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lecture 2 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

organic chemistry

A

the study of carbon-containing compounds

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2
Q

biological chemistry

A

the study of the chemistry of living cells, tissues, organs, and organisms

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3
Q

carbon atom

A

valence of 4 electron-form 4 chemical bonds w other atoms
-often form covalent bonds w CHONS

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4
Q

4 types of bonds

A

-covalent
-ionic (electrostatic)
-hydrogen
-van der waals

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5
Q

covalent bonds

A

a bond that is characterized by the sharing of eletrons between atoms

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6
Q

single bond

A

the sharing of one pair of electrons
ex. methane, ethanol, methylamine

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7
Q

double bond

A

the sharing of 2 pairs of electrons
ex. ethylene, carbon dioxide

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8
Q

triple bond

A

the sharing of 3 pairs of electrons
ex. molecular nitrogen, hydrogen cyanide, acetylene

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9
Q

single, double, triple: which of these need the most energy to be broken

A

triple

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10
Q

hydrocarbons

A

when hydrogen atoms are bonded to carbon atoms in linear, branched chains, or in rings
ex. hexane, octane, decane
-insoluble in water

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11
Q

functional groups

A

specific arrangements of atoms that confer characteristics and chemical properties on the molecules to which they are attached.
-usually 1-2 atoms of nitrogen, phosphorous, sulfur

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12
Q

ions

A

atoms/ molecules that are charged because they have gained/ lost an electron/a proton (a hydrogen atom wo its electron

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13
Q

negatively charged ion groups

A

carboxyl
phosphate
=acidic: given up protons

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14
Q

positively charged ion groups

A

amino
=basic: gained a proton

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15
Q

neutral but polar

A

hydroxyl
sulfhydryl
carbonyl
aldehyde
as a whole: no charge at pH values near neutrality
w/in: uneven distribution of charge- the presence of any oxygen/ sulfur atoms bound to carbon/ hydrogen result in a POLAR bond due to unequal sharing of electrons
(bc oxygen and sulfur have higher electronegativity than carbon and hydrogen [+})= when sharing, oxygen and sulfur tend to have more electrons (-)
-higher water solubility & chemical reactivity

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16
Q

oxidation

A

a loss of electrons; involves degradation and releasing of energy
-carbon compounds losing its electrons to molecular oxygen
ex. glucose->carbon dioxide and water

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17
Q

reduction

A

a gain of electrons, biosynthetic and requires energy
ex. carbon dioxide-> glucose

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18
Q

characteristics of water

A

*polarity (uneven distribution of e)
cohesiveness
temperature stabilizing capacity
solvent properties

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19
Q

polarity

A

uneven distribution of charge within the molecule

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20
Q

why is water polar

A

due to the shape of the molecule
-the molecule is bent with two hydrogen atoms to the oxygen at the angle of 104.5
-oxygen atom is electronegative= have 2 pairs of eletrons not shared w H

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21
Q

why is water cohesive

A

due to hydrogen bond (a type of noncovalent interaction; weak bond)
-water has the tendency to form hydrogen bonds between adjacent molecules, which makes water highly cohesive

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22
Q

water cohesiveness accounts for…

A

high surface tension (allows insects to move across the surface of a body of water & allows water to move upward through the conducting tissues of plants)
high boiling point
high specific heat
high heat of vaporization

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23
Q

why does water have high specific heat?

