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BMSC 200 > Module 1 > Flashcards

Module 1 Flashcards

1
Q

biochemistry is…

A

-the study of life at a molecular level
-the application of chem principals to explain bio
-the common set of reactions and pricipasl that underlies all living organisms
-the study of molecular logic of life

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2
Q

how are all living organisms simular

A

they are all remarkable uniform at a molecular level

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3
Q

all organism are uniform at a molecular level. all organisms use…

A

-a common repertoire of building blocks to create common categories of biomolecules
ie. (nucleic acid, proteings, polysaccharides, lipids)
-a common core essential biochemical prosess

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4
Q

living states can be considered from four different perspectives/foundations…

A

-chemical
-energy
-genetic
-evolutinary

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5
Q

are all living things made from simular ingredients

A

yes

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6
Q

what four elements account for all living things ingredients

A

carbon, oxygen, hydrogen, nitrogen account for 98% of most organisms (in order)

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7
Q

what accounts for most of the hydrogen in living things

A

water

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8
Q

what element are all life forms based

A

carbon

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9
Q

how do we accumulate our carbon

A

from air through plants

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10
Q

how do we accumulate our oxygen

A

from air

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11
Q

how do we accumulate our hydrogen

A

from water

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12
Q

why cant we get our nitrogen from air

A

because its in inert form N2

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13
Q

how do we accumulate our nitrogen

A

it comes from plants which extracts it from soil

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14
Q

what can nitrogen in soil limit

A

the growth of plants, limiting the amount of food we can produce

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15
Q

how much food could we grow with the amount of natural occurring nitrogens in the soil

A

enough food for 4 billion people

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16
Q

how would the sale value of the chemicals vs organs tissue biomolecs compare in the human body

A

the chemicals within the human body would cost less then a dollar but tissue, organs, biomolecs would cost around 45,000,000

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17
Q

carbon is versatile in terms of…

A

the number and variety of chemical bonds that it can form

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18
Q

when carbon is versatile in the shapes it can make it enables

A

creation of a wide array of complex molecs

ie. amino acids, sugars, nucleotides

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19
Q

after carbon what would be the next-best candidate as a chemical foundation for life

A

silicon

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20
Q

why is a carbon molecule better to be the foundation chemical for life over silicon

A

-carbon to carbon bonds are stronger then silicon to silicon
-more energy is released on the C to C bonds (more energy from C based nutrients)
-combustion products of carbon (CO2) are soluble and remain active in biosphere

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21
Q

how does the silicon combustion byproducts compare to the carbon combustion byproducts

A

-the SiO2 is insoluble and cannot be used again
-the CO2 is soluble and remains active in the biosphere (used by plants)

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22
Q

describe or draw a carbonyl (aldehyde) molecule function group

A

a C with a single bonded H and a double bonded O that attaches to a R group making a T shape

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23
Q

describe or draw a carbonyl (ketone) molecule function group

A

a double bonded C and O with two R groups on either ends creating a T shape

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24
Q

describe and draw a carboxyl molecule function group

A

a C attached to a double bonded O and a single bonded O- anion that attaches to a R group making a T

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25
Q

describe and draw a (alcohol) hydroxyl function group

A

a O and a H bonded together with an R group crating a liner molecule

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26
Q

describe or draw a amino function group

A

a N with two Hs and a R group

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27
Q

describe or draw a amido function group

A

a C with a N and a double bonded O. the N has two Hs

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28
Q

describe or draw a guanidino function group

A

-a N attached to a H and a c
-the C has a N and a double bonded N
-double bonded N has a H
-the single bonded N has two Hs

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29
Q

draw Imidazole function group

A

just draw then google it

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30
Q

describe or draw a sulfhydryl function group

A

a S and a H

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31
Q

what does the properties of a functional group determine

A

the properties determine the structure, function, and properties of the biomolecules

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32
Q

what does structure dictate

A

the function

molecules “do what they do” because of their structures

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33
Q

understanding the structure-function relationship of biomolecules allows one to…

A

predict molecular function, understand complex biology (and pathobiology, and rationale development of treatments

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34
Q

what is the conformation of a molecule

A

flexable spatial arrangement of atoms within a molecule
(can be changed without breaking covalent bonds)
(think paper plane you can change the shape with out breaking)

