Lecture #2 - Chemical bonds and Macromolecules Flashcards
Organic Molecules
- contain C-H, no dipoles
- C is the backbone of organic molecules
- C is weakly electronegative
Why is life carbon based?
- C can bond to 4 other atoms
- can form C-C chains
- can form double and triple bonds
- these all allow for molecular diversity
define monomer
- “single unit”
- building block of a polymer
- eg. nucleotide
define polymer
- “multiple unit”
- chain of monomers composed of similar or identical subunits
why are polymers more biologically important than monomers?
- allow for variations
eg. proteins = 20 a.a., DNA+ 4 nucleotides - in combination, the variety is infinite
Synthesis- condensation rxns/dehydration
- add monomers into a chain by catalyzing covalent bonds
- water is a product
- requires energy
breakdown - hydrolysis rxns
- cleavage of covalent bonds b/w monomers
- water is a reactant
- release energy
What is the function and structure of a carbohydrate/polysaccharide/sugar
- energy store
- gives cell strucutre
- cell-cell recognition
what is a glycosidic bond?
a covalent bond formed between monosaccharides
monosaccharide example: glucose
C6H12O6
- main energy source in all cells
- multiple chains of CH2O
- can either be linear or ring shaped
- alpha form is when the OH group is at the bottom, ring shape dominates in the cell
- alpha form is less common irl but more widely used
Disaccharides example: sucrose
- formed from the covalent (glycosidic) bond b/w glucose and fructose
- uses a dehydration rxn to join the two
polysacc eg: starch
- nutritional polysacc
- polymer of alpha glucose
- contains alpha 1-4 glycosidic bonds
polysacc eg: glycogen
- nutritional polysacc
- polymers of alpha glucose, connected by alpha 1-4 glycosidic bonds
- highly branched by alpha 1-6 glycosidc bonds
- function: energy storage in animals in muscle and liver
polysacc eg: cellulose
- structureal polysacc
- function: provide structure to plant cell walls
- contains beta 1-4 glycosidic bonds
polysacc eg: chitin
- structural polysacc
- polymer of monosacc
- found in insect exoskeleton and fungi
- peptidoglycan - function: structure to bacterial cell wall
Lips/fats - classification, function and structure
- not true polymers- not joined into polymers by covalent bonds
- hydrophobic: non-polar molecules made of mostly H-C
- non-polar lipids aggregate away from water
- they are single chains of mostly HC with a COOH end and is usually 16-18C long
- can esterify to a 3C glycerol backbone
fats/lips - triglyceride: saturated or unsaturated
- function: energy storage in animals
- it can be saturated or unsaturated
- sat: all c-c single bond, solid at room temp, linear fatty acids
- unsat: presence of C=C creates a kink in fatty acid tail, liquid at room temp
fats/lips - phospholipids
- structural component of biological membrane
- functions in the cell membrane
- 2HC chains attached to a glycerol backbone via ester linkages with a phosphate group attached to the 3rd glycerol
- phospholipids are amphipathic = both hydrophobic and hydrophilic domains
- hydrophilic head, hydrophobic tails
fats/lips - steroids
- class of lipids based on cholesterol
- slighty amphipathic
- planar/flat
2 major functions:
1. hormones eg.testosterone
2. membrane structure: in animals cholesterol in remembrance modulates membrane fluidity
Proteins
- polymers of a.a
- involved in every biological task
- 20 biologically relevant a.a
Draw a protein, indicate the directionally, and the types of variable groups
n-c directionality
variable groups:
- non-polar
- polar uncharged
- polar charged
- polar charged basic
Structure of protiens
- function in 3D
- synthesized as linear polypeptides
- product of dehydration reactions
what is a peptide bond?
bond formed between a.a, it links them together to make a protein
Primary sequence
- polymer of a.a
- sequence is determined by the DNA sequence of a gene
- primary sequence dictates fold and folding dictates function
secondary sequence
- local folding of a.a chain into an alpha helix or beta sheet
- R groups drive the folding, they don’t stabilize it
- stabilized by H-bonds b/w a.a backbones
tertiary sequence
- hydrophobic R groups bury into the middle of protein to aggregate away from water
- R group interactions stabilize the structure
1. covalent - disulfide bridge, very strong but rare
2. ionic bonds - b/w oppositely charged R groups
3. hydrogen bonds - b/w polar uncharged a.a
4. hydrophobic interactions - b/w non-polar a.a
quaternary sequence
- some proteins function as multisubunit complexes
- complex is stabilized by same R group interactions as tertiary sequence
- eg ribosomes
what are chaperones?
- proteins that assists in folding other proteins
- proper folding is essential for proper function
there are many diseases of protein folding - misfolded proteins are usually degraded
- if not degraded they can : refold with chaperones =good or aggregate = bad
Nucleic Acids( DNA/RNA) function
function:
- store and transmit hereditary information
- RNA tramits within cells
- DNA transmits b/w cells
DNA
- molecule of heredity
- polymer of nucleotides (ntds)
- deoxyribonucleotides
RNA
- polymer of ribonucleotides
many fxns: - info transmission
- translation
- splicing
- gene regulation
draw the basic structure of a nucleotide, define what each carbon is for, identify the directionality and the base stacking
- Pi = inorganic PO4-
- SC = sugar = ribose
- nitrogenous base
c1 = attaches to the NB
c2 = if DNA - just H group, if RNA - OH group
c3 = OH group
c4 = nothing boring
c5 = Pi attachment
5’ -> 3’ directionality
- hydrophobic base stack interactions stabilizes double helix
pyrimidines and purines and the complementary base pairing rule
A=T
G=- C
purine always pairs with a pyrimidine, this maintains the diameter of the helix
- pyrimidines = single ringed bases: cytosine, thymine, uracil
- purines = double ringed bases: adenine and guanine
What is a phosphodiester bond?
- monomers joined in a sugar-phosphate backbone
Why is RNA single stranded?
- 2’ OH makes helix more open
- 2’ OH makes RNA more reactive so it can base pair with: itself, other RNA and DNA
