Lecture 2 Flashcards
Molecules of life
Water
Macromolecules
What is the solvent of life
And why
Water
Dissolves more molecules than any other solvent
It’s a polar molecule (opposite charge on each end)
Dissolves polar and charged molecules
What are the macromolecules
Carbohydrate
Lipids
Protein
Nucleus acids
Polymers of sugars
Carbohydrates
What macronutrient isn’t a polymer
Lipid
Polymers of amino acids
Proteins
Polymers of nucleotides
Nucleus acids
Polymers
Chains composed of molecules called monomers
Polymerize and depolymerize
Polymerization
Go from a monomer to a polymer
Depolymerization
Go from polymer to monomer
Polymerization/ depolymerization reactions often involve loss or addition of what
Water
Therefor can also be described as
Dehydration synthesis(polymerization)
Hydrolysis (depolymerization)
Another word for polymerization
Dehydration synthesis
*Synthesis means making (making polymer from monomer)
Another word for depolymerization
Hydrolysis
Where does addition or loss of water happen in polymerization and depolymerization
Happens at the binds between monomers
Known as condensation polymerization
Enzymes
Catalyze the synthesis/ hydrolysis of polymers
What Catalyze the synthesis/ hydrolysis of polymers
Enzymes
enzymes in synthesis/ hydrolysis of polymer
Polymerases
Hydrolases
-ase suffix =?
Enzyme
What do biopolymers look like
They’re not simple chains
-twist and fold up
-chains arrange into varied levels of higher order structure
Examples: DNA double helix + protein folding
Higher order polymer structure example- proteins
1° structure- amino acids chain
2° structure- ex. Helix or a sheet
3° structure- folding
4° structure- assembling with other proteins into a complex
What determines a proteins structure
Properties and order of the amino acids
Amino acids
Contain nitrogen
Mildly acidic
R= sidechain
Sidechain properties define the chemistry of proteins
Amino acids are linked by
Covalent bonds called peptide bonds
Protein AKA
Polypeptides
How many different amino acids
20
What causes polypeptides to twist or form sheets
Hydrogen bonds between nearby amino acids
Protein twist name
Alpha helix
Protein sheet name
Beta sheets
Tertiary protein structure
Chemistry between side chains causes higher-order folding
Quaternary protein structure
Individual proteins interact to form complexes
Again determined by their structure and chemistry
Why was/is protein structure hard to predict
A- Central dogma of molecular biology means that for any gene we know exactly what amino acids will make up the protein
B- it’s HARD to predict what it will look like
C- it took years using X-ray crystallography to identify protein shape
D- machine learning: alpha gold and other ML based computer programs
Cell theory
1-All organisms are composed of one or more cells
2- cell is the basic structural and functional unit of all living organisms
3- cells arise only from the division of pre-existing cells
When were cells first observed
1600s
Robert Hooke
1600s
Looked at cork cells
Anton van Leeuwenhoek
Made a better microscope than Hooke and saw animacules
Animacules*
Why are cells small
- Surface area must be sufficient to allow exchange of stuff between the cell and its surroundings
- larger volumes require more surface area to achieve this
- larger volumes need more structural support
Trade off between cell surface area and volume
As volume increases, Surface area doesn’t increase proportionally
Ex. In a cube
V= a cubed
A= 6a squared
Volume is way higher the larger a gets
What if cells need a large surface area
They develop convoluted/ branch surface morphologies
Ex- brain cells, leaf epidermal cells, microvilli on intestinal epithelial cells
What if cells need a larger volume
They use cell walls
Example- xylem vessels from wood
Resolution- microscope
Ability of a microscope to distinguish 2 objects as being no separate
Higher magnification increases
Resolution
Higher contrast gives
More detail but can’t increase resolution
Microscopy types
Light microscopy
Electron microscopy
Light microscopy types
Reflected light
Transmitted light
Fluorescence
Electron microscopy types
Transmission
Scanning
Relflected light microscopy
- stereo microscope (aka dissecting microscope)
- lighting from top
- can see bigger size cells
Transmitted light
- stereoscopes (some can also use light from the bottom)
- compound microscopes
Variations on transmitted light compound
1- brightfield
2- darkfield
3- phase-contrast
4- DIC (differential interference contrast aka. Nomarksi)
2-4 are:
- contrast enhancing methods
- exploit refractive (light scattering) properties of specimens
- variations in specimen thickness and density influence how light passes through it
Brightfield
Ones we use in the lab
Staining of term required to see more details
Contrast enhancing methods
Darkfield
Phase contrast
Differential interference contrast (DIC/ nomarski)
Dark field
- illuminates sample at an angle so light does not hit the objective lens directly
- only light that is scattered upwards by the sample reaches the objective lens
Phase contrast
This method creates slight phase shifts in the illuminating light, which manifest as higher detailed images
DIC
Differential interference contrast
- similar to phase contrast
- gives a pseudo 3D appearance