A

due to the hydrogen bonding
-heat and boiling temp are much higher than liquids
-energy is used to break hydrogen bonds between water molecules

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24
Q

why is water a good solvent

A

the water molecule forms an ionic bond (formed by the attraction between opposite charged ions .
-water interacts with ions to form hydration shells to keep ions in solutions

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25
Q

hydrophilic

A

compounds/ solutes that have infinity for water
“water-loving”
ex. sugars, organic acids, certain amino acids
polar & ions

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26
Q

hydrophobic

A

compounds/solutes that are not soluble in water
“water-fearing”
ex.lipids & proteins in biological membranes
non-polar

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27
Q

amphipathic

A

a molecule that has one area of hydrophobic and one area of hydrophilic
ex. phospholipids, detergent molecule

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28
Q

what kind of bond make up the plasmamembrane

A

amphipathic bond \

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29
Q

the head of the phospholipid is

A

hydrophilic

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30
Q

the tail of the phospholipid is

A

hydrophobic

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31
Q

transport protein

A

specialized transmembrane proteins that serve either as a hydrophilic channel

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32
Q

what is the shape of a saturated phospholipid

A

straight

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33
Q

what is the shape of an unsaturated phospholipid

A

bent (water can get thru by hiding in the pockets of the bent angle

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34
Q

liposome

A

a structure that lipids make in water
function: it fuses w water to to deliver molecules “delivery” (2 circles)

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35
Q

micella

A

a structure that lipids make in water
function: solubilize fats
ex.makeup remover, detergent

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36
Q

what forms biological macromolecules?

A

monomers (small organic molecules)

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37
Q

the levels of molecules

A
  1. monomers
  2. macromolecules
  3. supramolecular
  4. organelles
  5. cells

*the macromolecules that are responsible for most of the form and order characteristics of living systems are generated by the polymerization of small organic molecules in long chains.

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38
Q

three types of biological macromolecules

A
  1. polysaccharides
  2. proteins
  3. nucleic acids
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39
Q

basic info of polysaccharides

A

monomer: monosaccharides, glucose
functions: storage, structural
ex. starch, glycogen
cellulose, chitin

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40
Q

basic info of proteins

A

monomer: amino acid (20)
functions: enzymes, hormones, antibodies, carriers, ion channels

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41
Q

basic info of nucleic acids

A

monomer: nucleotides (5)
function: informational
ex. DNA, RNA

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42
Q

What reaction add a monomer

A

condensation (the removable of water)

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43
Q

what reaction remove a monomer

A

hydrolysis (the addition of water)
aka degradation (the breakdown)

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44
Q

what is self-assembly and why is it important

A

self-assembly: a process in which molecules (or parts of molecules) spontaneously form ordered aggregates and involves no human intervention; the interactions involved usually are noncovalent

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45
Q

example of noncovalent bonds in macromolecules

A

hydrogen bonds
ionic bonds
vam der waals interactions
hydrophobic interactions

46
Q

hydrogen bonds

A

weak, attractive interactions between an electronegative atom ( O & N) and a hydrogen atom
*important in maintaining the 3d structure of proteins
* important in holding the 2 strands of DNA double helix

47
Q

ionic bonds

A

strong noncovalent between 2 oppositely charged ions
-form between + groups and - groups functional groups
*important in determining and maintaining the structure of proteins
* important in binding + proteins to - DNA molecules

48
Q

Van der Waals interactions

A

weak interactions between two atoms that occurs only when two atoms are close and are oriented properly
-when too close, will repel to due to overlapping outer electrons orbitals
*specifies personal space which limits how close atoms are to each other

49
Q

hydrophobic interactions

A

describes the tendency of nonpolar groups w/in a macromolecule to associate with each other as they minimize their contact with surrounding water molecules and with any hydrophilic group in the same or another macromolecule
*common in proteins

50
Q

list the monosaccharides

A

glucose
fructose
galactose

51
Q

list the disaccharides

A

maltose
lactose
sucrose

52
Q

what makes up maltose
what is the bond

A

glucose + glucose
a glycosidic bond

53
Q

what makes up lactose
what is the bond

A

galactose + glucose
b glycosidic bond

54
Q

what makes up sucrose (table sugar)

