Cell Biology

Purple Pages

Scientific Method

Acquiring knowledge by making observations about the natural world, developing explanations and testing them

Observations

Lead us to ask questions

Hypothesis

Predicted answer to a question

Must be testable and falsifiable

Can have more than one (First may not work)

Leads to predictions that can be tested by observing/experimenting

Failure to falsify does not prove hypothesis

Controlled Experiment

Is an experiment with a control group

Variable

Factor within the experiment

Independent Variable

A variable that is changed between test groups

Dependent Variable

A variable that depends on the independent variable

Controlled Variable

A variable that remains consistent

Bigger Sample Size

Gives a more specific/detailed result

Scientific Method Order

Observation, Hypothesis, Experimentation, Interpretation of Results, Conclusion, Peer Review (Research Paper), Scientific theory (Takes years)

Scientific Theory

Acceptable and well-substantiated explanation of some aspect of the natural world

  - takes many years to establish

  - supported by exhaustive experimentation

  - established truths that are unlikely to be contradicted by future research

Observational Science

Look for a pattern and cause in observations, relies on statistical techniques

Biology (Definition)

The study of living things

Bio- Living things

Logos- The study of

Cell (Definition)

Basic unit of life

Matter

Has a mass, occupies space and is made of pure element

Element

A substance that cannot be broken down into other substances by chemical reactions

Compound

A substance that consists of 2 or more elements using certain fixed ratios

Which elements make up 96% of living organisms

Carbon, Hydrogen, Oxygen, and Nitrogen

What makes living organisms so different

The ratios or organization of the main 4 elements (O,H,N,C)

Different shapes have different functions

Atomic Number

Number of Protons

Atomic Mass

Protons and Neutrons

(Electron mass is negligible)

Connection Between Protons and Electrons

Number of Protons is equal to number of Electrons and vise versa

Protons, Neutrons, and Electrons

Protons- Positive

Neutrons- Neutral

Electrons- Negative

Isotopes

Atoms with the same number of protons but a different number of electrons.

Same Atomic number different atomic mass

Orbitals

Stable orbitals have paired electrons

Orbitals are grouped into shells

Made up of protons moved in specific ways by electrons

Radioisotopes

Unstable isotopes that decay and release energy

Rate of Decay is constant

Used for nuclear medicine (Such as diagnostic testing)

Radioactive Tracer

A substance containing a radioisotope that is used to measure the speed of chemical processes and/or movement of substances.

(Nuclear Medicine)

Why was there a global radioisotope shortage between 2007-2010

Because the Chalk River reactor in Canada was shut down and we supplied 30-40% of the world’s supply

Valence Electrons

Electrons in the outermost shell (Valence Shell)

Determines reactivity of an atom

Full Valence shell = Inert (Stable/will not react)

4 types of Chemical Bonds

Ionic

Covalent

Hydrogen

Van der waals forces

Ionic Bonds

Transfer of electrons from one atom to another resulting in both atoms having charges. Which makes them ions

Intramolecular bond

Covalent Bonds

Sharing a pair of valence electrons by 2 atoms which makes a distinct 3D form. The 3D form (Structure) has to do with the functions.

Intramolecular bond

Hydrogen Bonds

Partial Positive charge of H atoms attracts partial negative charge of nearby atoms, only partial charges

Weaker than ionic and covalent bonds

Intermolecular bond

Van Der Waals Forces

Developed between non-polar bonds, constant motion of electrons causes them to accumulate by chance on one region of molecule this causes zones of negative and positive charge. (Holds molecules close together)

Weaker than hydrogen bonds

Intermolecular bond

Electronegativity

Measures atoms attraction for electrons in covalent bonds

(Polar or Non-polar)

Non-Polar Covalent

Equal Sharing of electrons

Polar Covalent

Unequal Sharing of electrons

One is slightly positive (Lower electronegativity)

One is slightly negative (Higher electronegativity)

Intramolecular Bonds

Intra means within

Applies to ionic and covalent bonds

Intermolecular Bonds

Inter means between

Applies to Hydrogen bonds and Van Der Waals forces

Cation

A positively charges ion that has lost one or more electrons

Anion

A negatively charged ion that has gained one or more electrons

Structure determines

Function

Cohesion

Attraction between water molecules (water “sticks” to itself ie, water droplets)

