Unit 1 Biochemistry

Energy & Atoms

Atoms

$Atoms$ - The smallest fundemental unit of matter

There are 120 different kinds of atoms ( $elements$ )
Biology is made up of 4 major elements, $CHON$ , ~10 minor, & ~30-50 trace elements

Energy

$Energy$ interacts with atoms in different ways.

Energy holds e- to the nucleus
When atoms absorb energy, e-’s are moved to higher energy levels
The movement of e-’s back to lower energy levels releases energy (As $EM radiation$ )

Atom bonds

Bonding is accomplished by electrons interacting between atoms (Due to $valence$ considerations)

2 major kinds of bonds hold atoms together:

$Ionic bonds$ - Transfer of e-’s from one atom to another, not many possible combinations.

$Covalent bonds$ - Sharing of e-’s. Funtionally infinite combinations. All important biological molecules are covalently bonded.

$Polarity$ - The unequal sharing of electrons in a covalent bond. Leads to unequal distribution of charge in molecule. Polar molecules are attarcted to other polar molecules.

$Hydrogen bonds$ - The strongest attractions between the most polar molecules. Common in biological systems (weakest bond of the bunch)

Bonds determine shape, shape is important because it is related to structure and function.

All chemical reactions result in the breaking and forming of bonds

In any reaction energy, mass, and charge are conserved

Compounds & Emergence

The properties of a compound can be very different from the properties of the elements that make them

$Emergence$ - Increasing levels of complexity in a system can demonstrate novel properties not seen in the levels below

Radioactivity

Atoms with unstable nuclei are $radioactive$
Radioactive atoms spontaneously emit high energy particles until stability is reached
Excess raditation is damaging to biological systems because high radiation kills cells
Radiation in biology is used as molecular labels

Water

Water’s unique properties

Water is one of the few substances that exists in all three phases at normal terrestrial conditions

Water’s unique properties are all due to the $polarity$ of water ( and its resulting $hydrogen bonds$ )

$Cohesion$ - sticking together (water wanting to be with water)

$Adhesion$ - sticking to other things (water sticking to glass)

The cohesiveness of water gives it a very high $surface tension$

$Transpiration$ - The movement of water through trees, very important

Water also has a very high $specific heat$

Specific heat- How much heat is absorbed/released before an increase/decrease in temperture

Water: 4.18 J/g C

Ethanol: 1.24 J/g C

Iron: 0.449 J/g C

Water as temp, $Buffer$

Ice floats because it is less dense then water

Water is known as the $universal solvent$ because of its ability to dissolve many things

Water dissasociates!

Water breaks apart easily because it is so polar.
This produces a Hydronium (H3O+) and hydroxide ion (-OH). In pure water the concentration of these ions are equal.
$Acids$ - donate protons (H3O+) > (-OH)
$Bases$ - Accept protons (H3O+) < (-OH)

$pH:$ a measure of acidity

The -log of the (H3O+)
In all (aq) solutions (H3O+) x (-OH) = 10E-14
You should be able to calculate pH/pOH if given the (H3O+) or (-OH) concentration
Biological systems can only live in a specific pH range

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Carbon

Biology is carbon based

Carbon’s unique properties

It’s abundant ( exists in large quantities )
It’s versatile
Carbon is $tetravalent,$ it makes 4 bonds to get stable which allows for almost infinite possibilities.

Isomers

$Isomers$ - Molecules with the same molecular formula, but different structures.

Any molecule more complex then propane has atleast one isomer
Isomerism is another example of an emergent property

Types of isomers

$Structural isomer$ - Same formula, different order

$Cis-trans$ - Same formula, different positioning around a double bond

$Enantiomers$ - Same formula, Mirror image, positioning around a central carbon

Functional groups

$Functional groups$ modify the properties of organic molecules

Hydroxyl

(-OH), may be written as (-HO)
Is polar
Found in some alcohols
Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars
Acidic
Hydrophilic

Carbonyl

(C=O)
Can be found in the carbon skeleton
Polar
Hydrophilic
basic

Carboxyl

(O=C-OH)
Acidic
Polar
Hydrophilic
Found in cells in the ionized form

Amino

Amines
(H-N-H)
Acts as a base (basic)
Hydrophilic
polar

Sulfhydryl

(-SH)
polar
Hydrophilic

Methyl

(H-C-H-H)
Usually found in DNA molecules
Found in male and female sex hormones, can affect their shape and function

Phosphate

Usually acidic
Charged
Can react with water to cause a release of energy

Macromolecules

Big! (Hence $macro$ )
Made of few, common atoms
Accomplishes all life functions
Put together in a special way
Can be incredibly comple

4 Main kinds

Carbohydrates
Lipids
Proteins
Nucleic acids

Except for lipids, macromolecules exist in two forms

$Monomer$ - The simplest unit
$Polymer$ - A large molecule made of repeating monomers

The movement between monomers and polymers is facilitated by adding/removing water

Dehydration synthesis

Builds more complex molecules from smaller ones by removing 2 H & 1 O, and replacing it with a bond
Water is produced!
Builds complexity ( $Anabolic$ )
Requires energy ( $endergonic$ )
Requires enzymes

Hydrolysis

Reverse of dehydration synthesis
-Lysis=breaking
Water is needed!
Reduces complexity ( $Catabolic$ )
Releases energy ( $Exergonic$ )
Enzymes are still required

Carbohydrates

$Sugar$ and $starches$
Made of C, H, and O (1:2:1 ratio in monomers)
Used for short term energy storage and structure
Monomers= $Monosaccharides$
Different sugar monomers have different #’s of carbon

Monosaccharides & Disaccharides

3 famous kinds of $monosaccharides$ , Typically shown as carbon rings

Glucose
Galactose
Fructose

Combine 2 by dehydration synthesis and you get a $dissacharide$

Glucose+Glucose= $Maltose$
Glucose+Fructose= $Sucrose$
Glucose+Galactose= $Lactose$