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Bio 107 > Lecture 2- Chemical Bonds and Macromolecules > Flashcards

Lecture 2- Chemical Bonds and Macromolecules Flashcards

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Biology 101 flashcards
1
Q

Why is water the solvent of life?

A
  • 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
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2
Q

explain the relationship between water and a nonpolar substance

A

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

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3
Q

organic molecules contain __ and ___

A

carbon and hydrogen

  • C is the backbone of organic molecules
  • C is weakly electronegative
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4
Q

Why is life carbon based? List 3 reasons

A
  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

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5
Q

Define monomer

A

“single unit”

single building block of a macromolecule

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6
Q

define polymer

A

“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

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7
Q

why are polymers more biologically important that monomers?

A

they allow for variation to promote biological diversity

  • eg. proteins have 20 amino acids- endless diversity
  • eg. DNA; 4 nucleotides in combination
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8
Q

polymers must be built up/ broken down by the ___

A

cell

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9
Q

synthesis of polymers is done by ____

A

condensation/ dehydration reactions

eg. DNA replication

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10
Q

explain a condensation/ dehydration rxn

A
  • add monomers to a growing chain; formation of covalent bonds
  • water is a product
  • requires energy (building up a polymer!)
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11
Q

the breakdown is polymers is done by a ___ reaction

A

hydrolysis

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12
Q

explain a hydrolysis rxn

A
  • 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!
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13
Q

function and structure of carbohydrates/ polysaccharides/sugars

A
  • energy storage
  • cell structure (cellulose in plant’s cell walls)
  • cell-cell recognition
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14
Q

monomers of carbohydrates

A

CH2O (monosaccharides)

  • monomers have a C chain of 3-7C long
  • can be linear or ring shaped
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15
Q

describe an example of a carbohydrate

A

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
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16
Q

Disaccharides are formed by

A

a covalent bond between monosaccharides

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17
Q

example of a disaccharide

A

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

- structural isomers (same formula, different shape)

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18
Q

bond type in carbohydrates

A

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.

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19
Q

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

A

nutritional
glucose
Function: energy storage in animals

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20
Q

polysaccharides are ____ of _____

A

polymers of monosaccharides

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21
Q

Difference b/w structures of starch vs cellulose

A

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

22
Q

name 4 polymers of glucose and their functions

A
  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
23
Q

True/ False

Lipids/ fats are true polymers

A

False

macromolecule? arguable

24
Q

How to you classify a lipid?

Fxn of lipids?

A

hydrophobic

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

fxn= energy storage and insulation

25
Q

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

A

16-18
COOH
esterify

26
Q

Fatty acids can be saturated or unsaturated. Explain the difference

A

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

27
Q

phospholipids are the structural component of ____

- they are ___(have both hydrophilic and hydrophobic domains)

A

membranes

-amphipathic

28
Q 
Steroids are a class of lipids based on \_\_\_\_\_
- characterized by the backbone of 4 \_\_\_\_ \_\_\_
A

cholesterol

4 fused rings

29
Q

2 major fxns of steroids

A
  1. hormones: eg estrogen, testosterone, progesterone

2. in animals, cholesterol sits in plasma membrane to maintain fluidity and increase membrane stiffness

30
Q

Proteins are polymers of ___ ____

- what’s the directionality?

A

amino acids

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

31
Q

why are amino acids extendible?

ie why is it possible to make the polymer (proteins)

A

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

32
Q

4 possible R (variable) groups of proteins:

A
  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
33
Q

what kind of bond do proteins have?

ie. a.a. are linked covalently by ___ bonds

A

peptide

34
Q

Are R groups involved in polymerization?

What happens to the directionality as the amino acids are polymerized?

A
  • no, R groups are not involved in polymerization

- N to C directionality is maintained in the polymer

35
Q

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

A

It dictates folding (what a.a. in what order?)

*a.a. sequence determines folding and folding dictates function

36
Q

Describe the secondary structure of proteins

A

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
37
Q

characteristics of alpha helix vs beta sheet

A

beta sheet: fully stretched out

alpha helix: coiled region of protein

38
Q

the tertiary structure is the ___ pattern of protein folding

A

3D

39
Q

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

A

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

40
Q

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

A
  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)
41
Q

Describe the quaternary structure.

What forces holds it together?

A
  • 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)
42
Q

____ are proteins that assist in the folding of other proteins

A

chaperones

43
Q

list some examples of human diseases of protein folding

A

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

44
Q

describe the steps of a bacterial chaperonin

A
  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
45
Q

Function of nucleic acids

A
  • store/ transmit heredity info
  • Rna transmits info within cell
  • DNA transmits info b/w cell generations
46
Q

Describe the 2 types of nucleic acids

A
  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
47
Q

Basic structure of a ntd (3 components)

A
  1. 5- carbon sugar = ribose
  2. nitrogenous base
  3. phosphate
48
Q

What does each carbon do in ntds?

A 
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
49
Q

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

A

phosphodiester linkages

  • negatively
50
Q

A and T have ___ H-bonds

G and C have ___ H-bonds

A 
A/T= 2 bonds
C/G= 3 bonds
51
Q

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

A

to maintain the diameter of the helix

52
Q

why is RNA single stranded?

A

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

Bio 107 (12 decks)

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