Lecture 2- Chemical Bonds and Macromolecules

Question 1

Why is water the solvent of life?

Answer 1

• 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

Question 2

explain the relationship between water and a nonpolar substance

Answer 2

they cannot form favorable interactions; they nonpolar molecule will aggregate (clump together away from the water) like oil

Question 3

organic molecules contain __ and ___

Answer 3

carbon and hydrogen

• C is the backbone of organic molecules
• C is weakly electronegative

Question 4

Why is life carbon based? List 3 reasons

Answer 4

1. C can bond to 4 other atoms (lots of diversity from one single backbone)
2. C can bond to form C-C chains (long!)
3. C can form double bonds and triple bonds

all of this results in a lot of molecular diversity

Question 5

Define monomer

Answer 5

“single unit”

single building block of a macromolecule

Question 6

define polymer

Answer 6

“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

Question 7

why are polymers more biologically important that monomers?

Answer 7

they allow for variation to promote biological diversity

• eg. proteins have 20 amino acids- endless diversity
• eg. DNA; 4 nucleotides in combination

Question 8

polymers must be built up/ broken down by the ___

Answer 8

cell

Question 9

synthesis of polymers is done by ____

Answer 9

condensation/ dehydration reactions

eg. DNA replication

Question 10

explain a condensation/ dehydration rxn

Answer 10

• add monomers to a growing chain; formation of covalent bonds
• water is a product
• requires energy (building up a polymer!)

Question 11

the breakdown is polymers is done by a ___ reaction

Answer 11

hydrolysis

Question 12

explain a hydrolysis rxn

Answer 12

• 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!

Question 13

function and structure of carbohydrates/ polysaccharides/sugars

Answer 13

• energy storage
• cell structure (cellulose in plant’s cell walls)
• cell-cell recognition

Question 14

monomers of carbohydrates

Answer 14

CH2O (monosaccharides)

• monomers have a C chain of 3-7C long
• can be linear or ring shaped

Question 15

describe an example of a carbohydrate

Answer 15

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

Question 16

Disaccharides are formed by

Answer 16

a covalent bond between monosaccharides

Question 17

example of a disaccharide

Answer 17

disaccharide of glucose(6C) = fructose (6C)

- structural isomers (same formula, different shape)

Question 18

bond type in carbohydrates

Answer 18

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.

Question 19

Glycogen is a _____ polysaccharide (a polymer of ___ that’s highly branched)
- Function of glycogen?

Answer 19

nutritional
glucose
Function: energy storage in animals

Question 20

polysaccharides are ____ of _____

Answer 20

polymers of monosaccharides

Question 21

Difference b/w structures of starch vs cellulose

Answer 21

starch: OH all on same side
Cellulose: OH on alternating sides

Question 22

name 4 polymers of glucose and their functions

Answer 22

1. starch: fxn= energy storage in plants
2. glycogen: fxn= energy storage in animals
3. Cellulose: fxn= plant cell wall
4. Chitin: fxn= insect exoskeleton and fungal cell wall

Question 23

True/ False

Lipids/ fats are true polymers

Answer 23

False

macromolecule? arguable

Question 24

How to you classify a lipid?

Fxn of lipids?

Answer 24

hydrophobic

• non-polar and aggregate away from water
• made up of mostly H and C

fxn= energy storage and insulation

Question 25

Fatty acids are a single chain (usually ___ C long) with a ____ end - they can attach ("____") to a glycerol backbone

Answer 25

16-18 COOH esterify

Question 26

Fatty acids can be saturated or unsaturated. Explain the difference

Answer 26

saturated: all single C-C bonds Unsaturated: double carbon bond (causes kink in the fatty acid tail)

Question 27

phospholipids are the structural component of ____ | - they are ___(have both hydrophilic and hydrophobic domains)

