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Bio 131 Exam 2 > Wk3 Lecture 1 Ch 3.1, 3.2, 3.3, 4.1, 5 > Flashcards

Wk3 Lecture 1 Ch 3.1, 3.2, 3.3, 4.1, 5 Flashcards

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1
Q

What are the 4 major types of organic molecules/macromolecules?

A
  1. Carbohydrates
  2. Lipids
  3. Proteins
  4. Nucleic Acids
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2
Q

What are the 5 main protein functions?

A
  1. Enzymes
  2. Structural
  3. Transport
  4. Protection
  5. Informational
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3
Q

What are the building blocks/monomers of proteins?

A

Amino Acids

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4
Q

How many amino acids are there?

A

20

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5
Q

What is a peptide?

A

Protein polymer; a compound composed of >2 amino acids

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6
Q

What is a polypeptide?

A

Protein polymer; a compound composed of >50 amino acids

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7
Q

What is the common chemical structure of all amino acids?

A

An amino group, carboxyl group, and a distinct side chain (R group) attached to a central carbon w/ a hydrogen atom

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8
Q

What happens to amino acids in water (pH=7)?

A

Amino acids ionize; amino and carboxyl groups ionize to NH3+ and COO- (net charge 0), respectively

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9
Q

Why are the charges on the functional groups of amino acids in water important?

A
  1. They help amino acids stay in solution
  2. Makes amino acids more reactive
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10
Q

What are the 4 general types of amino acid side chains?

A
  1. Acidic
  2. Basic
  3. Uncharged polar
  4. Nonpolar
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11
Q

How do you determine amino acid type? (4 questions)

A
  1. Does the side chain have a NEGATIVE charge?
    If yes, proton was lost => ACIDIC
  2. Does the side chain have a POSITIVE charge?
    If yes, proton was gained => BASIC
  3. If uncharged, does side chain have an OXYGEN atom?
    If yes, highly electronegative oxygen will result in polar covalent bond => UNCHARGED POLAR
  4. If no to all questions
    => NONPOLAR
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12
Q

What are the 3 special amino acids?

A
  1. Glycine
  2. Proline
  3. Cysteine
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13
Q

Why is glycine a special amino acid?

A

Only has H- as a side chain => smallest amino acid
Fits well in stretches of polar and non-polar amino acids, and is often at sites of protein-protein interactions

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14
Q

Why is proline a special amino acid?

A

Introduces bends and kinks in a peptides secondary structure (2 deg) => contorts basic tetrahedral structure

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15
Q

Why is cysteine a special amino acid?

A

It is the only amino acid that contains sulfur => used to form disulfide bonds/bridges (covalent) w/ another cysteine residue, which is one of the strongest ways to link amino acids

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16
Q

How do amino acids polymerize?

A

Peptide bonds = > DEHYDRATION SYNTHESIS between carboxyl group of one amino acid and amino group of a second amino acid

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17
Q

Why are peptide bonds so stable compared to other monomer linkages in other types of macromolecules? (textbook info)

A

The degree of electron sharing within peptide bonds is great enough that they have some of the characteristics of a double bond

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18
Q

What is a residue? (textbook info)

A

When amino acids are linked by peptide bonds into a chain; distinguishes them from free amino acid monomers

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19
Q

What are the 3 key characteristics of a peptide-bonded backbone?

A
  1. R-GROUP ORIENTATION: the side chains extend out from the backbone => they can interact w/ each other and water
  2. DIRECTIONALITY: backbones have an amino group (NH3+) and a carboxyl group (COO-) on each end; => biologists write amino acid residue sequences from N to C
  3. FLEXIBILITY: peptide bond cannot rotate b/c it acts like double bond, but single bonds on either side of peptide bond can rotate => structure is overall flexible
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20
Q

Why do proteins serve diverse functions?

A

They have diverse structure, which determines function:
diversity in size/shape, diversity in chemical properties of their amino acids

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21
Q

What are the 4 levels of protein structure?

A
  1. Primary structure (1 deg)
  2. Secondary structure (2 deg)
  3. Tertiary structure (3 deg)
  4. Quaternary structure (4 deg)
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22
Q

What is the primary structure of an amino acid?

