Works Cited:

Active transport. (n.d.). Retrieved April 10, 2017, from

https://www.khanacademy.org/science/biology/membranes-and-transport/active-transport/a/active-transport

Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland

Science; 2002. Chapter 10, Membrane Structure. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21055/

Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland

Science; 2002. The Lipid Bilayer. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26871/

Bulk transport. (n.d.). Retrieved April 10, 2017, from

https://www.khanacademy.org/science/biology/membranes-and-transport/bulk-transport/a/bulk-transport

Diffusion and passive transport. (n.d.). Retrieved April 10, 2017, from

https://www.khanacademy.org/science/biology/membranes-and-transport/passive-transport/a/diffusion-and-passive-transport

Endocytosis and Exocytosis. (n.d.). Retrieved April 10, 2017, from

https://www.wyzant.com/resources/lessons/science/biology/endocytosis-and-exocytosis

Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000.

Section 3.4, Membrane Proteins. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21570/

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