Solvent

Dissolves solute ie. water

Solute

Dissolved by solvent ie. salt

Hydrogen Shell

Water molecules surround polar molecules and ions

Allows for separation of molecules

Water Ionization

Separation of water = H⁺ and OH^-

Base

Proton acceptor

7.1-14 pH

Acid

Proton donor

1-6.9 pH

Acidity of a Solution

The concentration of H⁺ verses OH^-

Buffer

Controls pH by absorbing or releasing H⁺

Most are weak acids or weak bases

Carboxylic Acid Controls…

The pH of our blood

Tetravalence

Has 4 valence electrons

Allows for large complex molecules

example carbon can make 4 covalent bonds

Hydrocarbons

Molecule where carbon is only bonded to hydrogen

Vary in length and shape

Functional Group (Definition)

Reactive groups

Part of biological reactions

Bind to carbon

Hydroxyl

-OH

Carbonyl

-C=O

Carboxyl

-COOH

Amino

-NH₂

Phosphate

-PO₄^2-

Sulfhydryl

-SH

Synthesis of a Polymer

Dehydration Reaction

Removes water

Forms a bond

Breakdown of a Polymer

Hydrolysis Reaction

Add water

Break a bond

Carbohydrate

Sugars, Starches, Fiber

Main fuel source for cells

Helps as a building block for cell wall (In plants)

Monosaccharide

Means one sugar

CH₂O

Isomer

Same chemical formula, different structure

Enantiomer

Mirrored Isomer

Structural Isomer

Different position of carbonyl group

Disaccharide

Meaning two sugars

Two monosaccharides

Maltose=

Glucose + Glucose

Sucrose=

Glucose + Fructose

Lactose

Glucose + Galactose

Glycosidic Linkage

Covalent bond between sugars

Has H-bonds and N-groups

Polysaccharides

Meaning many sugars (Many monosaccharides)

Unbranched Vs Branched Polysaccharides

Unbranched is straight one continuous line

Branches has jut outs or branches

Proteins

Have many structures therefore many functions

“workhouse” of the cell

Structural support, storage, transport, enzymes in reactions, cellular communications, movement

Over 100,000 different functional proteins

Made of one or more polypeptides

Polypeptides

A continuous chain of amino acids held together by peptide bonds

Amino Acid

Organic molecule that bonds to form proteins

20 different ones

Nonpolar Amino Acids

10 out of 20

R group consists of carbon and hydrogen

Uncharged Polar Amino Acids

5 of the 20

R group consists of carbon, hydrogen and oxygen

Oxygen hogs electrons and becomes slightly negative making it polar

Charged Amino Acids

5 of the 20

2 types - negatively charged (Acidic)

-Positively charged (Basic)

Peptides

Covalent Bonds

Dehydration synthesis

Peptide bonds

Amino Acid added only to carboxyl end

Primary Protein Structure

Linear sequence of amino acids

tells us nothing about the structure

Secondary Protein Structure

Backbone of oxygen and hydrogen

Hydrogen bonds between amino acids

Folds into either a alpha helix or beta plated sheets

Tertiary Protein Structure

Polypeptide backbone

All types of bonds between R groups

3D shape

Now has function

Quaternary Protein Structure

Two or more polypeptides

All types of bonds

Heme Groups

Are prosthetic groups added to protein to help it function

Non protein component

Transport oxygen using iron to attract it (Oxygen is attracted to iron)

Prosthetic Groups

Non protein component

Needed for proper function in for example proteins

Nucleic Acids

Polymers of nucleotides

Stores genetic information like inherited genes

DNA

Deoxyribonucleic Acid

2 nucleotide chains

Sugar-phosphate backbone

Phosphodiester bonds

Read from 5’-3’

RNA

Ribonucleic Acid

Nitrogenous bases inside

H-bonds

mRNA

Messenger RNA

A single-stranded molecule that carries genetic instructions from DNA in a cell's nucleus to the ribosomes in the cytoplasm, where the cell builds proteins

tRNA

Transfer RNA

A small RNA molecule that helps build proteins by matching messenger RNA (mRNA) codes with the correct amino acids

rRNA

Ribosomal RNA

The main building block and working core of the cell's ribosome

Lipids

Nonpolar molecule

Hydrocarbon backbone

Not a true macromolecule

3 types- Fats, phospholipids, steroids

Saturated Fats

Maximum number of hydrogen bonds possible

No double bonds

At room temp it is a solid

Unsaturated Fats

One or more double bonds that cause a bend in the structure

At room temp it is a liquid (like oil)

Fatty Acid does what

Stores lots of energy when glucose isn’t available

Phospholipid

Found in cell membrane

Amphipathic (Has a polar head and a nonpolar end)

Polar head is hydrophilic, nonpolar end is hydrophobic

Forms primary structural foundation of all biological cell membranes

Steroids

4 carbon rings

Dual solubility

polar and nonpolar end