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IB Biology - Curriculum Notes 

2.1 Molecules to metabolism  

 ∑ - Understandings:



 ∑ - Molecular biology explains living processes in terms of the chemical substances involved.


Involves the explaining of biological processes from the structures of the molecules and how they interact with each other
There are many molecules important to living organisms including water, carbohydrates, lipids, proteins, and nucleic acids
Proteins are one of the most varied macromolecules, performing many cellular functions, including catalyzing metabolic reactions (enzymes)
The relationship between genes and proteins is important as well
Molecular biologists break down biochemical processes into their component parts (reductionism)
When they look at the sum of all these reactions as a whole, they can study the emergent properties of that system 



Applications and skills: β

β - Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

Video on how the synthesis of urea was discovered

https://cosmolearning.org/documentaries/100-greatest-discoveries-2004/4/ 



Urea is a component of urine which is produced when there is an excess of amino acids in the body; way to secrete nitrogen
A series of enzyme-catalyzed reactions produce urea in the liver, where it is transported by the blood to the kidney, where it is filtered out and excreted in the urine.
Urea can be produced artificially through different chemical reactions; however, the product is the same.
Urea is mainly used as a nitrogen source in fertilizers



Read the following article http://humantouchofchemistry.com/urea-and-the-beginnings-of-organic-chemistry.htm. In groups of 3-4 discuss the “Falsification of Vitalism”, with respect to the synthesis of artificial urea. After you have discussed this concept in small groups, come back together for a class discussion on your findings and opinions.

∑ - Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.



Carbon has a few unique bonding properties - the most important of which is its ability to form long chains of carbon. No other element can bond as carbon does.
The reason carbon can do this is that carbon-carbon bonds are extremely strong.  This allows carbon to make up many of the basic building blocks of life (fats, sugars, etc). 
Since carbon-carbon bonds are strong and stable, carbon can form an almost infinite number of compounds
In fact, there are more known carbon-containing compounds than all the compounds of the other chemical elements combined except those of hydrogen (because almost all organic compounds contain hydrogen too).
Carbon can also form rings eg. glucose
The simplest form of an organic molecule is the hydrocarbon—a large family of organic molecules that are composed of hydrogen atoms bonded to a chain of carbon atoms.  Eg. Methane
All bonding in hydrocarbons is covalent
Covalent Bonds are chemical bonds formed by the sharing of a pair of electrons between atoms. The nuclei of two different atoms are attracting the same electrons.
Carbon can form single, double and triple bonds



 
 









































Carbon has 4 valance electrons in its outer shell.

 
∑ - Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates


Carbohydrates are composed of carbon, hydrogen, and oxygen
The general formula for carbohydrates is (CH2O)n.
Many carbohydrates are used for energy or structural purposes



Lipids


Lipids are compounds that are insoluble in water but soluble in nonpolar solvents.
Some lipids function in long-term energy storage. Animal fat is a lipid that has six times more energy per gram than carbohydrates.
Lipids are also an important component of cell membranes.
Some examples of lipids are triglycerides, steroids, waxes, and phospholipids
Animal fats (saturated) are solid at room temperature and plant fats (unsaturated) are liquid at room temperature



Proteins


Proteins are composed of one or more chains of amino acids
All proteins are composed of carbon, hydrogen, oxygen, and nitrogen
Proteins are distinguished by their “R” groups. Some of these also contain sulphur






































                                          Generalized amino acid

 Nucleic Acids


Nucleic acids are composed of smaller units called nucleotides, which are linked together to form a larger molecule (nucleic acid).
Each nucleotide contains a base, a sugar, and a phosphate group. The sugar is deoxyribose (DNA) or ribose (RNA). The bases of DNA are adenine, guanine, cytosine, and thymine. Uracil substitutes for Thymine in RNA
They are made from carbon, hydrogen, oxygen, nitrogen and phosphorus



 
B - Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.

Amino Acid



Composed of an amine (NH2) group, a carboxyl (COOH) group, and an R group.
20 amino acids exist that compose all proteins
Each amino acid differs because the R groups are different




Glucose



Is a reducing sugar that contains C6H12O6
Most commonly found in a ringed structure and is the main product formed by photosynthesis
Energy molecule used in aerobic respiration
A monomer of starch, glycogen, and cellulose




Ribose



Pentose (5 carbon) sugar of RNA and RUBP (Calvin cycle)
C5H10O5
Differs from Deoxyribose (sugar in DNA) because it has an extra –OH group on the 2nd carbon of the ring




Fatty Acids



The main component of triglycerides and phospholipids
Fatty acids are non-polar and therefore hydrophobic
Chains consist of covalently bonded carbon with hydrogen
Saturated FA’s are all single bonds and are therefore saturated with hydrogen.
Unsaturated FA’s contain a double bond or double bonds.



          Saturated Fatty Acid                                          Unsaturated Fatty Acid 


 

 




















































£ - Skill: Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.



The generalized formula for carbohydrates is CH2O. All carbohydrate contain C, H, and O
Proteins also contain C, H, O but they all have N. Some proteins also contain S in their R-groups
Lipids contain C, H, and O as well, but in different ratios and much less O then carbohydrates. 



 ∑ - Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.



Metabolism is the set of life-sustaining chemical reactions within the cells of living organisms.
These reactions are catalyzed by enzymes and allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
Many of these reactions occur in the cytoplasm, but some are extracellular including digestion and the transport of substances into and between different cells
The word metabolism can refer to the sum of all chemical reactions that occur in living organisms



∑ - Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions. 



Metabolism is divided into two components; anabolism (building large molecules from smaller ones) and catabolism (breaking down of large molecules into their component parts)
Anabolic reactions require energy as you are building large molecules from small ones (takes energy to build things)
Some anabolic processes are protein synthesis, DNA synthesis and replication, photosynthesis, and building complex carbohydrates, such as cellulose, starch,   and glycogen
If you can’t remember which one is which, think anabolic steroids are used to build muscles in athletes and bodybuilders and catapults are used to break down walls in wars 





∑ - Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.



Catabolism is a reaction that breaks down larger molecules into smaller ones or their component parts
Catabolic reactions release energy (sometimes captured in the form of ATP)
Some examples of catabolic reactions are digestion of food, cellular respiration, and break down of carbon compounds by decomposers
Think of "catapults" used to break down enemy walls during wars



 **Note these reactions are condensation and hydrolysis which are outlined **



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