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MBB 231 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

What does cell theory (old one) state:

A
  • all organisms are composed of 1 or more cells
  • the cell is the structural unit of life
  • cells can only arise by division from pre existing cells
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2
Q

what does the updated cell theory state?

A
  • life: most basic property of cells
  • cells are highly complex and organized
  • cell possess a genetic program and the means to use it
  • cells acquire and use energy
  • cells carry out a variety of chemical reactions
  • cells engage in mechanical activities
  • cells are able to adapt and respond to stimuli
  • cells are capable of self regulation
  • cells evolve
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3
Q

what is metabolism

A

the sum total of all chemical reactions in cells

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4
Q

how is organization in cells achieved

A

though processes that are random

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5
Q

where is genetic info kept in cells

A

in chromosomes in either the nucleus (eukaryotes) or nucleoid (prokaryotes)

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6
Q

what do cells convert glucose into

A

ATP

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7
Q

what do virtually all chemical changes in a cell require ?

A

enzymes

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8
Q

what initiates cellular activity?

A

Based on mechanical changes within cells, which are often initiated by changes in shape of motor proteins

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9
Q

what bring cell back to the appropriate state

A

feedback circuits

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10
Q

what are the differences between prokaryotes and eukaryotes distinguished by

A

size and the type of organelles they contain

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11
Q

what do procaryotes and eukaryotes share, and why

A

because of shared ancestry

  • identical genetic language
  • common set of metabolic pathways
    -many common structural features
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12
Q

what are the two types of organization that eukaryotes have for biochemical events

A

temporal and spatial arrangements

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13
Q

what is the size range of bacteria cells

A

1-5 um (micro meter)

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14
Q

what is the size range of animals cells

A

10 - 100 um (micro meter)

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15
Q

what limits the size of a cell

A

-SA to volume ratio

-need to maintain adequate local concentrations of substances required for cellular function

  • rates at which molecules diffuse
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16
Q

what is lower size limit of cells because

A

due to cell needing enough volume to hold all its stuff

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17
Q

what is the upper size limit of cells because

A

due to rates of diffusion (bigger cells = slower diffusion)

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18
Q

how do cells overcome size limitations relating to nutrient uptake and release of waste

A

active transport

morphological specializations

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19
Q

what determines the amount of exchange a cell needs to make

A

cell volume

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20
Q

what is the cytoplasm

A

the volume of the cell excluding the nucleus

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21
Q

what is diffusion

A

unassisted motion that relies on concentration gradients

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22
Q

what is active transport

A

specialized machinery can move molecules/vesicles along the cytoskeleton from one place to another

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23
Q

what is a virus

A

an infectious agent that can only replicate inside a living cell

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24
Q

what is a virion

A

a complete viral partice, which includes the genome, capsid, and in some cases am envelope

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25
Q

what is a viroid?

A

an infectious agent that is composed solely of RNA (ie no coat proteins)

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26
Q

what is a prion

A

an infectious protein that can transmit its folded shape to other native folded proteins

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27
Q

in general what do virus particles (virions) consist of

A

nucleic acids (DNA or RNA) enclosed in a protein coat

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28
Q

what are the 3 types of proteins that all viral genomes encode

A
  • for replication
  • for packaging and delivery
    -for modification of host cell
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29
Q

what are covalent bonds

A

strong bonds formed by the sharing of electrons between adjacent atoms

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30
Q

what are ionic bonds

A

attractions between charged atoms

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31
Q

what do polar covalent bonds have, and where will electrons go to

A

unequal electron sharing

electron will go to more electronegative atom

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32
Q

where in a cell, are ionic bonds stronger

A

stronger in core of protein, since water is often excluded

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33
Q

what are hydrogen bonds

A

weak attractive interactions between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom

(the electronegative atom owns the hydrogen electron, creating an electropositive hydrogen