A

Unique amino acid sequence that is encoded directly by genes; fundamental to function and higher levels of protein structure

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23
Q

What is the secondary structure of an amino acid?

A

Formation of alpha helices and beta pleated sheets in a polypeptide; when a polypeptide bends in a way that puts carbonyl and amino groups close together for hydrogen bonding

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24
Q

What are the two secondary structures of an amino acid? What determines the diameter of a secondary structure?

A
  1. Alpha helix (coiled backbone)
  2. Beta pleated sheet (segments of peptide chain bend 180 deg and fold in same plane)

Distance b/t amino acids determine diameter

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25
What is the tertiary structure of an amino acid?
A protein's distinctive overall 3-D shape that results from interactions b/t residues that are brought together as the backbone bends and folds in space
26
What 3 things is protein folding of a tertiary structure driven by?
1. Total sequence 2. Interaction w/in a molecule 3. Interaction b/t molecule and solution
27
What is the difference b/t a cytosolic and membrane protein?
Cytosolic proteins have a hydrophobic amino acid core and hydrophilic amino acids on the exterior => not part of membrane Membrane proteins have hydrophilic amino acids outside the membrane (both sides) and hydrophobic amino acids inside the membrane => part of membrane
28
What 5 factors promote protein folding and stability?
1. Hydrogen bond: b/t side chain and carbonyl group on backbone 2. Hydrogen bond: b/t 2 side chains 3. Hydrophobic interactions + van der Waals interactions 4. Covalent bonding: disulfide bridges b/t 2 cysteines 5. Ionic bonding: form b/t groups that have full and opposing charges
29
What is the quaternary structure of a protein?
The shape produced by combinations of polypeptides (combinations of tertiary structures); can be same protein monomer or multimeric (different polypeptides)
30
Summary of protein structure
Protein structure is hierarchal -Quaternary based on tertiary, which is partly based on secondary -ALL based on primary Combined effects of all structures (final protein structure) allow for amazing diversity in protein form and function
31
What are the 3 main things that nucleic acids are responsible for?
1. Storage 2. Expression 3. Transmission of genetic information (they do more though)
32
What are the two classes of nucleic acids?
1. Deoxyribonucleic acid (DNA) 2. Ribonucleic acid (RNA)
33
What does DNA do?
Stores genetic info encoded in the sequence of nucleotide monomers
34
What does RNA do?
Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain (protein)
35
What are the monomers of nucleic acids?
Nucleotides
36
What 3 things are nucleotides composed of?
1. Phosphate group 2. 5 carbon sugar (4 carbon ring, 5th carbon is bonded to phosphate as substituent) 3. A single or double ring of carbon and nitrogen atoms known as a (nitrogenous) base Phosphate group is bonded to the sugar, which is bonded to the base
37
How to distinguish between RNA and DNA?
Look at second carbon of sugar -If there is hydroxy group => RNA -If there is no hydroxy group => DNA
38
What are the 5 nitrogenous bases for nucleotides?
Pyrimidines => Cytosine, Uracil, and Thymine Purines => Guanine and Adenine (double rings)
39
How do ribonucleotides and deoxyribonucleotides differ in nitrogenous bases?
RNA has Uracil and DNA has Thymine; they share the rest
40
Acronyms for remembering nitrogenous bases
CUT the PY PURe As Gold
41
How many different nucleotides are used to build nucleic acids? (textbook info)
8 => 4 ribonucletoides (A, G, C, and U) and 4 deoxyribonucleotides (A, G, C, and T)
42
How do nucleotides polymerize to form nucleic acids?
Phosphodiester linkage => DEHYDRATION SYNTHESIS b/t hydroxyl on the sugar of one nucleotide and phosphate group of a second nucleotide
43
What is ATP and what does it consist of?
ATP is a nucleotide (mother function is energy storage) that consists of 3 phosphate groups, ribose, and adenine
44
What does the phrase, "the sugar phosphate backbone of a nucleic acid is directional," mean?