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35
Q

what is the configuration of a molecule

A

fixed spatial arrangement of atoms within a molecule (cannot be changed with out breaking covalent bonds)
(think cutting off your finger)

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36
Q

configuration is conferred by either…

A

double bonds
chiral carbons(C bonded to 4 groups)

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37
Q

what are geometric (cis-trans) isomers

A

they have the same chemical formula but differ in the configuration of groups with respect to a non rotating double bond

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38
Q

what a cis bonds

A

groups on the same side of the double bond

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39
Q

what is a trans bond

A

groups on the opposite side of a double bond

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40
Q

can cis and trans change between each other

A

no. they stay this way there is so spontaneous conversations

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41
Q

what is a chiral carbon

A

it has four different substituents attached

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42
Q

can chiral carbons be arranged in different ways

A

yes. two different ways in space

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43
Q

because chiral carbons can be arranged in different ways in space what does this lead to

A

two different stereoisomers that differ in there configuration

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44
Q

how are steroisomers different

A

they tend to be identical but their biological properties are distinct

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45
Q

what are stereoisomers

A

they are molecules that are meior images of each other and take up space differently (think hands)

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46
Q

how many amino acids have a cyro alpha carbon

A

19 out of 20

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47
Q

Why is sterospecifity important

A

it is apparent in the construction and interactions of biomolecules

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48
Q

How many stereoisomers are bio molecules constructed from

A

biomolecules are often constructed exclusively from one stereoisomer
ie. proteins are built entirely from L-amino acids

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49
Q

what is the interactions between biomolecules, small molecules and biomolecules like

A

they are stereospicific

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50
Q

what does synthesis of chemical compounds (ie drugs) have a result of all the chiral forms

A

a asymmetric mixture of the chiral forms

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51
Q

why do not all forms of chiral carbons work for drugs

A

because these forms may have different biological activities
ie. thalidomide has two chiral forms one causes birth defects the other prevents moring sickness

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52
Q

what are biomolecules offten

A

polymers of simple building blocks

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53
Q

interms of biomolecule complexity what is more complex the structure and function or the the precursor molecules

A

the structure and function of resulting molecules are more complex then there precursor molecules; the whole is greater then the sum

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54
Q

what are the three advantages to constructing biomolecules as polymers

A

simplicity- simple and conserved reactions for synthesis and degradation

recycling-biomolecules can be digested back to component building blocks which can be recycled

diversity-incredibly complex molecules can be granted

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55
Q

what are the four major classes of biomolecules

A

proteins
carbohydrates
nucleic acids
lipids

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56
Q

what is the basic structure of DNA

A

two complementary strands

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57
Q

what are the two DNA complementary strands made up of

A

each strands is a linear polymer of four different types of building blocks

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58
Q

in DNA what is it that encodes information

A

the liner sequence within the strands

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59
Q

the nucleotide structure of genes dictates the…

A

sequence of amino acids incorporated into the corresponding protein

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60
Q

the amino acid sequence of proteins dictates…

A

the structure of the protein

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61
Q

the structure of protein dictates…

A

the biological activity

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62
Q

what is transcription

A

transcription of DNA into complementary RNA

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63
Q

what is translation

A

translation of RNA on ribosome to polypeptide chain

64
Q

what can random changes in genotype can result in…

A

changes in phenotype (observable characteristics)

65
Q

when a random change in genotype occurs when is it selected for

A

if the change offers a survival advantage it’ll be selected for

66
Q

when a random change in genotype occurs when is it selected against

A

if it disadvantages the organism it’ll be selected against

67
Q

do we have all or original proteins

A

no proteins in you today are not the same ones you had within you a month ago

68
Q

biochem reactions are…

A

steriospicific

69
Q

what do amino acids have attached to them

A

a carboxyl groups + amino group

70
Q

how do amino acids link together

A

link by carboxyl group of one amino acid to amino group of other

71
Q

what are proteins made of

A

linear polymers of amino acids

72
Q

how many amino acids are there

A

20

73
Q

what makes each amino acid different

A

they differ in there R group chains (which are different shapes/configurations)

