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BIOL 107 > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q

What elements makeup DNA?

A

carbon, hydrogen, oxygen, phosphorus, nitrogen

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2
Q

What elements make up protein?

A

carbon, hydrogen, oxygen, sulfur, nitrogen

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3
Q

Why is water a requirement of life?

A

-it is the solvent of life (universal solvent)

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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)
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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
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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.

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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.

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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.

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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.

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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.

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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

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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)
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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

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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

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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
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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

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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
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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)
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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)
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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)

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21
Q

Disaccharides

A
  • formed by a covalent bond between monosaccharides

eg: sucrose is a disaccharide of glucose and fructose

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22
Q

Structural Isomers

A

-they have the same molecular formula, but different structures

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23
Q

What type of bond is formed between sugars?

A
  • glyosidic bond

- is a type of covalent bind formed between sugars

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24
Q

Polysaccharides

A
  • are polymers of monosaccharides

- examples: starch, glycogen, cellulose, chitin

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25
Q

Starch

A
  • is a natural, nutritious polysaccharide and is a polymer of glucose
  • contains an alpha 1, 4 glyosidic bond
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26
Q

Glycogen

A
  • nutritional polysaccharide

- polymer of glucose that is highly branched

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27
Q

What is starch used for?

A

-function is energy storage in plants

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28
Q

What is glycogen used for?

A
  • 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
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29
Q

Cellulose

A
  • is a structural polysaccharide
  • polymer of glucose
  • contains a beta 1, 4 glycosidic bond
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30
Q

What is cellulose used for?

A

-function is forming the plant cell wall

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31
Q

Why can’t humans digest cellulose?

A
  • 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
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32
Q

What is the structural difference between cellulose and starch and why does it exist?

A
  • alpha bonds in starch forces all the OHs to point in the same direction
  • beta bonds in cellulose causes glucose to alternate orientations
33
Q

Chitin

A

-a structural polysaccharide (polymers of monosaccharides)

34
Q

Where is chitin found in?

A
  • insect exoskeleton

- fungal cell wall

35
Q

What characteristics classifies something as a lipid?

A
  • 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
Q

Why are lipids not true polymers?

A

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
Q

What are examples of lipids?

A

Fatty Acids, Fats, Phospholipids, Steroids

38
Q

Fatty Acids

A
  • 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
Q

Saturated Fatty Acid

A

-composed of only carbon-carbon single bonds

40
Q

Unsaturated Fatty Acid

A

-carbon-carbon double bonds cause a kink in the fatty acid tail (bend in the chain)

41
Q

What is a triglyceride and its structure

A
  • is animal fat

- consists of a glycerol backbone with 3 fatty acids attached (one on each carbon through an ester linkage)

42
Q

What is the function of a triglyceride?

A

energy storage, insulation

43
Q

Phospholipid function

A

-structural component of the biological cell membrane

44
Q

Phospholipid structure

A
  • 2 HC chains attached to a glycerol backbone via ester linkages
  • phosphate group attached to the 3rd C of glycerol
45
Q

Characteristics of Phospholipids

A
  • 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
Q

Amphipathic

A
  • to have both hydrophilic and hydrophobic domains

eg: phospholipids

47
Q

Steroid structure

A
  • 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
Q

What are the two major functions of steroids

A
  1. Hormones-eg: estrogen/ testosterone

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

49
Q

What are proteins?

A
  • they are polymers of amino aid monomers (there are 20 possible amino acid monomers)
  • are involved in every biological task
50
Q

What is the structure of amino acids?

A

-composed of an amino acid backbone (all amino acids have same backbone) and a variable group

51
Q

What are the characteristics of the amino acid backbone in amino acids?

A
  • 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
Q

What is the main characteristic of the variable group?

A

-it provides functional diversity

53
Q

What are the 4 different R groups that exist?

A
  • Non-polar (CH)
  • Polar Uncharged (OH, -SH)
  • Polar Charged Acid (COO-)
  • Polar Charged Basic (NH3+)
54
Q

How do we classify amino acids?

A

Ignore the amino acid backbone and use the R groups to classify

55
Q

What is the directionality of an amino acid chain?

A
  • 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
Q

Where are amino acids polymerized and during what process?

A

-during translation at the ribosome

57
Q

How are amino acids linked?

A
  • 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
Q

Primary Structure of Proteins

A
  • 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
Q

Secondary Structure of Proteins

A
  • 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
Q

What is a special property of B pleated sheets

A
  • 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
Q

Tertiary Structure of Proteins

A

-3D pattern of folding for proteins

62
Q

What is the driving force of folding?

A

-hydrophobic interactions of nonpolar R groups drive amino acids away from water and into the middle of the protein

63
Q

What are the forces that maintain the tertiary structure (ranked from strongest to weakest)

A
  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
Q

Quaternary Structure

A
  • 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
Q

Chaperones

A
  • proteins that assist in the folding of other proteins

eg: bacterial chaperonin (the “molecular changing room”), heat shock proteins

66
Q

Why is proper protein folding essential?

A
  • 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
Q

What is the function of nucleic acids?

A
  • store and transmit hereditary information

- DNA, RNA

68
Q

What is DNA?

A
  • 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
Q

What is RNA?

A
  • transmits information within the cell (from nucleus to cytoplasm to be used)
  • polymer of ribonucleotides
70
Q

List the functions of RNA

A
  • information=mRNA
  • translation=tRNA, rRNA
  • regulation=siRNA and miRNA
  • splicing=snRNA
71
Q

What is the basic structure of a nucleotide?

A
  • 5C sugar=ribose
  • nitrogenous base
  • phosphate
72
Q

Name the functions of all the carbons on a nucleotide

A
  • C1= attach to base
  • C2= DNA (no OH), RNA (OH)
  • C3=OH (essential for polymerization)
  • C4= nothing
  • C5= attaches to phosphate
73
Q

What are the pyrimidines?

A
  • single ringed bases (ntds)

eg: cytosine, thymine, uracil (RNA only)

74
Q

What are the purines?

A
  • double ringed bases (ntds)

- eg: adenine, guanine

75
Q

What is the directionality of a nucleotide

A
  • 5 prime to 3 prime (because polymerization happens on carbon 3)
76
Q

What is the directionality of a nucleic acid?

A
  • 5 prime to 3 prime (directionality is preserved in polymer)
  • monomers are joined into sugar-phosphate backbone by phosphodiester linkages (negative charge)
77
Q

Describe the general structure of DNA?

A
  • 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
Q

What are the complimentary based pairings and why are they important?

A
  • 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
Q

Describe the general structure of RNA

A
  • 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

BIOL 107 (3 decks)

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