A

glucose + fructose
a glycosidic bond

55
Q

a-d glucose

A

repeating unit of starch and glycogen

56
Q

b-d glucose

A

repeating unit of cellulose

57
Q

starch

A

alpha bond
sugars are oriented in the same direction

58
Q

cellulose

A

beta bond
every other sugar molecule is upside down

59
Q

glycogen

A

alpha bond
stored energy source ( in liver & muscles)
chain is branches/ forked

60
Q

Protein: enzymes

A

serves as a catalyst that increases chemical reactions
ex. digestive enzymes that hydrolyze the macromolecules in foods

61
Q

proteins: structural

A

provide physical support and shapes to cells and organelles, giving them their physical characteristic appearances
ex. collagen in animal connective tissues, keratin in hair, horns, and feathers

62
Q

protein: regulatory

A

control and coordination of cellular functions, ensuring that cellular activities are regulated to meet cellular needs

ex. transcription factors that bind DNA and regulate gene expression

63
Q

protein: Transport

A

movement of other substances into, out of, and within the cell

ex. glucose transporters and ion channels in membranes

64
Q

protein: hormonal

A

communication between distant parts of an organism

ex.insulin secreted by the pancreas to regulate blood glucose levels

65
Q

protein: receptor

A

response of cells to chemical stimuli

ex. receptors in nerve cell membranes sensing chemical signals from other nerves cells

66
Q

protein: defensive

A

provide protection against disease

ex. antibodies in the blood that detect and help destroy microorganisms

67
Q

protein: storage

A

storage (reservoir0 and release of amino acids

ex. seed proteins that are broken down during germination to provide nutrients

68
Q

what are proteins made out of?

A

monomer: amino acids

69
Q

what is the basic structure of amino acid

A

carboxyl group
amino group
hydrogen atom
r- group (side chain)

70
Q

what form of amino acid occur in biological proteins?

A

L-amino acid

71
Q

what determines the amino acid properties

A

the charge and polarity of the r group

72
Q

characteristics of group A (aa)

A

9
-nonpolar (hydrophobic)-cannot make hydrogen bonds
-hydrocarbon (with few/ no oxygen & nitrogen atoms)
-found in the interior

73
Q

characteristics of group B (aa)

A

6
-polar (hydrophilic), uncharged
(uneven distribution of charge)
-found on the surface of proteins

74
Q

characteristics of group C (aa)

A

5
-polar (hydrophilic), charged
-found on the surface of proteins
acidic aa= -
basic aa=+

75
Q

what are polymers of amino acids?

A

polypeptides
proteins

76
Q

the addition of new aa to a growing chain is done by what process?

A

condensation
3 atoms of h20 are removed, the carboxyl carbon of 1 aa and the amino nitrogen of a second are linked directly by a covalent bond

77
Q

what is a peptide bond?

A

a C-N bond linking two aa tgt

78
Q

the direction of chains of aa

A

intrinsic directionally because it always has an amino group at one end and a carboxyl group at the other end

79
Q

N- (amino) terminus

A

the amino group end of the chain

80
Q

C-(carboxyl) terminus

A

the carboxyl group end of the chain

81
Q

what is a polypeptide

A

the immediate product of aa polymerization
-chains of 3d shape and is biologically active

82
Q

monomeric proteins

A

proteins that are consist of a single polypeptide and their final shape is due to the folding and coiling that occur spontaneously as the chain is being formed

83
Q

multimeric proteins

A

proteins consists of two or more polypeptides that are often called POLYPEPTIDE subunits

84
Q

conformation

A

the inital folding of a polypeptide into its proper shape

85
Q

what causes denaturation in proteins?

A

disruptions by heat, high salt, chemical treatment

86
Q

when is a protein inactive?

A

in its denatured, unfolded state

87
Q

what are the forces stabilizing protein structure?

A

covalent disulfide bonds
hydrogen bonds
ionic bonds
van der Waals and hydrophobic interactions

88
Q

what is a disulfide bond?

A

a bond that forms between the sulfur atoms of two cysteine aa residues
-covalently linked by oxidation (removes 2 H atoms from the sulfhydryl group)

89
Q

what do hydrogen bonds do in protein structure?