74
Q

when amino acids have different R group chains what does this mean

A

it means they have different properties associated with them

75
Q

what do the different properties of amino acids determine

A

how the strands interact with eachother

76
Q

what happens when amino acids link together

A

they link together to form linear chains that fold into complex patterns with distinct biological activities

77
Q

what is protein folding a characteristic of

A

the amino acids that determines how it will fold

78
Q

what does the structure of a protein determine

A

biological activity

79
Q

what happens when when you have changes with in the structure

A

you change the function

80
Q

what can you look at on the the amino acids to predict the behavior of a protein

A

if the amino acids are polar or non polar (that is one of the main determinants of protein folding)

81
Q

what kind of chains do amino acids make

A

they make linear chains

82
Q

how are polysaccharides constructed

A

they are monosaccharides linked together to form linear or branched polymers

83
Q

what important biological roles do higher order polysaccharides serve

A

roles including structural, energy storage, and cellular recognition

84
Q

how do we link individual monosaccharides

A

they are linked together through glycosidic linkages (covalent linkages)

85
Q

what can carbohydrates do that can lead to very complex structures

A

they can form more then one covslent linkage to other sugars (branch points)

86
Q

what are some roles polysaccarides can play

A

they play a number of different roles such as energy storage, cellulose, joint lubricants

87
Q

how is nucleic acids constructed

A

linear polymers of nucleotide building blocks

88
Q

how many building blocks is there for DNA and RNA

A

5

89
Q

what is nucleic acids involved in

A

all aspects of storage and utilization of genetic information

90
Q

what are the 5 DNA/RNA buliding blocks

A

cytosine
uracil
thymine
adenine
guanine

91
Q

how do nucleic acids link together and what shape is it

A

they use covalent linkages creating linear structures

92
Q

how are nucleic acids bonded together

A

they are bonded with covalent phosphodiester bond

93
Q

what are lipids

A

they are aggregates (rather then defined polymers) of building blocks

94
Q

how do lipids serve

A

in energy storage, formation of membranes and signalling

95
Q

what is the structure of lipids

A

they have a hydrophilic head and two hydrophobic tails

96
Q

how are lipids bonded together

A

they are agrogating together through non covalent forces

they come together through hydrophobia

97
Q

why are lipids different from other biomolecules

A

because they aren’t bonded through covalent linkages but rater they are aggregating together through non covalent forces

98
Q

in lipids what are some concequences of not being linked together

A

lots of freedom of rotation

99
Q

how are lipids diffrent then the other 3 biomolecules

A

they done come together through covalent linkages and instead they aggregated together through non covalent forces

100
Q

what kind of structure can you build from lipids

A

structures that are consistant with there biological functions

101
Q

what are the two basic classes of living organisms

A

prokaryotes and eukaryotes

102
Q

how big are prokaryotes

A

around 1 micrometer (they are small)

103
Q

what can prokaryotes do because of there rapid cell growth

A

because of there rapid they can adapt to there environmental conditions easily

104
Q

what is contained with in a prokaryote cell

A

a single compartment, the nucleoid, which contains nucleic acid
other biomolecules (protein, metabolites, etc) in a complex, organized mix

105
Q

what are prokaryotes

A

they are single celled organisms and one cell represents the entirety of the organism

ie.. bacteria

106
Q

are there specialized cells when it comes to prokaryotes

A

no. one cell represents the whole organism (homogeneous soup of together)

107
Q

what are some advantages associated with prokaryotes

A

they can very easily adapt to changing circumstances
(change rapidly as new pressures are introduced)

108
Q

how quickly can prokaryotes devide

A

they can devide every 20 minutes

109
Q

how big are eukeryotes

A

around 100 micro meters (large)

110
Q

what kind of organisms do eukaryotes make up

A

multi-cellular organisms such as yeast, plants, fungi, vertebrates

111
Q

what do eukaryotes make up to support specialized functions

A

organells (nucleus, mitochondria, etc)

