Lecture 2 Flashcards
1
Q
What elements makeup DNA?
A
carbon, hydrogen, oxygen, phosphorus, nitrogen
2
Q
What elements make up protein?
A
carbon, hydrogen, oxygen, sulfur, nitrogen
3
Q
Why is water a requirement of life?
A
-it is the solvent of life (universal solvent)
4
Q
What chemical properties of water allow it to be a universal solvent?
A
- water is polar, meaning that there is an unequal distribution of electrons across the bond where electrons sit loser to oxygen than hydrogen-creates a dipole
- therefore anything with a charge/dipole interacts well with water (like dissolves like)
5
Q
Why does water have high boiling points and low freezing points?
A
- Water can associate with other water molecules because opposite charges attract-positive hydrogen interacts with negative oxygen creating a hydrogen bond
- many hydrogen bonds stabilize the molecule
6
Q
What happens when nonpolar molecules are mixed with water?
A
They will not form favorable interactions with water, they will aggregate and clump together away from water.
7
Q
What is a covalent bond and what is its relative bond strength?
A
A covalent bond is one where electrons are shared. It forms a strong bond.
8
Q
What is an ionic bond and what is its relative bond strength?
A
An ionic bond is one where electrons from one atom is fully dissociated from that atom. It forms a strong bond.
9
Q
What is a hydrogen bond and what is its relative bond strength.
A
A hydrogen bond is one where hydrogen is involved in dipole-dipole interactions. It forms a weak bond but there is strength in numbers.
10
Q
What is a Van der waals bond and what is its relative bond strength?
A
A bond with transient interactions of charges. When electrons move around atoms sometimes a temporary dipole is formed and dipole-dipole interactions can occur. The likelihood of this happening increases with mass and electron number. It forms a weak bond.
11
Q
How an you tell if something is an organic macromolecule?
A
- It will contain a carbon-hydrogen bond
- carbon is the backbone of organic molecules
12
Q
Why is life carbon based?
A
- carbon can bond to 4 other atoms (can have more diversity)
- can bond to form carbon-carbon chains (can have long, complex molecules)
- carbon an form double and triple bonds (can have more diversity)
13
Q
What other element could be a potential backbone to life?
A
Silicon-because it has the same properties, so it could potentially be a backbone to life-it just has more molecular weight
14
Q
What is a monomer?
A
It is a single building block of a macromolecule eg: DNA is composed of A, T, G, C
15
Q
What is a polymer?
A
- It is a chain of monomers composed of similar but non-identical subunits eg: a molecule of DNA
- must be built up broken down by the cell
16
Q
Why are polymers more biologically important than monomers?
A
They allow for variation to promote biological diversity eg: with DNA having 4 nucleotides and proteins being made of 20 amino acids, in combination you can get endless/ infinite diversity
17
Q
Condensation/ Dehydration Reaction
A
- synthesis reaction
- add monomers to a growing chain (functionally have two sides that can react and form a covalent bond)
- water is a product
- needs energy
eg: used in DNA replication
18
Q
Hydrolysis Reaction
A
- breakdown reaction
- cleavage of covalent bonds between monomers in a polymer
- water is a reactant
- releases energy (because breaks bond)
19
Q
Function and Structure of Carbohydrates
A
- used in energy storage
- used in cell-cell recognition (found on outer membrane and helps identify us-blood type based on the sugar you present on your red blood cells)
- cell structure (plant cell wall has cellulose-sugar)
20
Q
Monosaccharides
A
-monomers of carbohydrates
-multiples of CH2O
-can have a C chain of 3-7 C long
can be linear/ ring shaped
eg: glucose (main energy source of the cell and is broken down by respiration)
21
Q
Disaccharides
A
- formed by a covalent bond between monosaccharides
eg: sucrose is a disaccharide of glucose and fructose
22
Q
Structural Isomers
A
-they have the same molecular formula, but different structures
23
Q
What type of bond is formed between sugars?
A
- glyosidic bond
- is a type of covalent bind formed between sugars
24
Q
Polysaccharides
A
- are polymers of monosaccharides
- examples: starch, glycogen, cellulose, chitin
25
Starch
- is a natural, nutritious polysaccharide and is a polymer of glucose
- contains an alpha 1, 4 glyosidic bond
26
Glycogen
- nutritional polysaccharide
| - polymer of glucose that is highly branched
27
What is starch used for?
