Lecture 2 - Chemical Bonds and Macromolecules Flashcards
1
Q
DNA contains which elements
A
C,H,O,P,N
2
Q
Protein contains which elements
A
C,H,O,S,N
3
Q
Fat contains which elements
A
C,H,O
4
Q
Sugars contains which elements
A
C,H,O
5
Q
life is dominated by compounds composed of what
A
CHOPSN, ions, and trace elements
6
Q
polar
A
unequal distribution of e- across a covalent bond
7
Q
why is water polar
A
oxygen is highly electronegative and pulls electrons towards the oxygen side and away from hydrogen side
8
Q
H - bond
A
if H is in a dipole-dipole interaction then it is considered a hydrogen bond
weak bond but is common and when many H - bonds present becomes strong
9
Q
dipole-dipole bond
A
attraction between the - end and + end of two polar molecules
10
Q
how does waters polarity affect it
A
water can associate with other water molecules or any polar molecule
non-polar molecules will aggregate away from water (oil in water)
11
Q
covalent bond
A
electrons shared between two non-metals. this is a strong bond
12
Q
ionic bond
A
electrons are “stolen” from one atom and “given” from another atom. this is a strong bond
13
Q
van der waals
A
transient interaction of induced dipoles (when e- happen to be clustered on one side of the atom) and becomes momentarily polar
This is a very weak bond
14
Q
organic macromolecules contain
A
C and H
C is the backbone of organic molecules
15
Q
why is life carbon based (3 reasons)
A
- carbon can bind to 4 other atoms
- carbon can bind to other carbons
- carbon can form double and triple bonds (with itself)
this allows for molecular diversity
16
Q
monomer
A
single unit - single building blocks of molecules
17
Q
polymer
A
chain of monomers containing similar or identical subunits
18
Q
synthesis
A
AKA condensation or dehydration reactions
- monomers are added to a growing chain
- requires input of energy
- water is a product
19
Q
hydrolysis reactions
A
- breaking covalent bonds between polymers
- water is a reactant
- releases energy
20
Q
carbohydrates
A
AKA polysaccarides or sugars
-for energy, storage, cell structure, and cell-cell recognition
21
Q
carbohydrates monomers
A
- multiples of CH2O
- Can have a C chain of 3-7 long
- can be linear or ring shaped
ex: glucose, fructose, galactose
22
Q
glucose
A
monomer of carbohydrates / monosaccharide
ring shape
OH and H are functional groups that link glucose together
23
Q
disaccharides
A
formed by covalent bonds between two monosaccharides
EX: sucrose - nutritional disacc.
-made of glucose and fructose
24
Q
structural isomer
A
two or more molecules that have the same number of each atom, but have different structures
ex: glucose and fructose
25
glycosidic bond
a bond between two monomers of carbohydrate or sugar monomers
ex: bond between glucose and fructose in sucrose
26
what forms a glycosidic bond?
a condensation/dehydration/synthesis reaction
27
what does glucose looks like
5 C is numbered as so
|
4⬠ 1
3 2
28
polysaccharides
polymers of monosaccharides held together by glycosidic bonds
Ex: starch
29
Starch
nutritional polysaccharide
polymer of glucose
contains α glucose which makes α 1-4 glycosidic bonds (bonds C1 and C4 together)
storage form of energy for plants (like potatoes!🍠)
somewhat branched
30
glycogen
nutritional polysaccharide
energy storage in animals
polymer of glucose with α bonds that is highly branched because of α 1-6 bonds
broken down (metabolized) in liver and released in blood during fasting
stored in the muscles to fuel muscle contraction
31
cellulose
structural polysaccharide
polymer of β glucose
contains β 1-4 glycosidic bonds
BBBB - bacteria break β bonds (only bacterial enzymes can break β bonds)
32
β bonds vs α bonds
α bonds- OH groups all align the same direction
β bonds- OH groups alternate up and down
assuming they are oriented and bonded in the same way (ex all 1-4 bonds)
33
Chitin
structural polysaccharide in insects + fungi
- polymer of monosaccharides
- create insect cytoskeleton
34
Lipids
fats and are not true polymers
| classified as a lipid if they are hydrophobic
35
Hydrophobic
-fear water
-aggregate away from water
-non-polar
-in lipids, H and C are equally shared b/c H and C are weakly electronegative
∴no dipoles, non-polar
36
fatty acids
lipids of single chains of HC with a COOH (carboxylic acid) end
can esterify to attach to a 3C glycerol backbone
37
esterify
the process of two reactants forming an ester bond
typically a COOH and OH bond to form
O
|| + water
O–C
AKA carboxylic acid and alcohol group undergo a dehydration reaction to produce an ester bond
38
glycerol
the backbone of fats, or specifically triacylglycerol / triglyceride
39
fats
triacylglycerol/triglyceride
energy storage and insulation in animals
can be saturated or unsaturated
made of a 3C glycerol backbone and 3 fatty acid tails, ester bonded together
40
Saturated fats
no double bond C═C
3 fatty acid tails are straight
animal fat
41
unsaturated fats
contains a double bond C═C which forms kink in the fatty acid tails chain
in plant fats
in cis
42
in cis
means when the carbon chain is bent due to a double bond C═C
43
phospholipids
structural component of the cell membrane
phosphate head connected to a glycerol with two fatty acid tails
amphipathic
44
amphipathic
having both hydrophilic and hydrophobic parts
45
steroids
```
a class of lipids based on cholesterol
characterized by a backbone of 4 fused HC rings
have a small polar functional group, but overall hydrophobic
Function: hormones and membrane integrity
```
46
Proteins
polymers of amino acids
| proteins are involved in every biological task
47
amino acid
monomer of proteins
| 20 biologically relevant amino acid
48
appearance of amino acids
```
_________R
_________|
NH3+ -------C-------COO-
_________|
_________H
```
49
R
variable group
| can have multiple different "things" elements, etc. in that spot
50
Variable group in amino acids
1) non-polar - mostly H+C
2) polar uncharged - contains -OH
3) polar charged acidic (-) - contains COO-
4) polar charged basic (+) - contains NH3+
51
Structure of Proteins
proteins function in 3D form but are synthesized as linear polypeptides
4 degrees of structure
!!primary structure dictates folding, folding dictates function!!