112
Q

what are some consequences associated with eukaryotes

A

much slower evolution and adaptation

113
Q

how many eukaryotes and prokaryotes do we contain within our bodies

A

we have around 30 trillion eukaryotic cells

around 100 trillion prokaryotic cells

114
Q

are the prokaryotes good for us

A

yes they are critical for our health

115
Q

what does the bacteria in out guts do

A

they help digest food and maintain a functional immune system

116
Q

what does out gut including microflora in it impact

A

our mental health, obesity and intelligence

117
Q

what are some possible ways to influence the microbiota in us

A

diet, pro and prebiotic, and fecal transplants

118
Q

if we put all the bacteria in our body how much we have

A

something the size of our brains (think of it as a extra organ)

119
Q

what are the two experimental approaches of studying molecules

A

in vitro
in vito

120
Q

what is in vitro

A

(in glass) studies behavior of molecules outside the context of the cell and organism

121
Q

what is in vivo

A

(in the living) studies occur within the complexity of the cell or organism

122
Q

why do experiments that are successful in vitro fail in vivo

A

because the behavior of molecules is context dependent

123
Q

what is the ideal way of studying molecules

A

in there natural habitat

124
Q

what are some pros associated with in vitro

A

you limit variables

125
Q

what are some in vitro cons

A

sometimes isolating molecules makes them harder to study

126
Q

what does the order of testing subjects go like

A

first mice then pigs then humans

127
Q

what animal is most ideal to study to compare to humans

A

pigs

128
Q

what are some pros and cons of experimenting on mice

A

pro: they are easy to keep
con: they have very different biological systems then humans

129
Q

how must energy for life be obtained

A

from the environment

130
Q

how much ATP does your body go through a day

A

about your body weight

131
Q

what is the first law of thermodynamics

A

the amount of energy in the universe remains constant energy cant be created nor destroyed

132
Q

how are cells highly effects transducers of energy

A

they convert the energy metabolized nutrients, or the energy of the sun, into work, heats or the generation of complex molecules

133
Q

what is the second law of thermodynamics

A

the tendency in nature is toward even greater disorder: the total entropy of the universe if continually increasing

134
Q

how do living systems and their biomolecules like to be interms of there organization

A

they require a high level or organization

135
Q

what theory did willard gibbs develop

A

the theory of energy changes during chemical reactions

136
Q

how did willard gibbs demonstrate that free energy (G) of any closed system can be defined in terms of

A

-enthalpy(H)
-entrophy(S)
-temperature

137
Q

what is enthalpy (H)

A

reflects number and kinds of bonds

138
Q

what is entrohpy (S)

A

the degree of randomness

139
Q

what is the equation of the definition of energy

A

G=H-TS

140
Q

what is the equation of free energy change

A

delta G = delta H - T delta S

141
Q

if the delta G is is bigger then 0…

A

(it is +) (endergonic meaning it absorbs energy in the form of work)
it is a non spontaneous process, needs input of energy to proceed

142
Q

if the delta G is smaller the 0…

A

(it is -) (exergonic meaning occurs with out the input of energy)
it is a spontaneous process, releases free energy which can be used to do work

143
Q

for a spontaneous process for free energy, what is meant by spontaneous

A

it means nothing about the time frame. just that it wants to be like this (with out energy imput)

144
Q

in spontaneous processes for free energy how long do they occur for?

A

it proceeds until equilibrium is reached

145
Q

if the delta free energy is 0…

A

system is at equilibrium, there is no change in free energy in the system

146
Q

what does G mean

A

free energy

147
Q

what does H mean

A

enthalpy

148
Q

what does S mean

A

entropy

149
Q

how can cells drive thermodynamically unfavourable reactions

A

by coupling energy requiring (endergonic) to energy releasing (exergonic) reactions

150
Q

if the sum of the free energy changes is negative the overall process is…

A

exergonic (spontanious)

151
Q

ATP serves as the link between…

A

catabolic and anabolic rxns

152
Q

the perpetunation of life requires that genetic info be…

A

-stored in a stable form
-expressed accurately in the form of gene products
-reproduce with minimal efforts

153
Q

for many organisms DNA provides…

A

-the instructions for forming all other cellular components
-a template for producing of identical DNA molecules to be distributed to the progeny when the cell devides

154
Q

DNA must be…

A

stable, usable, easy mechanism to make a copy

155
Q

What is the monomer of nucleic acid

A

Nucleotides

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