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Biochemistry - Coggle Diagram
Biochemistry
Enzymes and Energy
Glycolysis
During glycolysis which is the splitting of the glucose molecule into two molecules of pyruvate, four molecules of ATP are formed but two molecules of ATP are consumed.
Overall two molecules of ATP are produced in this process.
This process involves 3 enzymes hexokinase , phosphofructokinase and pyruvate kinase.
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Krebs Cycle
The pyruvic acid is converted into acetate by the enzyme PAD (pyruvic acid dehydrogenase). The acetate is assisted into the mitochondria by the action of coenzyme A.
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Electron Transport Chain
The electron transport chain also occurs within the mitochondria. In this process, electrons are passed from one molecule to another.
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This chain involves a series of multienzyme complexes. Some of the enzymes involved include ATP synthase complex and NADH dehydrogenase complex.
The mitochondria
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The enzyme complexes that conduct these reactions are found on the surface of the folds of the inner membrane.
The chloroplast
The reactions of photosynthesis takes place in thylakoids. A collection of Thylakoids is called a Granum
These are a type of specialized plastids that exist in plant cells . This type of plastid produces and stores a molecule known asa chlorophyll. Plastids produce and store other pigment molecules such as carotenes.
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water
as a solvent
One of the unique properties of water is the ability to act as a solvent. This property is due to the polarity of the water molecule.
Polarity depends on two factors, the first being the difference of electronegativity values of the atoms within the said molecule. The second factor is the molecular geometry of the said molecule.
Water would only dissolve polar substances, due to the hydrophilic/hydrophobic interactions. Polar molecules and ions are attracted to water molecules are referred to as hydrophilic. Non-polar molecules are not attracted to water and are referred to as hydrophobic
Hydrogen Bonding
Hydrogen bonding is one of the strongest types of intermolecular forces that can hold molecules together in a particular arrangement. Hydrogen bonding can only occur with molecules of which a hydrogen atom is bonded directly to a fluorine atom, an oxygen atom or a nitrogen atom.
Water can form intermolecular bonds with other polar molecules. The ability to form these interactions allow water to act as a solvent.
Surface Tension
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The hydrogen bonding in water is responsible for the phenomenon known as surface tension. Since the water molecules are incapable of forming hydrogen bonds with air molecules and in turn creates an imbalance. The water molecules on the surface creates a tension and makes the molecules at the surface more resistant to separation.
Thermal Energy
Water also have a high heat capacity due to its strong hydrogen bonds. The specific heat capacity can be defined as the amount of heat required to heat one gram of a substance by one degree.
In addition to the high specific heat capacity, water also has a rather high heat of vaporization value. Both of these characteristics allows water to absorb thermal energy.
This can allow living organisms to help maintain a constant body temperature due to the high specific heat capacity. In addition, this allows water to act as a cooling agent especially in the form of sweat which dissipates heat.
as a lubricant
Water can act as a lubricant by maintaining the optimum levels of moisture in certain areas of the body. Water helps protect the spinal cord and help cushion the joints in the human body.
Water also acts as a lubricant in the defecation process. When there is too little water within the large intestine, rectum and anus constipation can occur.
Cellular Transportation
Endomembrane System
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These organelles of this system all participate in the synthesis, modification and transportation of proteins and lipids.
After examining the various organelles involved in the endomembrane system, create a mind map and write down the organelles in the endomembrane system and state what roles they play within this system.
Cell membrane
Cell membranes exist as two layers of phospholipids.; each phospholipid has a hydrophilic, water-soluble end and a hydrophobic, non-water-soluble end. One of the water-soluble end faces the outer environment and the other water-soluble end faces the cytoplasm.
Glycoproteins and other proteins are embedded in the phospholipid bilayer; they impart a unique identity to the cell. Some proteins act as doors opening and closing the paths through the cell membranes and some proteins are involved in transport.
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Passive transport
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Diffusion is the movement of molecules from an area of higher concentration to an area of lower concentration. Molecular collisions are responsible for diffusion and it is not confined to gases but can occur with liquids as well. Oxygen and carbon dioxide move across the cell membrane by diffusion.
