BIO1011 Lecture Notes - Hydrogen Atom, Hydrogen Bond, Systems Biology
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Lecture 1 - Chemical Elements and Chemical Bonds
Learning outcomes
● Understand hierarchy of structural and functional levels in biology
● Understand the properties associated with life
● Understand the concept of scale in biological systems - from organelle to cell
to tissue to organ
● Distinguish between different forms of bonding
● Understand the structure and geometry of a water molecule
● Explain the relationship between the polar nature of water and its ability to
form hydrogen bonds
Hierarchy
Reductionism → systems biology
Simple → complex, however, it depends on what level you’re looking at it from
Characteristics of living organisms
● Reproduction
● Nutrition of themselves
● Respiration
● Homeostasis
● Movement
● Dna rna proteins
● Carbon-based
● Metabolism
● Growth
What organisms are made of
Major constituents of living matter
-92 natural, 23 in living matter
● Elements in organisms
○ Major: hydrogen, oxygen, carbon, nitrogen
○ Minor: phosphorus, sulphur, calcium, sodium, potassium
○ Trace: manganese, iron, cobalt, copper, zinc
Hydrogen atom
● Nucleus with 1 proton with +ve chage and one electron with -ve charge
● If electron is lost, becomes +ve charged
● When the outer orbit is full (the shell) the atom is most stable → so as the
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electron number increases, the stability increases
Why hydrogen, carbon, nitrogen and oxygen
● Can form covalent bonds
○ With themselves, each other and other elements
○ Covalent bonds are strong bonds
○ Occurs by atoms sharing electrons with one another
● The lightest elements
○ The lighter the element, the stronger the covalent bonds are (the bonds
are shorter, making them stronger)
Covalent bonds
● Not easily broken without special catalysts
○ (eg. enzymes)
Hydrogen bonds
● They are not a bond, more of a weak electrostatic attraction
● Oxygen atoms are highly electronegative creating polarity
● Can break and reform more easily
● Can form between water molecules and other groups of chemicals
● Important in
○ Determining the shape of macromolecules
○ Surface tension
○ Capillary action (sucking water up into the organism from a source)
Other ‘weak’ bonds
● Ionic bonds
● Hydrogen bonds
● van der Waals interactions
● Hydrophobic interactions
● Disulfide bonds
Carbon atom
● Autotrophs
○ Self feeder using inorganic carbon as its source of carbon
○ Eg plants
● Heterotrophs
○ Other feeders using organic compounds as its source of carbon
○ Eg animals (also some fungi and other organisms)
● Carbon atoms accept/donate 4 electrons to complete an outer shell
○ Each carbon atom can covalently link with up to 4 other atoms
○ This gives the wide variety of 3D structures
Carbon vs. silicon
● Carbon
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Document Summary
Lecture 1 - chemical elements and chemical bonds. Understand hierarchy of structural and functional levels in biology. Understand the concept of scale in biological systems - from organelle to cell. Understand the structure and geometry of a water molecule. Explain the relationship between the polar nature of water and its ability to to tissue to organ form hydrogen bonds. Simple complex, however, it depends on what level you"re looking at it from. Nucleus with 1 proton with +ve chage and one electron with -ve charge. When the outer orbit is full (the shell) the atom is most stable so as the. If electron is lost, becomes +ve charged electron number increases, the stability increases. With themselves, each other and other elements. Occurs by atoms sharing electrons with one another. The lighter the element, the stronger the covalent bonds are (the bonds are shorter, making them stronger) Not easily broken without special catalysts (eg. enzymes)