Lecture #2 - Chemical bonds and Macromolecules

Question 1

Organic Molecules

Answer 1

• contain C-H, no dipoles
• C is the backbone of organic molecules
• C is weakly electronegative

Question 2

Why is life carbon based?

Answer 2

• C can bond to 4 other atoms
• can form C-C chains
• can form double and triple bonds
• these all allow for molecular diversity

Question 3

define monomer

Answer 3

• “single unit”
• building block of a polymer
• eg. nucleotide

Question 4

define polymer

Answer 4

• “multiple unit”
• chain of monomers composed of similar or identical subunits

Question 5

why are polymers more biologically important than monomers?

Answer 5

• allow for variations
  eg. proteins = 20 a.a., DNA+ 4 nucleotides
• in combination, the variety is infinite

Question 6

Synthesis- condensation rxns/dehydration

Answer 6

• add monomers into a chain by catalyzing covalent bonds
• water is a product
• requires energy

Question 7

breakdown - hydrolysis rxns

Answer 7

• cleavage of covalent bonds b/w monomers
• water is a reactant
• release energy

Question 8

What is the function and structure of a carbohydrate/polysaccharide/sugar

Answer 8

• energy store
• gives cell strucutre
• cell-cell recognition

Question 9

what is a glycosidic bond?

Answer 9

a covalent bond formed between monosaccharides

Question 10

monosaccharide example: glucose

Answer 10

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

Question 11

Disaccharides example: sucrose

Answer 11

• formed from the covalent (glycosidic) bond b/w glucose and fructose
• uses a dehydration rxn to join the two

Question 12

polysacc eg: starch

Answer 12

• nutritional polysacc
• polymer of alpha glucose
• contains alpha 1-4 glycosidic bonds

Question 13

polysacc eg: glycogen

Answer 13

• 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

Question 14

polysacc eg: cellulose

Answer 14

• structureal polysacc
• function: provide structure to plant cell walls
• contains beta 1-4 glycosidic bonds

Question 15

polysacc eg: chitin

Answer 15

• structural polysacc
• polymer of monosacc
• found in insect exoskeleton and fungi
• peptidoglycan - function: structure to bacterial cell wall

Question 16

Lips/fats - classification, function and structure

Answer 16

• 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

Question 17

fats/lips - triglyceride: saturated or unsaturated

Answer 17

• 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

Question 18

fats/lips - phospholipids

Answer 18

• 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

Question 19

fats/lips - steroids

Answer 19

• 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

Question 20

Proteins

Answer 20

• polymers of a.a
• involved in every biological task
• 20 biologically relevant a.a

Question 21

Draw a protein, indicate the directionally, and the types of variable groups

Answer 21

n-c directionality
variable groups:
- non-polar
- polar uncharged
- polar charged
- polar charged basic

Question 22

Structure of protiens

Answer 22

• function in 3D
• synthesized as linear polypeptides
• product of dehydration reactions

Question 23

what is a peptide bond?

Answer 23

bond formed between a.a, it links them together to make a protein

Question 24

Primary sequence

Answer 24

• polymer of a.a
• sequence is determined by the DNA sequence of a gene
• primary sequence dictates fold and folding dictates function

Question 25

secondary sequence

Answer 25

- 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

Question 26

tertiary sequence

Answer 26

- 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

Question 27

quaternary sequence

Answer 27

- some proteins function as multisubunit complexes - complex is stabilized by same R group interactions as tertiary sequence - eg ribosomes

Question 28

what are chaperones?

Answer 28

- 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

Question 29

Nucleic Acids( DNA/RNA) function

Answer 29

function: - store and transmit hereditary information - RNA tramits within cells - DNA transmits b/w cells

Question 30

DNA

Answer 30

- molecule of heredity - polymer of nucleotides (ntds) - deoxyribonucleotides

Question 31

RNA

Answer 31

- polymer of ribonucleotides many fxns: - info transmission - translation - splicing - gene regulation

Question 32

draw the basic structure of a nucleotide, define what each carbon is for, identify the directionality and the base stacking

Answer 32

1. Pi = inorganic PO4- 2. SC = sugar = ribose 3. 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

Question 33

pyrimidines and purines and the complementary base pairing rule

Answer 33

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

Question 34

What is a phosphodiester bond?

Answer 34

- monomers joined in a sugar-phosphate backbone

Question 35

Why is RNA single stranded?

Answer 35

- 2' OH makes helix more open - 2' OH makes RNA more reactive so it can base pair with: itself, other RNA and DNA