Osmosis is the diffusion of water molecules across a selectively permeable membrane. Osmosis is just the diffusion of water and will follow the concentration gradient which is the difference in the number of molecules or ions of a substance between adjoining regions. Without energy substances tend to diffuse from an area of higher concentrations to areas of lower concentration until equilibrium is achieved.
Equilibrium a condition in which acting influences are balanced, resulting in a stable environment.
The movement of water in and out of cells is important to life processes and cells are immersed in isotonic solutions – which are solutions in which the concentration of the solution outside the cell is equal to the concentration of the solution inside the cell.
One of the blood’s major function is to maintain an isotonic balance which is part of homeostasis. Homeostasis is the process in which a constant internal environment is maintained in spite of various changes in the internal and external environment..
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Acids, Bases and Buffers
Acids
Acids are substances that release hydrogen ions when they are dissolved in water. The Lowry-Bronsted theory describes acids as proton donors, since the hydrogen ion is basically a proton. The higher the concentration of hydrogen ions in a solution the lower the ph of the solution.
Acids can be regarded as weak or strong depending on their strength of ionization. A strong acid is fully ionized in water whilst a weak acid is only partially ionized in water.
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Bases
Like acids, bases can be classified as either strong or weak depending on the strength of ionization.
These are substances that dissolve in water to yield hydroxide (oh-) ions. The Bronsted-Lowry definition of a base is one that a hydrogen ion (H+) acceptor. Bases increase the concentration of the hydroxide ions in a solution and in turn results in an increase in ph.
A weak base is partially ionized in water and the ph range is from 8 - 10
A strong base is fully ionized in water and the ph range is from 11 – 14
Buffers
A buffer is a mixture of a conjugate acid-base pair that maintains a nearly constant pH when diluted or strong acid/base is added.
A buffer resists pH changes by reacting with H3O+ ions or OH- ions when they are added to the buffer solution. When a small amount of sodium hydroxide is added to an acetate buffer the following occurs:
Neutralization
A neutralization reaction is one in which where the hydronium ions (h3o+) reacts with hydroxide ions (oh-) to form water molecules. During the reaction between an acid and a base, in addition to the formation of water a salt is also formed.
However, the neutralization reaction itself is a reaction between the hydronium ions and the hydroxide ions to form water.
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Micromolecules
Carbohydrates
These are divided into 2 groups, sugars and polysaccharides.
Sugars are crystalline solids which can be subdivided into 2 groups. The first being monosaccharides which is made up of pentoses (C5H10O5) or hexoses (C6H12O6). The second is the disaccharides which have a formula of C11H22O11
Monosaccharides
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They contain an aldehyde and a ketone group respectively and are referred to as aldoses and ketoses. Both of these compounds are cyclic but when dissolved can exist as both as two cyclic and one noncyclic structures. This is known as mutarotation.
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Protein Structure
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The secondary structures are when the chains are organized into regular structures called alpha helices or beta pleated sheets. Which are held together by hydrogen bonds.
The tertiary structure is the description of the whole chain folds itself into a 3-dimensional shape. Held together mostly by, hydrogen bonding, London forces, ionic interactions and Sulfur bridges . The number of interactions in tertiary structures is fewer compared to the secondary structure. These bonds are weak and are influenced by environmental conditions.
Genes are patterns of nucleotides in DNA and this pattern is transcribed on the mRNA (messenger RNA)which leaves the nucleus of the cell and attaches itself to ribosomes in the cytoplasm. There another type of RNA called tRNA (transfer RNA)is brought into position with mRNA on the ribosome. As this takes place, each amino acid is brought into its correct position in the chain to build the protein. This is known as translation.
Nucleic Acids
ATP
Adenosine triphosphate (ATP) is an RNA nucleotide with an adenine base. Adenine + ribose = adenosine with two additional phosphate groups attached to its phosphate group.
The phosphate-to-phosphate bonds are unique and despite being weak their bonds are rich in energy. Cells store energy in this way in the form of chemical bond energy.
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