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34
Q

is hydrogen bond strength additive

A

yes

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35
Q

are hydrophobic interactions a bond or attraction

A

no, neither

based on desire of hydrophobic molecules to not interact with each other

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36
Q

are polar molecules hydrophobic to hydrophilic

A

hydrophilic

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37
Q

are non-polar molecules hydrophobic or hydrophilic

A

hydrophobic

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38
Q

what are van der waals forces

A

weak attractive forces between uncharted molecules that are very close to each other

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39
Q

does it take more energy to break covalent bonds or non-covalent bonds

A

covalent

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40
Q

is more energy used to break single bond or double/triple bonds

A

double/triple

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41
Q

what is the universal solvent in biological systems

A

water

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42
Q

how many bonds can a water molecule form simultaneously

A

4

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43
Q

what allows water to dissolve a large variety of substances

A

its polarity

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44
Q

what is the hydrophobic effect and why is it energetically favourable

A

the tendency of non-polar molecules and non-polar portions of molecules to aggregate in water

aggregated form has less order = more entropy = energetically favoured (less order since more free water)

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45
Q

why does water have a high specific heat

A

most of the energy used to disrupt H-bonds rather than increase the molecular motion (ie increase temp)

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46
Q

how efficient are metabolic reactions and what happens to “wasted” energy

A

50% efficient

wasted energy warms body

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47
Q

what do acids and bases of in regards to protons

A

acids: release protons

bases: accept protons

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48
Q

what is a amphoteric molecule

and what is an example

A

can act as acid or base

ex: water

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49
Q

what do buffers do

A

resist changes in pH

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50
Q

why are hydrocarbons less common in living cells

A

they are of limited importance since they aren’t soluble in water

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51
Q

what is a macromolecule

A

large highly organized molecules that form cellular structures and carry out the activities of cells

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52
Q

what are the 4 major categories or macromolecules

A
  • proteins
  • nucleic acids
  • polysaccharides
  • lipids
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53
Q

are most macromolecules short lived

A

yes

expect DNA which is continually broken down and replaced

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54
Q

what is the most abundant form of organic matter on earth

A

carbohydrates

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55
Q

what are the roles of carbohydrates

A

energy

metabolic intermediates

structural components of DNA/RNA

structural components of cell walls (bacteria and plants)

glycoproteins and glycolipids

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56
Q

what is the structure of sugar’s backbone

A

backbone of carbons linked in a linear array of single bonds

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57
Q

when is it a ketose

A

if carbonyl group is located at internal position

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58
Q

when is it an aldose

A

if carbonyl is located at end of molecule

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59
Q

what happens to sugars with more than 5 carbons

A

they self react to form a ring containing molecule

60
Q

what is the anomeric carbon

A

carbon derived from the carbonyl (C=O) of the open chain form of the carbohydrate molecule

61
Q

what are glycosidic bonds

A

formed between OH groups on 2 separate monosaccharides (or monosaccharide + another molecule)

62
Q

what is a polysaccharide

A

long chain polymers of sugars and sugar derivatives

63
Q

what are the functions of polysaccharides

A

storage
structural
signalling

64
Q

what do the multiple OH groups in monosaccharides participate in

A

glycosidic bonds

65
Q

what is cellulose

A

plant product made of unbranched polymers (glucose)

66
Q

what re GAGs

A

composed of 2 different sugars found in intracellular space

67
Q

what do alpha - glycosidic bonds allow for

A

spontaneous formation of helical shapes

68
Q

what do beta - glycosidic bonds form

A

rigid linear rods

69
Q

what are glycoconjugates

A

signalling carbohydrates covalently joined to a protein or lipid

(glycoproteins or glycolipids)

70
Q

what are blood types determined by

A

cell surface carbohydrates of red blood cell

71
Q

what are nucleic acids and what do they do

A

linear polymers of nucleotides

they store, transmit, and express genetic info

72
Q

what direction are nucleotide sequences written

A

5’ to 3’

