Unit 1: Bio Chemistry and Macromolecules

Slogan: Structure determines Function

Pre Unit 1: Statistics

Null hypothesis- States that there is no difference between groups or no relationship between variables

Positive Control Group- Experiment with definite results from the variable

• used to confirm the system is working correctly

Negative Control Group- Experiment where no response to the variable occurs

• used to check false positive

Independent Variable- The part of the experiment you change

• Always on the x-axis

Dependent Variable- The part of the experiment that changes as a result of manipulation

• Found on the y-axis

Standard Deviation- A measure of how each value in a data set varies of deviates from the mean

• 68% of data will be within 1 standard deviation

• 95% of data will be within 2 standard deviations

• 99% of data will be within 3 standard deviation

• Formula: SD : $\sqrt{\frac{\sum\left(x-x̄\right)^2}{n-1}}$

Standard error- A statistical measure of how far the sample average of the data is likely to be from the true population mean

• Standard error bars- lines that represent the variability in the data

  • If they overlap, the data is NOT significant

Unit 1

Cohesion (Company)- the same molecules interact

• Water + water

Adhesion (Alternate)- different molecules come together

• Water + Penny

What property of water has to do with heat capacity?

• Hydrogen bonding

Functional Groups

Group	Alt. Name	Structure	Characteristics
Methyl	Alkyl		Found at the ends of hydrocarbon chains NONPOLAR / hydrophobic
Amino	Amines		Ionize NH3+ to create basic conditions (Accepts H+ ion) R group will determine Polarity
Phosphate	Organic Phosphate		POLAR Soluble in water Abundant in ATP and DNA Commonly found as Pi (inorganic) when removed from hydrocarbon chains
Hydroxyl	Alcohol		Typically names end in “-ol(s)“ POLAR Large quantities found in carbohydrates
Carbonyl	Aldehydes /ketones		POLAR Aldehydes have O=C<HR Ketones have O=C<RR All sugar molecules have at least one carbonyl Carbonyl needs a double bond to oxygen
Sulfhydryl	thiols		POLAR Important to the structure/function of proteins Forms disulfide bridges with other S
Carboxyl	Carboxylic Acids		Frequently Ionize to make weak acids (Donates H+ ion) POLAR Soluble in water Common in fatty acids and amino acids -COOH is carboxyl group

Macromolecules

CHONPS- Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur

Chemical reactions:

• Anabolic: using energy to build larger molecules from smaller molecules

  • dehydration synthesis takes out water to combine two monomers

• Catabolic: releases energy by breaking down larger molecules into smaller molecules

  • Hydrolysis breaks down monomers by “splitting“ water and “adding” it to the respective monomers

• Metabolism: the sum of all the chemical reactions in your body

Carbohydrates

ONLY CONTAIN: Carbon, Hydrogen, Oxygen

• has a 1:2:1 ratio of the above (C₁:H₂:O₁)

Monomers are called monosaccharides

• Monomers are single sugar units

• Examples↴

  • Glucose

  • Ribose

  • Galactose

  • Glyceraldehyde

Disaccharides are covalently bonded

• known as Glycosidic linkage (A dead giveaway that something is a carb.)

• A weak Glycosidic Bond: ⬠\_o/⬠\_o/⬠ [down:down:down / up:up:up]

• A strong Glycosidic Bond: ⬠\_o/⬠/^_o\⬠\_o/⬠ [Alternate- up:down:up ]

Lipids

ONLY CONTAIN: Carbon, Hydrogen, Oxygen

• Doesn’t have the 1:2:1 ratio for the above

• Forms long chains of hydrocarbons

Are always hydrophobic

Saturated fats: Carries all the possible hydrogen atoms a carbon chain can hold

• Solid at room temperature

• Maintains a straight hydrocarbon chain

• A diet in saturated fats can lead to cardiovascular disease

  • Butter and lard are saturated fats

Unsaturated fats: Does not have all the possible hydrogen atoms that the carbon chain could fit

