BIOA01H3 Study Guide - Midterm Guide: Ionic Bonding, Chemical Polarity, Protein Structure

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Published on 14 Nov 2017
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How do we differentiate living from non-living?
Characteristics of living:
1.Complexity with precise spatial organization
2. Ability to respond to the environment (take cues from their environment and undergo major
changes in physiology and gene expression)
3. Reproduction
4. Evolve (genetics can change over time)
-Earth evolved in a highly reduced condition, living could have evolved from non-living but in
this world today, no living entity can evolve from non-living,
-Back then there was no free oxygen, therefore chemical synthesis was used to make biological
molecules
All living entities must follow rules of thermodynamics and biological systems must obey 2 laws
of thermodynamics:
First Law
-Energy can be neither created or destroyed
-It is transformed from one form to another
-Therefore, the total energy of the universe is constant
Second law
- within the universe degree of disorder increases, energy is required to create order
-Entropy is the amount of disorder
-Higher level of organization would appear to violate the second law but it is prevented by the
release of heat
ex: when we organize DNA into a double stranded molecule, it creates order which decreases
entropy and theoretically breaks the second law of thermodynamics. So, the system then
generates and releases heat which creates a disorder. A path requires a dissipation of heat.
Cells
-Cells vary in size, and shape and they are the simplest self-replicating entity that can exist as an
independent unit of life.
Classification
Major classification: bacteria and archaea bacteria (prokaryotes) and then there is eukaryotes
which are plants, animals, algae and fungi
There are more prokaryotes, much more complexity and diversity exist among them. They have
lived here much longer and will most likely live longer than us as they have the ability to
undergo major changes in evolution over time.
Question 1: Which one of the following is characteristic of all living organisms and all
nonliving material?
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A. the capacity to evolve
B. the ability to reproduce
C. complexity, with spatial organization of several levels
D. the ability to change in response to the environment
E. subject to the basic laws of chemistry and physics
The answer is E because everything living must obey the laws of thermodynamics
Atoms
•The atom is the fundamental unit of matter.
•Atoms can combine to form molecules linked by chemical bonds.
Water is essential for life. (living cells are mostly water, therefore reactions must be able to take
place in water)
•Carbon is the backbone of organic molecules.
•Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which
is built from simpler units. (made chemically before but now are made by biological systems and
enzymes)
•Life likely originated on Earth through a set of chemical reactions that gave rise to the
molecules of life.
-high abundance (oxygen, carbon, phosphorus, etc) in living systems
- Believe silicon can support some kind of life because they form similar bonds to carbon
Atoms can combine with one another to form molecules, held together by chemical bonds.
There are four types of chemical bonds:
a. Covalent e.g. gaseous hydrogen (H2) or oxygen (O2)
b. Polar covalent e.g. water
c. Hydrogen
d. Ionic
-most important chemical bonds for proteins to fold, are polar covalent, hydrogen and ionic
bonding because they are weaker than covalent so they can be easily broken (covalent bond form
the backbone). However, many of them together adds strength to the molecules within the bond
Ex: DNA strands are able to come apart because of hydrogen bonds, if they were held by
covalent bond they would not separate because they are much stronger.
Water
-Water is a polar molecule
What makes it so advantageous? - Water has a structure that allows it to have a partial negative
side due to oxygen and a partial positive side due to hydrogen. It has a V-like structure, this
allows water to disrupt ionic interactions as ionic interactions will carry negative or positive
charges (they would rather like to interact with water then themselves)
-the structure of water is critical for function
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Ionic Bonds
Ex: NaCl sodium and chloride are interacting. The sodium gives up an electron to be positively
charged, and the chloride accepts an electron to be negatively charged, it dissolves in water as
water is a good medium, the sodium will interact with the negative oxygen creating a solvent
ring and the chloride will interact with positive hydrogen
-Ionic bonds will break in the presence of water, therefore water has to be kept away from them
to function
Liquid water versus water in ice form
- Ice would float on liquid water, ice becomes more organized and more hydrogen bonds
form
Hydrogen bonds have a clear lattice structure in ice, however in liquid water the solution is
denser and has a less clear structure
-Part of waters role is to dissipate heat
-Water is able to resist temperature change; in order for its temperature to increase, hydrogen
bonds must first break.
-This property is important for living organisms: water resists temperature changes that would
result from the biochemical reactions taking place within them.
If ice was denser scenario: ice forms on the surface and if the lake froze from the bottom up to
the top, then nothing would survive as ice provides insulation for aquatic organisms and
regulates temperature
Carbon
-Carbon structures are really important, carbon molecules are needed to create a living system
-These molecules can take a lot of different forms. Simple structures like ethane
-It is the largest dry mass element in the human body (oxygen is second, hydrogen third and
nitrogen fourth)
The following are all dependent on carbon (chemical backbone for macromolecules) to build
these building blocks:
-Need C to build amino acids for proteins
-Need C to build nucleotides to make DNA and RNA
-Need C to build sugar to build complex carbohydrates
-Need C to build fatty acids to build Lipids
•Proteins: structural, enzymatic function, carrying out reactions, signaling
•Nucleic acids: DNA and RNA: genetic blueprints (DNA- hereditary, RNA-intermediate that
leads to synthesis of protein)
•Carbohydrates: storage (energy), for structures like cell wall (eukaryotes, fungi and algae) and
prokaryotes, and signaling (extra-cellular matrix), excellent source of energy
•Lipids: membranes, energy, signaling, important source of energy, long term storage
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Document Summary

1. complexity with precise spatial organization: ability to respond to the environment (take cues from their environment and undergo major changes in physiology and gene expression, reproduction, evolve (genetics can change over time) Earth evolved in a highly reduced condition, living could have evolved from non-living but in this world today, no living entity can evolve from non-living, Back then there was no free oxygen, therefore chemical synthesis was used to make biological molecules. All living entities must follow rules of thermodynamics and biological systems must obey 2 laws of thermodynamics: It is transformed from one form to another. Therefore, the total energy of the universe is constant. Within the universe degree of disorder increases, energy is required to create order. So, the system then generates and releases heat which creates a disorder. Cells vary in size, and shape and they are the simplest self-replicating entity that can exist as an independent unit of life.

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