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Spring 2013 / Biochemistry > Week 2 > Flashcards

Week 2 Flashcards

1
Q

biological molecules are almost always found operating in liquid environment of water, why?

A

bc it is dynamic, being polar, and bc it SOLUBILIZES so many substances

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2
Q

in liquid and gaseous environments, where molecules can circulate easily amongst themselves, what dominates all motion?

A

random motion of atoms and molecules

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3
Q

2nd law of thermodynamics explains…? which means…?

A

ENTROPY

the desire of matter and energy to EQUILIBERATE if not constrained

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4
Q

when can you see entropy?

A

in diffusion of heat from a hotter area to colder area

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5
Q

what type of process is diffusion?

A

a spontaneous and irreversible process

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6
Q

can particles that have been spread out by diffusion spontaneously re-order themselves?

A

NO

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7
Q

what is Brownian Motion?

A

random motion

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8
Q

what is concentration gradient?

A

tendency of substance x to diffuse toward area of cell where it is less concentrated (2nd law of thermodynamics)

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9
Q

the surface area of red blood cells are large or small? why?

A

small, compact, smooth, to not expose itself to environment as easily

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10
Q

the surface area of neuron is large or small? why?

A

has numerous extensions increasing surface areas for maximum exposure to environment

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11
Q

what is hydraulics?

A

study & application of using pressures of liquids to do work

liquids & solids do not compress, so it creates hydraulic pressure

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12
Q

gases create a pressure in direct ratio to…

A

tje amount of pressure they are exerting, or being exerted upon

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13
Q

what is partial pressure?

A

when gases dissolve in liquids, such as oxygen or carbon dioxide does in blood

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14
Q

when does a chemical reaction takes place?

A

when molecules and/or atoms interact and a CHANGE (delta) in one or more molecules or atoms occurs

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15
Q

what is a catalyst?

A

(without the use of energy) causes a reaction to occur almost spontaneously

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16
Q

the amount of energy needed to start a reaction is called?

A

activation energy

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17
Q

what is the rate of reaction?

A

the speed of a reaction to completion (catalysts usually speed up the reaction rate)

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18
Q

the sign “+” is…

A

where the activation energy and catalysts act to create an interaction bt 2 atoms or molecules

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19
Q

what is redox reactions?

A

red-uction and ox-idation

1 molecule will oxidize, the other will be reduced, thus maintaing balance

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20
Q

when does oxidation occur?

A

when a molecule LOSES electrons or ACCEPTS oxygen

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21
Q

when does reduction occur?

A

when molecule ACCEPTS electrons or hydrogen ions and LOSES oxygen

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22
Q

when does oxidative stress occur?

A

when there is an abundance of oxidized molecules or atoms in the tissue

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23
Q

what does antioxidants do?

A

“mop up” oxidative stress, which damages tissues by restoring electrons to an environment.
they are inherently recycled so they can re-donate electrons again and again

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24
Q

why are oxidants damaging to tissues?

A

bc they react with atoms or molecules and change the molecules, which changes the CONFORMATIONAL STRUCTURE and/or the electrochemistry of molecule

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25
Q

what is a toxin?

A
  • a molecules that strips electrons from biological molecules
  • toxins keep their electrons, leaving molecules in oxidized state
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26
Q

what is chronic inflammation?

A

an oxidative cellular and tissue state

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27
Q

what is nuclear chemistry

A

chemistry of atom’s nucleus

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28
Q

what is radioactivity?

A

result of decay of that nucleus

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29
Q

does radioactivity affect electrons?

A

NO

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30
Q

what results in nuclear radiation?

A

from unstable atomic nuclei releasing particles from unstable nucleus leading to nucleus decay

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31
Q

what is an isotope?

A

different numbers of NEUTRONS in nucleus

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32
Q

what happens in an unstable isotope

A

the nucleus decays by losing both protons and neutrons, spewing radioactive particles into the environment

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33
Q

how are the unstable isotopes of cesium and strontium created?

A

by disintegration of uranium from fission

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34
Q

how do cesium and strontium (metals, relatives of sodium and potassium) damage biological systems by their radiation?

A

they will substitute for sodium and potassium in biological systems, and release their radiation directly into the organism they have been incorporated

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35
Q

What are the 4 major types of decay particles from atomic disintegration?

What are they called?

A

beta particles
positron emission
gamma rays
alpha particles

ionizing radiation

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36
Q

how do radiation damage atoms and molecules (2 ways)?

A
  1. disrupting their electron clouds and bonds to other atoms, causing oxidative stress
  2. damage an atomic nucleus by absorption of a neutron in a stable isotope (which emits more radiation)
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37
Q

molecules damaged by radiation can be progenitors of…?

A

cancerous growth bc beyond cell’s capacity to repair the DNA

38
Q

what are beta particles?

A

high energy electrons with NEG charge

39
Q

why do beta particles not act like normal electrons?

A

bc they are ejected from decaying nucleus of a radioactive atom at high speed

40
Q

what are alpha particles?