• Liquid at room temperature

• Creates a bend in a hydrocarbon chain

• Good for a blood stream as it flows smoothly

  • Oils are an example of unsaturated fats

Phospholipids: molecules that contain a fatty acid attached to phosphate

• The head (Phosphate) is hydrophilic whilst the tail (the two lipid chains) is hydrophobic

Proteins

ONLY CONTAIN: Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur

• NEVER contains Phosphorus

Monomers of Proteins are called Amino acids made up of:

• Amino Group Terminus

• Central Carbon (known as the α carbon)

• Carboxyl Terminus

• Central R group

Peptide bonds hold amino acids together

• through dehydration synthesis, the -OH from the carboxyl and H from the amino group is removed to form HOH or H₂O

• This leads to the formation of two amino acids bonded together + H₂O

The R-group determines the chemical properties of the amino acids (there are 20)

• 9 are non-polar

  • None of them contain Oxygen

• 6 are polar

  • All contain Oxygen except Cysteine which contains an “SH“ instead

• 2 are acidic

  • Contain negatively charged atoms

• 3 are basic

  • Contain positively charged atoms

There are 4 levels of protein structure

• All structures contain primary, secondary, and tertiary

Primary- Covalent Peptide bonds

• forms the initial chains

Secondary- 3-Dimensional folding arrangement of the Primary structure into either coils (α) or pleats (β).

• Held together by hydrogen bonds

• Alpha (α) Helix

• Beta (β) pleated sheets

Tertiary- Formed as secondary structure is bent and folded into a more complex 3D arrangement

• The R-groups interactions play a role in how it bends/folds (hydrophobic/philic)

• Bonds can be: hydrogen bonds, ionic bonds, and disulfide bridges

  • A polypeptide folds into compact 3-D shape stabilized by interaction between r groups of amino acids

• These structures can be referred to as Protein Subunits

Quaternary- Composed of two or more protein subunits

• Not all proteins have a quaternary structure

• Quaternary structures are in a globular shape

  • Enzymes are a quaternary structure

Enzymes: Help speed up metabolic reactions

• Activation energy allows the reaction to take place faster using less energy, making it more convenient

• Most enzymes end in “-ase”

• Enzymes are reusable

Nucleic Acids

ONLY CONTAIN: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus

• NEVER contains sulfur

The monomers of nucleic acids are called nucleotides

• Made up of a nitrogen base, pentose sugar, and a phosphate

  • A nucleoside refers to the nitrogen base and pentose sugar alone

• Two types of Nucleotides ↴

Chargaff’s rule:

• Adenine will always pair with Thymine

• Guanine will always pair with Cytosine

Phosphodiester bonds: Connect nucleotides to each other on a single strand

• hydrogen bonds connect the nitrogen bases of the two strands in a DNA molecule

DNA

• stands for Deoxyribonucleic acid

• The Phosphate end is considered 5’ (five prime)

• the hydroxyl group on the pentose sugar is considered 3’ (three prime)

  • This orientation when they come together is known as antiparallel

RNA

• Stands for Ribonucleic acid

• Three types: mRNA, rRNA, tRNA

  • mRNA: a messenger between DNA and the ribosomes

  • rRNA: combines with proteins to form the large and small subunits of the ribosome

    • decodes DNA by making and RNA copy

  • tRNA: assembles amino acids into proteins through Protein synthesis

The sequence of protein synthesis goes like ↴

DNA → RNA → Protein

DNA vs RNA

Extra Notes!

STRUCTURE DETERMINES FUNCTION

The oxygen atoms of a water molecule- is more electronegative than hydrogen atoms

Essential Questions

1. What properties of oxygen and hydrogen lead to the unique properties of water?

2. Which elements are used to build which macromolecules?

3. How do these contribute to their properties?

4. What types of bonds are used to create molecules, macromolecules, and most organic compounds?

5. What reactions are used to make and break polymers?

6. Which macromolecules are polar vs. non-polar? why?

7. How does the structure of these components help determine or influence the function of the molecules discussed in this unit?

8. How do small changes in the structure impact function