One end has an unlinked 5' carbon and the other end has an unlinked 3' carbon => nucleotides are only added at the 3' end of a growing nucleic acid molecule => nucleotide sequence is written in the 5' to 3' direction
45
What is a carbohydrate (glycan)?
A macromolecule, also known as a sugar, composed of carbon, hydrogen, and oxygen atoms
46
What is the molecular formula for a carbohydrate?
Cn(H2O)n
47
What are the monomers of carbohydrates?
Monosaccharides
48
What structures do carbohydrate molecules take on and prefer?
They can exist as straight chains or rings, but rings are more common b/c they are more stable as rings in water
49
Why do carbohydrates dissolve so easily in water/aqueous solutions? (textbook info)
They can have carbonyl groups and/or multiple polar hydroxyl groups, which means that even the simplest sugars have many reactive/hydrophilic/polar functional groups
50
Compare glucose (aldose) and fructose (ketose)
Same molecular formula, different arrangement; glucose has an aldehyde at the end of its chain, whereas fructose has a ketone within its chain; glucose is a 6 membered ring and fructose is a 5 membered ring (both have CH2Oh as a substituent for the last carbon)
51
How are sugars named?
Based on the number of carbons -3 carbons => triose -4 carbons => tetrose -5 carbons => pentose -6 carbons => hexose
52
Why is structure of a carbohydrate important? Give an example
Structure determines function (imagine a flipped pencil); glucose and galactose have the same molecular formula, but different spatial arrangement (downward v upward hydroxyl on 4' carbon) Glucose is a fuel source and galactose (more abundant in the body) needs to be converted via enzyme-catalyzed reaction to be used in the same ways
53
How do monosaccharides polymerize to form complex carbohydrates?
Glycosidic linkage => DEHYDRATION SYNTHESIS between two hydroxyl groups resulting in a covalent connection (-O-)
54
Difference between polymerization of amino acids and nucleotides vs monosaccharides (textbook info)
Peptide bonds and phosphodiester linkages form between the same locations in their monomers => proteins and nucleic acids have a standard backbone structure Glycosidic linkages form between hydroxyl groups => every monosaccharide contains at least 2 hydroxyls => location/geometry of glycosidic linkages can vary
55
What is a disaccharide?
When only 2 sugars link together; it is the most common polymerization of monosaccharides
56
What are the 5 main types of polysaccharides?
1. Starch 2. Glycogen 3. Cellulose 4. Chitin 5. Peptidoglycan
57
What is starch?
Plants store sugar as starch It is a mixture of branched (amylopectin) and unbranched (amylose) alpha glucose polymer
58
What is glycogen?
Animals store sugar as glycogen It is a highly branched alpha glucose polymer
59
What is cellulose?
A structural polymer found in plant cell walls It is a polymer of beta glucose monomers
60
What is chitin?
A structural polymer found in fungi cell walls, some algae, and may animal exoskeletons Comprised of N-acetylglucosamine (NAc) monomers
61
What is peptidoglycan?
A structural support for bacterial cell walls It is a backbone of alternating monosaccharides; determines gram positive/negative bacteria
62
What are the 3 main roles of polysaccharides?
1. Energy storage 2. Structure 3. Cellular identity
63
Explain energy storage role of polysaccharides
Many mono/disaccharides form long polymers as both energy source and storage; increased branching permits more rapid glucose release Energy storage as starch or glycogen
64
What are glycosaminoglycans (GAGs)?
Also known as mucopolysaccharides, are complex polysaccharides containing a number of disaccharide repeating units; they can act as mucus and are on the external surface of a cell membrane
65
What are proteoglycans?
GAGs that are linked to a core protein -highly negatively charged - attracts positive ions and water -provide "gel-like" squishiness, lubrication, rubbery texture => critical components of extracellular matrix
66
Explain cellular identity role of a carbohydrate
Carbohydrates can display information on the outer surface of cells in the form of glycoproteins
67
What is a glycoprotein?
A protein linked to carbohydrates; each cell in your body has glycoproteins on its surface Key molecules in... -cell to cell recognition -cell to cell signaling

Bio 131 Exam 2 (5 decks)

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