-function is energy storage in plants
28
What is glycogen used for?
- function is energy storage in animals (we store access sugar in long chains for later use)
- broken down and released from liver into the blood as glucose during fasting
- used by all cells (especially for muscle contraction and powering brain)-but not used by red blood cells
29
Cellulose
- is a structural polysaccharide
- polymer of glucose
- contains a beta 1, 4 glycosidic bond
30
What is cellulose used for?
-function is forming the plant cell wall
31
Why can't humans digest cellulose?
- only bacteria can hydrolyze the B 1, 4 bond and make methane, since humans don't host bacteria we cannot metabolize the bond and get energy out of cellulose
- other animals like cows and goats host bacteria that can break down cellulose for them
32
What is the structural difference between cellulose and starch and why does it exist?
- alpha bonds in starch forces all the OHs to point in the same direction
- beta bonds in cellulose causes glucose to alternate orientations
33
Chitin
-a structural polysaccharide (polymers of monosaccharides)
34
Where is chitin found in?
- insect exoskeleton
| - fungal cell wall
35
What characteristics classifies something as a lipid?
- being hydrophobic (non-polar and aggregate away from water, are highly attracted to themselves)
- made of mostly hydrocarbons (H-C) (H and C are both equally weakly electronegative, therefore the electrons sit in the middle and there are no dipoles formed)
- made by life
36
Why are lipids not true polymers?
Because they don't actually form bonds between monomers (in fact, they have no true monomers-come in diverse forms), they just clump up with similar fat molecules instead of interacting with water
37
What are examples of lipids?
Fatty Acids, Fats, Phospholipids, Steroids
38
Fatty Acids
- single chains of mostly HC, with a COOH at the end
- usually 16-18 carbons long
- can attach (esterify) to a glycerol backbone (3 carbon chain that acts as an anchoring/attachment point for fatty acids
- an be saturated/ unsaturated
39
Saturated Fatty Acid
-composed of only carbon-carbon single bonds
40
Unsaturated Fatty Acid
-carbon-carbon double bonds cause a kink in the fatty acid tail (bend in the chain)
41
What is a triglyceride and its structure
- is animal fat
| - consists of a glycerol backbone with 3 fatty acids attached (one on each carbon through an ester linkage)
42
What is the function of a triglyceride?
energy storage, insulation
43
Phospholipid function
-structural component of the biological cell membrane
44
Phospholipid structure
- 2 HC chains attached to a glycerol backbone via ester linkages
- phosphate group attached to the 3rd C of glycerol
45
Characteristics of Phospholipids
- phosphate head carries a negative charge, therefore it is polar and hydrophilic (attracted towards water)
- fatty acid tail is nonpolar and hydrophobic (pulled away from water)
46
Amphipathic
- to have both hydrophilic and hydrophobic domains
| eg: phospholipids
47
Steroid structure
- is a class of lipids based on cholesterol-cholesterol is backbone, if you add functional groups you get different molecules
- characterized by 4 fused HC rings with a small polar functional group (has small polar character but overall is hydrophobic)
48
What are the two major functions of steroids
1. Hormones-eg: estrogen/ testosterone
| 2. In animals, cholesterol sits in plasma membrane to maintain membrane fluidity and increase stiffness
49
What are proteins?
- they are polymers of amino aid monomers (there are 20 possible amino acid monomers)
- are involved in every biological task
50
What is the structure of amino acids?
-composed of an amino acid backbone (all amino acids have same backbone) and a variable group
51
What are the characteristics of the amino acid backbone in amino acids?
- consists of an amino group on one end and a carboxy group on the other (these groups are reactive and therefore are able to extend the amino acid)
- both groups carry charges at a pH of 7
- amino group has a positive charge, carboxylic acid has a negative charge
52
What is the main characteristic of the variable group?
-it provides functional diversity
53
What are the 4 different R groups that exist?
- Non-polar (CH)
- Polar Uncharged (OH, -SH)
- Polar Charged Acid (COO-)
- Polar Charged Basic (NH3+)
54
How do we classify amino acids?
Ignore the amino acid backbone and use the R groups to classify
55
What is the directionality of an amino acid chain?