Answer 27

membranes | -amphipathic

Question 28

``` Steroids are a class of lipids based on _____ - characterized by the backbone of 4 ____ ___ ```

Answer 28

cholesterol | 4 fused rings

Question 29

2 major fxns of steroids

Answer 29

1. hormones: eg estrogen, testosterone, progesterone | 2. in animals, cholesterol sits in plasma membrane to maintain fluidity and increase membrane stiffness

Question 30

Proteins are polymers of ___ ____ | - what's the directionality?

Answer 30

amino acids | - N to C (amino- NH3+ to carboxy- COO-)

Question 31

why are amino acids extendible? | ie why is it possible to make the polymer (proteins)

Answer 31

amino acids carry both a negative (COO-) and positive (NH3+) charge. Therefore the amino and carboxy (acid) groups are reactive/ extendible

Question 32

4 possible R (variable) groups of proteins:

Answer 32

1. non-polar (R=CH) 2. polar uncharged (R= -OH or -SH) 3. Polar uncharged acidic (R= COO-) *neg charge 4. Polar charged basic (R= NH3+) *pos charge

Question 33

what kind of bond do proteins have? | ie. a.a. are linked covalently by ___ bonds

Answer 33

peptide

Question 34

Are R groups involved in polymerization? | What happens to the directionality as the amino acids are polymerized?

Answer 34

- no, R groups are not involved in polymerization | - N to C directionality is maintained in the polymer

Question 35

the primary structure of a protein is the polymer of a.a. (N to C) What does the primary structure dictate?

Answer 35

It dictates folding (what a.a. in what order?) | *a.a. sequence determines folding and folding dictates function

Question 36

Describe the secondary structure of proteins

Answer 36

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

Question 37

characteristics of alpha helix vs beta sheet

Answer 37

beta sheet: fully stretched out | alpha helix: coiled region of protein

Question 38

the tertiary structure is the ___ pattern of protein folding

Answer 38

3D

Question 39

what is the driving force of folding for the tertiary structure?

Answer 39

hydrophobic interactions of non-polar R groups drive a.a. away from water into middle of the protein

Question 40

The forces that maintain the tertiary structure are interactions between R-groups. List the types of stabilizing interactions from strongest to weakest.

Answer 40

1. (strongest): Covalent bonds: disulfide bridges b/w 2 cysteine 2. ionic bonds (b/w oppositely charged a.a.) 3. Hydrophobic interactions: b/w non-polar a.a. 4. (weakest): H-bonds (b/w polar, uncharged a.a. (dip-dip)

Question 41

Describe the quaternary structure. | What forces holds it together?

Answer 41

- 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)

Question 42

____ are proteins that assist in the folding of other proteins

Answer 42

chaperones

Question 43

list some examples of human diseases of protein folding

Answer 43

mad cow disease Alzheimer's Parkinson's sickle cell anemia (can be caused by a few things)

Question 44

describe the steps of a bacterial chaperonin

Answer 44

1. unfolded protein enters folding chamber 2. chamber provides a favorable environment for folding 3. chamber spits out a correctly folded protein * can refold protein that's been unfolded by heat for ex

Question 45

Function of nucleic acids

Answer 45

- store/ transmit heredity info - Rna transmits info within cell - DNA transmits info b/w cell generations

Question 46

Describe the 2 types of nucleic acids

Answer 46

1. DNA: - polymer of deoxynucleotides (DNA ntds are deoxygenated at carbon 2 of ribose sugar) - contains all info essential for life 2. RNA: - polymer of ribonucleotides - many functions for RNA: - info= mRNA - translation= tRNA and rRNA - regulation= siRNA, miRNA - splicing= snRNA

Question 47

Basic structure of a ntd (3 components)

Answer 47

1. 5- carbon sugar = ribose 2. nitrogenous base 3. phosphate

Question 48

What does each carbon do in ntds?

Answer 48

``` 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 ```

Question 49

monomers are joined into sugar-phosphate backbone by ______ linkages. - the backbone is ____ charged with the bases pointing off of the backbone

Answer 49

phosphodiester linkages - negatively

Question 50

A and T have ___ H-bonds | G and C have ___ H-bonds

Answer 50

``` A/T= 2 bonds C/G= 3 bonds ```

Question 51

why does a purine (A and G) always pair with a pyrimidine (C and T- or C and U)?

Answer 51

to maintain the diameter of the helix

Question 52

why is RNA single stranded?

Answer 52

2' OH makes helix more open and reactive therefore the free base pairs with itself, other RNA, or DNA