A
  • a helium nucleus that has no electrons

- weak radiation, disperse quickly

41
Q

what are positrons emissions?

A
  • decay product of a proton with POS charge

- high energy particle

42
Q

why is positron emission called B+?

A

bc it is the antimatter particle to an electron

43
Q

what is gamma rays?

A

high energy and dangerously destructive particle emission (form of light energy)

44
Q

what is organic chemistry

A

chemistry of carbon

45
Q
  1. are all carbon-containg molecules “organic”?

what are examples of organic molecules and why are they considered organic?

A

NO

coal or oil, bc they are created by plants, a result of production in biological system

46
Q

what are examples of inorganic molecules and why?

A

cell salts or oxygen, bc they don’t contain carbon in their structure

47
Q

what are the most common elements in organic compounds?

A

hydrogen, oxygen, carbon, nitrogen

48
Q

what elements (2) will [primarily] bond to the 4 basic compounds of carbon?

A

sulfure

phosphorus

49
Q

carbon compounds are exclusively bonded with what type of bond?
what other bond is common?

A
  • covalent bond

- hydrogen weak bond

50
Q

soap is an example of what type of infrequent bond of carbon compound?

A

ionic bond

51
Q

which metal ions (7) will be CHELATED into biological molecules?

A

iron, magnesium, copper, potassium, sodium, calcium, manganese, etc.

52
Q

what is CHELATED?

A

not technically bonded, but held in place within an enzyme or PORPHYRIN structure

53
Q 
CARBON
# of bonds
charge
A
  • 4 bonds

- NEUTRAL charge

54
Q 
OXYGEN
# of bonds
charge
A
  • 2 bonds

- NEG charge

55
Q 
NITROGEN
# of bonds
charge
A

3 bonds

NEG charge

56
Q 
HYDROGEN
# of bonds
charge
A

1 bond

POS charge

57
Q

“meth-“

A

1

58
Q

“eth-“

A

2

59
Q

“prop-“

A

3

60
Q

“but-“

A

4

61
Q

“pent-“

A

5

62
Q

“hex-“

A

6

63
Q

“hept-“

A

7

64
Q

“oct-“

A

8

65
Q

“acet-“

A

2-carbon chain

66
Q

-ol

A

alcohol

67
Q

-ase

A

enzyme

68
Q

-ose

A

sugar

69
Q

-amine

A

amino acid

70
Q

Carbon is element #?
valence?
name 2 other characteristics that it is ALWAYS in

A

element #6
valence -4
always has its 4 bonds filled
always covalently bonded

71
Q

what shape does Carbon’s bond have?

A

tetrahedral distribution around the nucleus

72
Q

is carbon polarized? why?

A

NO, bc both POS and NEG atoms bond to it, maintaining 109 degrees

73
Q

organic molecules can dissolve in water or not, the degree of dissolution in water or solubility are defined as…?

A

hydrophobicity

hydrophilicity

74
Q

which large biological molecules create more solubility and why?

A

OH-, H+, or O- are exposed and more apt to mix with water, creating more solubility

75
Q

which group on a molecule is hydrophobic in nature (name 2)?

A

methyl group (-CH) and benzene ring, they will reject interaction with water

76
Q

what are saturated molecules?

A

more solid and dense bc they have MORE HYDROGEN atoms bonded to the molecule per carbon
ex. coconut oil (solid at a little below room temp)

77
Q

what are unsaturated molecules?

A

more liquid and light bc they have LESS HYDROGEN per carbon

ex. olive oil

78
Q

what are ENANTIOMERS?

A

organic molecules that have mirror image constructions (both right- and left-handed mirror)

79
Q

the right configuration of ENANTIOMERS are signified as? the left?

A

RT: “D-form” (dextrorotatory)
LEFT: “L-form” (levorotatory)

80
Q

most amino acids (building block of protein) in biological systems are which form?

A

L- form

81
Q

sugar molecules that are of use in biological systems are which form?

A

D- form

82
Q

How can enantiomer become useable as fuel or building block for macromolecules when they often taste and smell different, and have different effects due to their different conformational structures?

A

many enzymes exist to “flip” an enantiomer from one form to the other

83
Q

what are aliphatic molecules?

A

based on c-c-c linear backbone

84
Q

what are the subdivisions of aliphatic molecules (3)?

A
  1. alkAne (single-bond)
  2. alkEne (double-bond)
  3. alkYne (triple-bond)
85
Q

what are some examples of aliphatic compounds?

A

fats, sterols, waxes, fules like gasoline or butane

86
Q

what are aromatic compounds?

A

based on benzene ring structure and are known for their ability to create aromas

87
Q

what is benzene’s formula, and what is its special quality?

A

C6H6

has 3 bonds that move around at the next moment (not static)

88
Q

alkAnes are…

A

saturated

89
Q

alkEnes and alkYnes

A

unsaturated or polyunsaturated

90
Q

what is an alkyle group?

A

alkAne or alkEne attached to a primary molecular structure

Spring 2013 / Biochemistry (13 decks)

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