52
polymerization
Polymerization, any process in which monomers, combine chemically to produce a polymer.
53
translation
The process in living cells in which the genetic information encoded in messenger RNA (mRNA) in the form of a sequence of nucleotide triplets (codons) is translated into a sequence of amino acids in a polypeptide chain during protein synthesis. Translation takes place on ribosomes in the cell cytoplasm.
54
1º
Primary structure-polymerization of amino acids
Determined by the sequence of DNA (in genes)
formed by peptide bonds that link amino acids together
55
peptide bonds
```
bonds that link together amino acids
δ-
O
॥
C—N
........|
.......H δ+
```
56
directionality in polymer and monomer
- amino acids connects N to C ends
| - amino acids each have a C and N end
57
amino terminus
the N or NH₃ end of the amino acid
58
carboxyl terminus
the COO- end of the amino acid
59
2º
secondary structure
interaction between the backbones of the polypeptide chain (R groups do not stabilize folding, only drive it!)
-local folding of the amino acid chain into either 𝝰 helix or β sheet
-R group interactions drive folding
-2 structure is stabilized by H bonds between amino acid backbones
60
3º
tertiary structure
| hydrophobic interactions of non-polar R groups drive the amino acids away from water and into the middle of the protein
61
What forces maintain the 3º structure?
4 interactions between R groups
1. covalent bonds between 2 cysteine a.a.
2. ionic bonds between oppositely charged a.a.
3. hydrophobic interactions between non-polar a.a.
4. hydrogen bonds between polar uncharged a.a.
62
4º
quaternary structure
not all proteins have 4º
some folded peptides form multi subunit complexes
4º held together by the same forces that stabilize 3º
63
peptide
Any of a group of organic compounds comprising two or more amino acids linked by peptide bonds. Used to describe proteins that do not have their full structure (usually either incomplete in being made, or are being broken down in digestion)
64
what are chaperones?
proteins that assist in the folding of other proteins
65
why are chaperones important?
proper folding is essential to protein function
chaperones can target misfolded proteins for degradation
diseases can arise from incorrect protein folding
66
What are some diseases of incorrect protein folding and how can they arise?
Can be by mutation (heritable) or spontaneous or chaperone function disorders
(misfolded proteins can aggregate and cause cell death)
-madcow/creutzfeld-Jacob
-alzheimers
-parkinsons
-Huntington's
-sickle cell anemia
67
Why might misfolded proteins aggregate?
There are hydrophobic components on the outside and hydrophobic substances will aggregate in water
68
nucleic acids
store and transmit hereditary information
RNA - transmits info within the cell
DNA - transmits info to next cell generation
69
DNA
polymer of deoxyribose nucleotides (dNTD)
DNA nucleotides (ntds) are deoxygenated @ C₂ of ribose sugar
DNA genome contains all info essential for life
70
RNA
```
polymer of ribonucleotides
Functions:
-information (mRNA)
-splicing (snRNA)
-regulation (siRNA and miRNA)
```
71
structure of nucleotides includes...
- 5C ribose sugar
- nitrogenous base
- phosphate (PO₄⁻⁻)
72
What are the nitrogenous bases and how are they grouped?
cytosine, thymine, uracil, adenine, guanine
| purines and pyrimidines
73
Which nitrogenous bases are used for DNA vs RNA
DNA : A - T, G - C
| RNA: A - U, C - G
74
Purines are?
double ringed nitrogenous bases
| A and G
75
Pyrimidines are?
single ringed nitrogenous bases
| U, T, C
76
role of C's in ribose
1: attaches the base
2: OH in RNA, H in DNA
3: OH
4: boring/H
5: phosphate attached
77
directionality of DNA
5' to 3'
the C3 and C5 join for the direction
bonded using phosphodiester bonds
78
phosphodiester bond
The covalent bond that links a phosphate group and a sugar group, by means of an oxygen bridge, in the sugar-phosphate backbone of a nucleic acid molecule.
79
Why is RNA single stranded?
- 2OH makes helix more open / more reactive b/c it will interact with water
- RNA can make a base pair with itself, with other RNA or with DNA
80
How do base pairs pair together and why?
C㆔G aka they triple H bond
A═T (or U) aka they double H bond
Purine and pyrimidines always pair together to maintain the diameter of the DNA helix
H bonds give base pairing specificity
