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Unit 3 - Life Chemistry and Energy

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Nick Budziszewski

on 22 October 2015

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Transcript of Unit 3 - Life Chemistry and Energy

Proteins are made of amino acids, which consist of an amino functional group (-NH2) as well as a carboxylic acid group (-COOH).






Amino acids all have what is known as an R group, or side chain. These parts of the amino acid give them many different properties (acidic, basic, polar, nonpolar, charged, ring shapes, etc.)

Why are these R groups important in organisms? How could they affect protein structure?
Unit 2 and 3 - Biochemistry
Lipids
Lipids are a macromlecules that are mostly made of carbons and hydrogens (hydrocarbons). Since they have many nonpolar covalent bonds, they are usually insoluble in water (hydrophobic).
Carbohydrates
Carbohydrates are a macromolecule with the general formula C (H O) - for example glucose, C (H O) , or C H O as we commonly write it.
The structure of chemicals affects their biological properties
In other words, how a molecule looks has a lot to do with how it works. Take chemical bonding, for example:
Nucleic Acids
So far, everything we have talked about has consisted mostly of carbon, hydrogen, and oxygen. Nucleic acids contain nitrogen and phosphorus as well. They are made up of monomers called
nucleotides
.
Proteins
Proteins display a huge range of structures and functions:
Can speed up reactions (enzymes)
Can serve as body defenders (i.e. antibodies)
Regulate processes in the body (i.e. hormones)
Receive signals from the outside environment
Storage of chemicals
Make up body structures and allow for movement (i.e. muscle)
Transportation (i.e. hemoglobin)
Regulate gene expression
- the structure of the outermost (valence) electron shells in an atom determine the bonding that can take place (covalent, ionic)
Even among similar types of bonds, structure is important.
The structure of molecules greatly influences how they interact with one another.
These functional groups give molecules many properties, and allow monomers to be linked together through
condensation
or broken apart through
hydrolysis
.

Condensation allows for several different types of biologically important macromolecules to be formed.
2
n
n
6
6
2
6
12
6
Carbohydrate - hydrates of carbon, or carbon mixed with water. On a molecular scale, however, the carbons aren't actually bound with water molecules -- most of the carbons are actually bound with hydrogen by itself (-H) or with a hydroxyl group (-OH)
Monosaccharides - the building blocks of carbohydrates
Dehydration of monosaccharides yield complex di-, poly-, or oligosaccharides.
Carbohydrates - who cares?
Can be used as immediate energy
Can be used as energy transportation (broken down later)
Structure (think cellulose in plant cell walls)
Recognition/signaling molecules on membranes (oligosaccharides)
Many lipids are triglycerides, which can take the form of fats or oils (depending on whether they are saturated or unsaturated).
Triglycerides consist of a molecule of glycerol (three -OH groups) bound with three fatty acids (which each have a -COOH group).
The resulting molecules has lots of C-H bonds and C-C bonds, which are not polar.
Lipids - who cares?
Energy can be stored in C-C and C-H bonds (why is it harder to release the energy in a lipid rather than a carb?)
Make up a lot of the structure of membranes (phospholipids - amphipathic)
Insulation in animals
Both carbohydrates and lipids play important roles in organisms, but these molecules are not always available to use.

Fortunately, organisms can make these molecules (or break them) when necessary, although they must obey the
laws of thermodynamics
when doing so.
1st Law of Thermodynamics
- Energy is neither created nor destroyed
Energy is simply converted into different forms. The amount of energy before a reaction is the same as the of energy after a reaction
2nd Law of Thermodynamics
- Disorder (Entropy) tends to increase in a system over time
Just because the amount of energy does not decrease after a reaction does not mean that all of the energy left is useable.
This doesn't make any sense! Organisms are super organized! Look at all their cells and tissues and organs! How could you possibly say that disorder (entropy) is constantly increasing?!
Some reaction terms:

1)
Anabolic reactions
- "build up" reactions; require a source of energy to occur (also called
endergonic
or
endothermic
reactions)

2)
Catabolic reactions
- "break down" reactions; release energy as they occur (also called
exergonic
or
exothermic
reactions)

Many times these reactions are linked. The total of all the reactions happening at a given time in your body is your
metabolism
.
Carbohydrates and lipids both play an important role in the metabolism of organisms, but usually they are just the starting reactants or the end products of reactions.
In other words, something other than carbohydrates and lipids must be pulling the strings behind the metabolism of living things.

This looks like a job for...
NUCLEIC ACIDS and PROTEINS!
Nitrogen bases with a single six-carbon ring structure are known as pyrimidines. (adenine and guanine)

Nucleotides with a fused double-ring structure are known as purines. (thymine/uracil, cytosine)

The structure of these nitrogen bases allow them to bind in very specific ways (A-T/U, G-C). Yet another example of structure being intertwined with function.
Nucleotides consist of a
nitrogen base
, deoxyribose or ribose
sugar
(base + sugar = nucleoside), and a
phosphate

group
(nucleoside + phosphate = nucl
e
otide).
Nucleotides are connected to each other through (surprise!) a dehydration/condensation reaction. The phosphate group on the nucleotide being added (which is found on the fifth, or 5', carbon of the nucleotide) is linked to the hydroxyl group attached to the third, or 3', carbon of the existing nucleotide. Therefore, nucleic acids grow from phosphate group to hydroxyl group, or in the 5' to 3' direction.

HUH?
DNA vs RNA
What are some similarities? Differences?
n
Nucleic Acids - who cares?
Specify the specific amino acid sequence of proteins
Allow for transfer of genetic information
Allow us to analyze evolutionary relationships

Kind of boring for something so important, right?
Protein structure can be described in many different ways:
primary structure
secondary structure
tertiary structure
quaternary structure
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