A

stabilize helical & sheet structure
-donors: H atom covalently linked to a more electronegative (high affinity for electrons= neg charged) atom
-acceptors: have an electronegative atom that attracts this hydrogen atom

90
Q

what is the role of ionic bonds in protein structure?

A

noncovalent
since some r groups are + and -, the folding is dictated by the tendency of charged groups to repel/ attract

-able to exert a big force over large distances–> nondirectional (not limited to discrete angles)

91
Q

four hierarchical levels of protein organizations

A

primary
secondary
tertiary
quarternary

92
Q

primary structure

A

amino acid sequence linked tgt by peptide bonds, forming a polypeptide
-give the protein its conformation (3d)

93
Q

secondary structure

A

local interactions between aa residues that are closed tgt along the chain
-the polypeptide is then coiled into an alpha helix

94
Q

tertiary structure

A

results from long-distance interactions between stretches of aa residues
-the final folding of the polypeptide

95
Q

tertiary structure

A

interactions of 2 or more polypeptides to form a single multimeric proteins as they interact to form the final, functional protein

96
Q

nucleic acids

A

important in storing, transmitting, and expressing genetic info

97
Q

what is the monomer of nucleic acids?

A

nucleotides

98
Q

DNA

A

deoxyribonucleic acid
sugar: deoxyribose
genetic info
shape: double helix

99
Q

RNA

A

ribonucleic acid
sugar: ribose (5)
gene regulation + protein synthesis

100
Q

what does each nucleotide consist of

A

phosphate group
a nitrogen
1 out of 4 bases

101
Q

purine bases

A

adenine
guanine
-two rings structure

102
Q

pyrimidine bases

A

cytosine
uracil
thymine
-one ring

103
Q

nucleoside

A

a base and sugar

104
Q

phosphodiester bonds

A

the form between sugar and phosphate
-5’ of 1 nucleotide linked by a second phosphodiester bond to the 3’ carbon

105
Q

what is the direction of dna

A

anti-parallel complimentary
5’ 3’
3’ 5’

106
Q

what is the bond between the bases

A

hydrogen bonds

107
Q

the number of hydrogen bonds between the bases

A

A-T/U= 2 hydrogen bonds
C-G= 3 hydrogen bonds

108
Q

what are polysaccharides

A

long chains of polymers of sugars and sugar derivatives
function: energy storage

109
Q

what are oligosaccharides

A

shorter polymers
when attached to proteins on cell surface- cellular recognition of extracellular signal molecules

110
Q

discovery of membrane structure

A

a) lipid nature of membrane
when: 1895
who: Charles Overton
how: proposes that lipid coats exist (lipoids) + dissolved in these permeate the cell walls

b) lipid monolayer
when: 1917
who: Langmuir
how: published a paper on the chemistry of oil films
-Langmuir films: aliphatic chain and hydrophilic orient the molecules in a film on a water molecule

c) lipid bilayer
when: 1925
who: E Gorter + F Grendel
how: extracted membrane lipids from RBC and calculate the surface area
= found the surface was 2x that of the surface area of RBC—> membranes consist of 2 layers of lipids

d) lipid bilayer + protein sheets
When: 1935
who: davson + daniel
how: the sandwich model- importance of proteins in biological membranes

e) unit membrane
when: 1960
who: Robertson
how: EM structure represents trilaminar pattern

f) fluid mosaic model
when: 1972
who: SInger + Nicolson
how: viewed membranes proteins as discrete globular entities within the lipid bilayer
-lipid components are in constant motion
strength:
- explains the hydrophobic nature and globular structure of most protein membranes
- eliminate the need to accommodate membrane proteins in thin surface layers of unvarying thickness

g) membrane protein structure
when: 1975
who: Unwin & Anderson
how: used em, protein bacterial rhodopsin has 7 hydrophobic transmembrane domains + hydrophilic domains

cell & molecular biology (8 decks)

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