Lecture 2- Chemical Bonds and Macromolecules Flashcards
Why is water the solvent of life?
- polar (has partial charges- unequal distribution of e- across a bond)
- oxygen has a high affinity for e- (high electronegativity) so the e- sit closer to O than to H
- anything that can interact with a charge can interact with water
explain the relationship between water and a nonpolar substance
they cannot form favorable interactions; they nonpolar molecule will aggregate (clump together away from the water) like oil
organic molecules contain __ and ___
carbon and hydrogen
- C is the backbone of organic molecules
- C is weakly electronegative
Why is life carbon based? List 3 reasons
- C can bond to 4 other atoms (lots of diversity from one single backbone)
- C can bond to form C-C chains (long!)
- C can form double bonds and triple bonds
all of this results in a lot of molecular diversity
Define monomer
“single unit”
single building block of a macromolecule
define polymer
“multiple units”
a chain of monomers composed of similar yet non-identical subunits (similar in that they’re all amino acids, but there are 20 amino acids)
eg. a molecule of DNA is a polymer
why are polymers more biologically important that monomers?
they allow for variation to promote biological diversity
- eg. proteins have 20 amino acids- endless diversity
- eg. DNA; 4 nucleotides in combination
polymers must be built up/ broken down by the ___
cell
synthesis of polymers is done by ____
condensation/ dehydration reactions
eg. DNA replication
explain a condensation/ dehydration rxn
- add monomers to a growing chain; formation of covalent bonds
- water is a product
- requires energy (building up a polymer!)
the breakdown is polymers is done by a ___ reaction
hydrolysis
explain a hydrolysis rxn
- cleavage of covalent bonds between monomers in a polymer (the bonds holding the polymer together)
- water is a reactant
- releases energy
- breakdown of a polymer!
function and structure of carbohydrates/ polysaccharides/sugars
- energy storage
- cell structure (cellulose in plant’s cell walls)
- cell-cell recognition
monomers of carbohydrates
CH2O (monosaccharides)
- monomers have a C chain of 3-7C long
- can be linear or ring shaped
describe an example of a carbohydrate
glucose (C6H12O6)
- main energy source in cell
- reactive H and OH groups allows extensibility (react w/ reach other –> long chains)
- ring shape dominates in the cell
Disaccharides are formed by
a covalent bond between monosaccharides
example of a disaccharide
disaccharide of glucose(6C) = fructose (6C)
- structural isomers (same formula, different shape)
bond type in carbohydrates
glyosidic bond
- Carbohydrates are made up of monosaccharides linked together into polysaccharide chains by a type of covalent bond known as a glycosidic bond. These glycosidic bonds are formed in a dehydration synthesis reaction.
Glycogen is a _____ polysaccharide (a polymer of ___ that’s highly branched)
- Function of glycogen?
nutritional
glucose
Function: energy storage in animals
polysaccharides are ____ of _____
polymers of monosaccharides
Difference b/w structures of starch vs cellulose
starch: OH all on same side
Cellulose: OH on alternating sides
name 4 polymers of glucose and their functions
- starch: fxn= energy storage in plants
- glycogen: fxn= energy storage in animals
- Cellulose: fxn= plant cell wall
- Chitin: fxn= insect exoskeleton and fungal cell wall
True/ False
Lipids/ fats are true polymers
False
macromolecule? arguable
How to you classify a lipid?
Fxn of lipids?
hydrophobic
- non-polar and aggregate away from water
- made up of mostly H and C
fxn= energy storage and insulation
Fatty acids are a single chain (usually ___ C long) with a ____ end
- they can attach (“____”) to a glycerol backbone
16-18
COOH
esterify
Fatty acids can be saturated or unsaturated. Explain the difference
saturated: all single C-C bonds
Unsaturated: double carbon bond (causes kink in the fatty acid tail)
phospholipids are the structural component of ____
- they are ___(have both hydrophilic and hydrophobic domains)
membranes
-amphipathic
Steroids are a class of lipids based on \_\_\_\_\_ - characterized by the backbone of 4 \_\_\_\_ \_\_\_
cholesterol
4 fused rings
2 major fxns of steroids
- hormones: eg estrogen, testosterone, progesterone
2. in animals, cholesterol sits in plasma membrane to maintain fluidity and increase membrane stiffness
Proteins are polymers of ___ ____
- what’s the directionality?
