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cell & molecular biology > lecture 2 > Flashcards

lecture 2 Flashcards

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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
hydrophilic
compounds/ solutes that have infinity for water "water-loving" ex. sugars, organic acids, certain amino acids polar & ions
26
hydrophobic
compounds/solutes that are not soluble in water "water-fearing" ex.lipids & proteins in biological membranes non-polar
27
amphipathic
a molecule that has one area of hydrophobic and one area of hydrophilic ex. phospholipids, detergent molecule
28
what kind of bond make up the plasmamembrane
amphipathic bond \
29
the head of the phospholipid is
hydrophilic
30
the tail of the phospholipid is
hydrophobic
31
transport protein
specialized transmembrane proteins that serve either as a hydrophilic channel
32
what is the shape of a saturated phospholipid
straight
33
what is the shape of an unsaturated phospholipid
bent (water can get thru by hiding in the pockets of the bent angle
34
liposome
a structure that lipids make in water function: it fuses w water to to deliver molecules "delivery" (2 circles)
35
micella
a structure that lipids make in water function: solubilize fats ex.makeup remover, detergent
36
what forms biological macromolecules?
monomers (small organic molecules)
37
the levels of molecules
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.
38
three types of biological macromolecules
1. polysaccharides 2. proteins 3. nucleic acids
39
basic info of polysaccharides
monomer: monosaccharides, glucose functions: storage, structural ex. starch, glycogen cellulose, chitin
40
basic info of proteins
monomer: amino acid (20) functions: enzymes, hormones, antibodies, carriers, ion channels
41
basic info of nucleic acids
monomer: nucleotides (5) function: informational ex. DNA, RNA
42
What reaction add a monomer
condensation (the removable of water)
43
what reaction remove a monomer
hydrolysis (the addition of water) aka degradation (the breakdown)
44
what is self-assembly and why is it important
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
45
example of noncovalent bonds in macromolecules
hydrogen bonds ionic bonds vam der waals interactions hydrophobic interactions
46
hydrogen bonds
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
ionic bonds
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
Van der Waals interactions
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
hydrophobic interactions
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
list the monosaccharides
glucose fructose galactose
51
list the disaccharides
maltose lactose sucrose
52
what makes up maltose what is the bond
glucose + glucose a glycosidic bond
53
what makes up lactose what is the bond
galactose + glucose b glycosidic bond
54
what makes up sucrose (table sugar)
glucose + fructose a glycosidic bond
55
a-d glucose
repeating unit of starch and glycogen
56
b-d glucose
repeating unit of cellulose
57
starch
alpha bond sugars are oriented in the same direction
58
cellulose
beta bond every other sugar molecule is upside down
59
glycogen
alpha bond stored energy source ( in liver & muscles) chain is branches/ forked
60
Protein: enzymes
serves as a catalyst that increases chemical reactions ex. digestive enzymes that hydrolyze the macromolecules in foods
61
proteins: structural
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
protein: regulatory
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
protein: Transport
movement of other substances into, out of, and within the cell ex. glucose transporters and ion channels in membranes
64
protein: hormonal
communication between distant parts of an organism ex.insulin secreted by the pancreas to regulate blood glucose levels
65
protein: receptor
response of cells to chemical stimuli ex. receptors in nerve cell membranes sensing chemical signals from other nerves cells
66
protein: defensive
provide protection against disease ex. antibodies in the blood that detect and help destroy microorganisms
67
protein: storage
storage (reservoir0 and release of amino acids ex. seed proteins that are broken down during germination to provide nutrients
68
what are proteins made out of?
monomer: amino acids
69
what is the basic structure of amino acid
carboxyl group amino group hydrogen atom r- group (side chain)
70
what form of amino acid occur in biological proteins?
L-amino acid
71
what determines the amino acid properties
the charge and polarity of the r group
72
characteristics of group A (aa)
9 -nonpolar (hydrophobic)-cannot make hydrogen bonds -hydrocarbon (with few/ no oxygen & nitrogen atoms) -found in the interior
73
characteristics of group B (aa)
6 -polar (hydrophilic), uncharged (uneven distribution of charge) -found on the surface of proteins
74
characteristics of group C (aa)
5 -polar (hydrophilic), charged -found on the surface of proteins acidic aa= - basic aa=+
75
what are polymers of amino acids?
polypeptides proteins
76
the addition of new aa to a growing chain is done by what process?
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
what is a peptide bond?
a C-N bond linking two aa tgt
78
the direction of chains of aa
intrinsic directionally because it always has an amino group at one end and a carboxyl group at the other end
79
N- (amino) terminus
the amino group end of the chain
80
C-(carboxyl) terminus
the carboxyl group end of the chain
81
what is a polypeptide
the immediate product of aa polymerization -chains of 3d shape and is biologically active
82
monomeric proteins
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
multimeric proteins
proteins consists of two or more polypeptides that are often called POLYPEPTIDE subunits
84
conformation
the inital folding of a polypeptide into its proper shape
85
what causes denaturation in proteins?
disruptions by heat, high salt, chemical treatment
86
when is a protein inactive?
in its denatured, unfolded state
87
what are the forces stabilizing protein structure?
covalent disulfide bonds hydrogen bonds ionic bonds van der Waals and hydrophobic interactions
88
what is a disulfide bond?
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
what do hydrogen bonds do in protein structure?
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
what is the role of ionic bonds in protein structure?
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
four hierarchical levels of protein organizations
primary secondary tertiary quarternary
92
primary structure
amino acid sequence linked tgt by peptide bonds, forming a polypeptide -give the protein its conformation (3d)
93
secondary structure
local interactions between aa residues that are closed tgt along the chain -the polypeptide is then coiled into an alpha helix
94
tertiary structure
results from long-distance interactions between stretches of aa residues -the final folding of the polypeptide
95
tertiary structure
interactions of 2 or more polypeptides to form a single multimeric proteins as they interact to form the final, functional protein
96
nucleic acids
important in storing, transmitting, and expressing genetic info
97
what is the monomer of nucleic acids?
nucleotides
98
DNA
deoxyribonucleic acid sugar: deoxyribose genetic info shape: double helix
99
RNA
ribonucleic acid sugar: ribose (5) gene regulation + protein synthesis
100
what does each nucleotide consist of
phosphate group a nitrogen 1 out of 4 bases
101
purine bases
adenine guanine -two rings structure
102
pyrimidine bases
cytosine uracil thymine -one ring
103
nucleoside
a base and sugar
104
phosphodiester bonds
the form between sugar and phosphate -5' of 1 nucleotide linked by a second phosphodiester bond to the 3' carbon
105
what is the direction of dna
anti-parallel complimentary 5' 3' 3' 5'
106
what is the bond between the bases
hydrogen bonds
107
the number of hydrogen bonds between the bases
A-T/U= 2 hydrogen bonds C-G= 3 hydrogen bonds
108
what are polysaccharides
long chains of polymers of sugars and sugar derivatives function: energy storage
109
what are oligosaccharides
shorter polymers when attached to proteins on cell surface- cellular recognition of extracellular signal molecules
110
discovery of membrane structure
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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