- Amino group to carboxy group (N to C)
- amino acids are added to the carboxy side always
- always linked "head to tail" (can keep adding more blocks infinitely)
56
Where are amino acids polymerized and during what process?
-during translation at the ribosome
57
How are amino acids linked?
- they are covalently linked by a peptide bond connecting the carboxy end of one amino acid and the amino end of another
- R groups are not involved in polymerization
58
Primary Structure of Proteins
- determined by the sequence of DNA (in genes)
- involves the polymerization of amino acids to form a primary sequence (which is written and translated N to C at the ribosome)
- primary structure dictates folding, folding (shape) dictates function)
59
Secondary Structure of Proteins
- the local folding of amino acid chain into either an alpha helix or beta sheets
- interactions between the amino acid backbones of the peptide chain through hydrogen bonds stabilize the structure
- R groups are not involved in stabilizing the secondary structure
- is a spontaneous process
60
What is a special property of B pleated sheets
- is fully stretched out
| - silk is made out of a protein that is a B sheet, silk is the strongest material because it is un-stretchable
61
Tertiary Structure of Proteins
-3D pattern of folding for proteins
62
What is the driving force of folding?
-hydrophobic interactions of nonpolar R groups drive amino acids away from water and into the middle of the protein
63
What are the forces that maintain the tertiary structure (ranked from strongest to weakest)
1. covalent bonds-disulfide bridges between 2 cysteines (rare-found in proteins released outside the cell, not usually inside)
2. ionic bonds- between oppositely charged amino acids
3. hydrophobic interactions between nonpolar amino acids
4. hydrogen bonds-between polar uncharged amino acids
64
Quaternary Structure
- some proteins form multicellular complexes that create a functional protein
- is held together by the same forces as a tertiary structure
eg: collagen and hemoglobin
65
Chaperones
- proteins that assist in the folding of other proteins
| eg: bacterial chaperonin (the "molecular changing room"), heat shock proteins
66
Why is proper protein folding essential?
- misfolded proteins aggregate in cell and cause cell death
| - most impactful in brain because neurons do not regenerate (eg: Parkinson's, Alzheimer's, Mad Cow, Sickle Cell Anemia)
67
What is the function of nucleic acids?
- store and transmit hereditary information
| - DNA, RNA
68
What is DNA?
- is the molecule of heredity and transmits information between cell generations (is more stable than RNA)
- is a polymer of deoxynucleotides
- contains all information essential for life
69
What is RNA?
- transmits information within the cell (from nucleus to cytoplasm to be used)
- polymer of ribonucleotides
70
List the functions of RNA
- information=mRNA
- translation=tRNA, rRNA
- regulation=siRNA and miRNA
- splicing=snRNA
71
What is the basic structure of a nucleotide?
- 5C sugar=ribose
- nitrogenous base
- phosphate
72
Name the functions of all the carbons on a nucleotide
- C1= attach to base
- C2= DNA (no OH), RNA (OH)
- C3=OH (essential for polymerization)
- C4= nothing
- C5= attaches to phosphate
73
What are the pyrimidines?
- single ringed bases (ntds)
| eg: cytosine, thymine, uracil (RNA only)
74
What are the purines?
- double ringed bases (ntds)
| - eg: adenine, guanine
75
What is the directionality of a nucleotide
- 5 prime to 3 prime (because polymerization happens on carbon 3)
76
What is the directionality of a nucleic acid?
- 5 prime to 3 prime (directionality is preserved in polymer)
- monomers are joined into sugar-phosphate backbone by phosphodiester linkages (negative charge)
77
Describe the general structure of DNA?
- forms a double helix with bases pointing in
- complimentary based pairing
- DNA helix is antipararellel (5 prime to 3 prime on one side and 3 prime to 5 prime on the other)
78
What are the complimentary based pairings and why are they important?
- A is paired with T (2 hydrogen bonds)
- C is paired with G (3 hydrogen bonds)
- purines always pair with pyrimidines to maintain the diameter of the helix
79
Describe the general structure of RNA
- is single stranded
- the OH on the second carbon makes the helix more open and more reactive, therefore it is free to base pair with itself, other RNA, or DNA
- it could be double stranded, but is more stable single stranded