amino acids
- N to C (amino- NH3+ to carboxy- COO-)
why are amino acids extendible?
ie why is it possible to make the polymer (proteins)
amino acids carry both a negative (COO-) and positive (NH3+) charge. Therefore the amino and carboxy (acid) groups are reactive/ extendible
4 possible R (variable) groups of proteins:
- non-polar (R=CH)
- polar uncharged (R= -OH or -SH)
- Polar uncharged acidic (R= COO-) *neg charge
- Polar charged basic (R= NH3+) *pos charge
what kind of bond do proteins have?
ie. a.a. are linked covalently by ___ bonds
peptide
Are R groups involved in polymerization?
What happens to the directionality as the amino acids are polymerized?
- no, R groups are not involved in polymerization
- N to C directionality is maintained in the polymer
the primary structure of a protein is the polymer of a.a. (N to C)
What does the primary structure dictate?
It dictates folding (what a.a. in what order?)
*a.a. sequence determines folding and folding dictates function
Describe the secondary structure of proteins
interaction b/w the backbone of the peptide chain (r-groups drive the folding, but do NOT stabilize it)
- the secondary structure= local folding of a.a. chain into either alpha helix or beta sheet
- stabilized w/ H-bonds b/w a.a. backbones
characteristics of alpha helix vs beta sheet
beta sheet: fully stretched out
alpha helix: coiled region of protein
the tertiary structure is the ___ pattern of protein folding
3D
what is the driving force of folding for the tertiary structure?
hydrophobic interactions of non-polar R groups drive a.a. away from water into middle of the protein
The forces that maintain the tertiary structure are interactions between R-groups. List the types of stabilizing interactions from strongest to weakest.
- (strongest): Covalent bonds: disulfide bridges b/w 2 cysteine
- ionic bonds (b/w oppositely charged a.a.)
- Hydrophobic interactions: b/w non-polar a.a.
- (weakest): H-bonds (b/w polar, uncharged a.a. (dip-dip)
Describe the quaternary structure.
What forces holds it together?
- some proteins form multisubunit complexes that create a functional protein
- quaternary structure held together by the same forces as the tertiary structure (R-group interactions)
____ are proteins that assist in the folding of other proteins
chaperones
list some examples of human diseases of protein folding
mad cow disease
Alzheimer’s
Parkinson’s
sickle cell anemia (can be caused by a few things)
describe the steps of a bacterial chaperonin
- unfolded protein enters folding chamber
- chamber provides a favorable environment for folding
- chamber spits out a correctly folded protein
* can refold protein that’s been unfolded by heat for ex
Function of nucleic acids
- store/ transmit heredity info
- Rna transmits info within cell
- DNA transmits info b/w cell generations
Describe the 2 types of nucleic acids
- DNA:
- polymer of deoxynucleotides (DNA ntds are deoxygenated at carbon 2 of ribose sugar)
- contains all info essential for life - RNA:
- polymer of ribonucleotides
- many functions for RNA:- info= mRNA
- translation= tRNA and rRNA
- regulation= siRNA, miRNA
- splicing= snRNA
Basic structure of a ntd (3 components)
- 5- carbon sugar = ribose
- nitrogenous base
- phosphate
What does each carbon do in ntds?
C1: attaches to the base C2: in DNA, there's no OH, in RNA there is an OH C3: 3' OH (essential for polymerization) C4: boring carbon C5: attaches to PO4
monomers are joined into sugar-phosphate backbone by ______ linkages.
- the backbone is ____ charged with the bases pointing off of the backbone
phosphodiester linkages
- negatively
A and T have ___ H-bonds
G and C have ___ H-bonds
A/T= 2 bonds C/G= 3 bonds
why does a purine (A and G) always pair with a pyrimidine (C and T- or C and U)?
to maintain the diameter of the helix
why is RNA single stranded?
2’ OH makes helix more open and reactive therefore the free base pairs with itself, other RNA, or DNA