73
Q

how many hydrogen bonds does AT form

A

2

74
Q

how many hydrogen bonds does GC form

A

3

75
Q

what is coenzyme A notable for

A

its role in the synthesis and oxidation of fatty acids

76
Q

what cAMP

A

second messenger for intracellular signal transduction in many different organisms

77
Q

what is the central dogma of MBB

A

DNA males RNA, RNA makes protein

78
Q

what are the non-coding RNAs

A

small nuclear/nucleolar RNA

microRNA (miRNA)

transfer RNA (tRNA)

rRNA

long non coding RNA (lncRNA)

79
Q

are lipids formed by the same type of linear polymerization as proteins, nucleic acids, and polysaccharides

A

no

80
Q

why are lipids considered macromolecules

A

because of their high molecular weight and importance in membranes

81
Q

lipids are a heterogenous category, what classifies them together

A

solubility properties (hydrophobic)

82
Q

what are the functions of lipids

A

energy storage

membrane structure

specific biological functions (ex: signal transmission)

83
Q

what are the 6 classes of lipids

A

fatty acids

triacyglycerols

phospholipids

steroids

glycolipids

terpenes

84
Q

what is a fatty acid

A

long unbranched hydrocarbon with a carboxyl group at one end

85
Q

why are even numbers of carbons favoured

A

because fatty acid synthesis occurs via the stepwise addition of 2 carbon units to growing chain

86
Q

why do fatty acids release a high amount of energy upon oxidation

A

since they are highly reduced

87
Q

what is a saturated fatty acid like

A

long and straight

no double bonds

88
Q

what is an unsaturated fatty acid like

A

bent

at least 1 double bond

89
Q

what is the orientation around the double bond in unsaturated fatty acids

A

cis

since they reduce van der Waals interactions

90
Q

what is hydrogenation

A

chemical process by which hydrogen atoms are added to unsaturated fats to reduce number of double bonds

allows the chains to pack more closely together to form a solid structure

91
Q

what kind of bond does hydrogenation create

A

trans bonds

92
Q

why are phospholipids important to membrane structure

A

due to their amphipathic nature (has both hydrophobic and hydrophilic parts)

93
Q

what is a diacylglycerol

A

phospholipid molecule that has 2 fatty acid chains (not 3) attached to a glycerol backbone

94
Q

what is a steroid

A

derivatives of 4 ringed hydrocarbon skeleton

95
Q

are steroids non polar or polar

A

non polar = hydrophobic

96
Q

what is the most common steroid in animals cells

A

cholesterol

97
Q

what is cholesterol the starting material for

A

the synthesis of steroid hormones ( sex hormones, glucocorticoids, mineralocorticoids)

98
Q

what is membrane fluidity determined by

A

phospholipid/steroid content

length and degree of saturation of fatty acyl chains and temperature

99
Q

what are terpenes synthesized from

A

5 carbon compound: isoprene

100
Q

what are involved in almost every cellular pathway

A

proteins

101
Q

what are the 4 levels of protein organization

A

primary structure : amino acid sequence

secondary structure: folding of polypeptide backbone

tertiary structure: describes conformation of entire polypeptide

Quaterary structure: assembled subunits

102
Q

what do all amino acids have

A

carboxyl group

amino group

single carbon atom ( alpha carbon)

r group

103
Q

what happens to the carboxyl group and the amino group at pH 7

A

carboxyl group looses a proton (negatively charged)

amino group accepts a proton (positively charged)

104
Q

what kind of amino acids are used in the synthesis of a protein on a ribosome

A

L-amino acids

105
Q

what charge do acidic amino acids have

A

negatively charged

106
Q

what charge do basic amino acids have

A

positively charged

107
Q

where do polar amino acids tend to be found

A

surfaces of proteins

108
Q

where do non-polar amino acids tend to be found

A

buried in the core of proteins or membranes

109
Q

what are the unique amino acids and what do they do

A

glycine: flexible and can tightly pack

cysteine: disulphide bond formation

proline: breaks secondary structures

110
Q

what kind of reaction are involved in the addition new amino acids

A

condensation (dehydration reaction)

111
Q

when does a polypeptide become a protein

A

after it has assumed a unique 3D stable shape and is biologically active

(after folding)

112
Q

what is protein synthesis

A

the process of elongating a chain of amino acids

113
Q

where is all info necessary for secondary structure contained

A

primary structure

114
Q

what is the difference between configuration and conformation

A

configuration: molecular composition

conformation: proper shape

115
Q

what kind of bond are necessary for a protein to adopt its proper shape

A

covalent and non-covalent bonds

116
Q

what generates secondary structure

A

hydrogen bonding between amino acids (polypeptide backbone)

117
Q

what is an alpha helix

A

spiral in shape, consisting of the peptide backbone wth the R groups jutting out from the spiral

118
Q

how may amino acids are there per turn of an alpha helix

A

~3.6

119
Q

is an alpha helix hydrophilic or hydrophobic

A

can be either

120
Q

in an alpha helix where do the H-bonds occur

A

between the NH group of one and the CO or another that is one turn from the first

121
Q

what are the 4 constraints affecting formation/stability of am alpha-helix

A

-electrostatic repulsion/attraction between successive amino acid residues with charged R groups

-bulkiness of adjacent R group

-helix forming amino acids (leucine, methionine, glutamate)

-helix breaking amino acids (proline and glycine)

122
Q

what is a beta sheet

A

extended sheet like conformation with several segments of a polypeptide (strand) lying side by side in a folded or pleated formation

123
Q

where do R groups jut out in beta sheets

A

on alternating sides of the sheet

124
Q

what amino acids are beta sheet formers

A

isoleucine, valine, phenylalanine

125
Q

what are the major internal supportive elements in a protein

A

alpha helices and beta sheets

126
Q

where on the polypeptide chain is there the greatest biological activity

A

hinges, turns, loops, or finger like extensions (most flexible parts)

127
Q

what is a motif

A

unit of secondary structure that consist of short stretches of alpha helices and beta sheets connected by turns and loops

128
Q

what do people use to classify proteins into protein families

A

motifs

129
Q

what is tertiary structure stabilized by

A

covalent and non-covalent binds between R groups

130
Q

what does the weak nature of stabilizing forces result in for proteins

A

being able to change shape

131
Q

what give proteins considerable stability to proteins

A

disulphide bonds

132
Q

what is often used to decide if 2 proteins have similar structure/function

A

primary sequence

133
Q

what is a domain

A

discrete locally folded unit (substructure) of the overall tertiary structure, usually with a specific function

134
Q

Are proteins static and inflexible

A

no

135
Q

what accompanies nearly every activity that a protein takes part in

A

conformational changes

136
Q

what is quaternary structure

A

assembled subunits

137
Q

what is a homodimer

A

protein composed of 2 identical subunits

138
Q

what is a heterodimer

A

protein composed of 2 non-identical subunits

139
Q

what are monomeric proteins

A

proteins that consist of a single polypeptide

140
Q

what are multimeric proteins

A

consist of 2 or more polypeptides

141
Q

what is native conformation

A

a stable 3D structure for a particular polypeptide

lowest energy

142
Q

what are the two categories that proteins are divided into

A

fibrous: have extensive regions of secondary structure, giving them a highly ordered repetitive structure
- most common in structural material that resides outside of cell

globular: different segments of polypeptide chain (or multiple chains) fold back on each other generating a compact structure
-most proteins within cell are globular

143
Q

what is denaturation

A

unfolding of a protein

144
Q

how do proteins get their final conformation

A

explore a range of conformations, then funnel down to the most energetically favourable state

145
Q

what do molecular chaperons do

A

bind to short structures of hydrophobic amino acids that are exposed in non-native proteins to facilitate proper folding

(having these regions exposed is unfavourable since proteins can stick together when they are not supposed to)

146
Q

where are larger polypeptides transferred to to provide a proper folding environment

A

chaperonins

MBB 231 (5 decks)

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