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General Chemistry 111 > Biology Midterm: Lectures 1-8 and 27 > Flashcards

Biology Midterm: Lectures 1-8 and 27 Flashcards

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1
Q

What is biology the study of

A

life

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2
Q

characteristics of life (7)

A
  • reproduction
  • ability to metabolize
  • growth and development
  • homeostasis
  • sense + respond to stimulus
  • has order/organization
  • adaptation
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3
Q

reproduction

A

the ability to generate offspring with new combinations of (parent) DNA

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4
Q

ability to metabolize (2 types)

A
  • catabolism: break down molecules to yield energy

- anabolism: building up of molecules by using energy

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5
Q

growth and development

A
  • growth: size

- development: maturation

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6
Q

homeostasis

A

the ability to maintain a controlled internal environment

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7
Q

sense + respond to stimulus (2 types)

A
  • immediate: fight or flight, phototropism

- overtime: evolutionary adaptations that do not just occur in 1 individual

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8
Q

has order/organization

A

made up of at least one cell that has chemical structure and cellular processes

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9
Q

adaptation

A

changes that occur over time due to natural selection and mutation

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10
Q

are viruses living?

A

no, because they require a host to reproduce

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11
Q

Classification of Living Organisms (9)

A
  • domain (most inclusive and least genetically identical)
  • kingdom
  • phylum
  • class
  • order
  • family
  • genus
  • species
  • sub species/strain (least inclusive and most genetically identical)
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12
Q

How were domains discovered and how many are there?

A
  • discovered by woese and fox
  • sequenced 165 rRNA genes and found 3 different types
  • 3 domains of life
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13
Q

What are the 3 domains and their characteristics?

A 
-Archaea:
prokaryotes 
single celled extremophiles
no nucleus
-Bacteria:
prokaryotes
-Eukarya
eukaryotes
have a nucleus
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14
Q

What organisms are classified as Archaea?

A
  • methanogens (organisms that produce methane)
  • extreme halophiles (salt loving)
  • extreme thermophiles
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15
Q

What organisms are classified as bacteria?

A
  • gram positive (thick cell walls of peptidoglycan)
  • gram negative/proteobacteria (thin cell walls of peptidoglycan)
  • cyanobacteria (photosynthesis bacteria)
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16
Q

What organisms are classified as eukarya

A
  • protista
  • fungi
  • plantae
  • anamalia
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17
Q

what is the organism naming system called

A

binomial nomenclature

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18
Q

what are the 5 unifying themes of life

A
  • organization
  • information
  • energy and matter
  • interactions
  • evolution
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19
Q

What is organization

A

heirarchy used to organize the study of life

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20
Q

what is the order of the heirarchy of life

A
  • biosphere
  • ecosystem
  • community
  • population
  • organism
  • organs
  • tissues
  • cells
  • organelles
  • molecules
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21
Q

biosphere

A

all life on eart and all of the places where life exists

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22
Q

ecosystem

A

all the living things in a particular area, along with all of the nonliving components that life interacts with

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23
Q

community

A

the array of organisms that live in an ecosystem

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24
Q

population

A

all of the individuals within a species that live in a certain area

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25
Q

organism

A

individual living thing

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26
Q

organs

A

a bodypart made up of multiple tissues, with a specific function

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27
Q

tissues

A

a group of cells that works together to perform a function

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28
Q

cells

A

lifes fundamental unit, the smallest unit of organization that can perform all activities required for life

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29
Q

organelles

A

functional components of cells

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30
Q

molecules

A

a chemical structure consisting of two or more atoms

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31
Q

reductionalism

A

reduces complex systems to simpler components that are more manageable to study

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32
Q

emergent properties

A

new properties emerge at each level that are absent from the one before because complexity increases at higher levels of organizations

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33
Q

systems biology

A

exploring biological systems by analyzing interactions among its parts

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34
Q

how do structure and function corralate

A

you can analyze a structure to find clues about how it’s function works

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35
Q

cell theory

A

all living organisms are made up of cells-and the actions of organisms are based on the activities of cells

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36
Q

what are the differences between eukaryotic cells and prokaryotes

A 
EUKS
-membrane bound organelles
-has a nucleus
PROKS
-lack a nucleus
-no membrane bound organelles
-generally smaller than euks
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37
Q

where is DNA contained

A

chromosomes

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38
Q

what does DNA contain

A

genes

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39
Q

what are genes

A

units of inheritance, code the info necessary to build all molecules synthesized in a cell (identity and function)

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40
Q

structure of DNA

A

2 chains arranged in a double helix

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41
Q

what are nucleotides

A

they make up the strands of the double helix

chemical building blocks A,T,C,G

specific sequences of nucleotides encode info in genes (many times it is making protein)

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42
Q

producers

A

photosynthetic organisms that consumers feed on

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43
Q

consumers

A

organisms that feed on other organisms, or their remains

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44
Q

what happens when an organism uses chemical energy to do work

A

some of that energy is lost to the surroundings, in the form of heat

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45
Q

how does energy flow through an ecosystem

A
  • in 1 direction

- usually enters as light and exits as heat

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46
Q

how are chemicals recycled in an ecosystem

A

when chemicals that the plant absorbs have passed through the host’s body, the plants re-uptake the chemical again

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47
Q

why is feedback regulation important

A
  • interactions between components that make up organisms are crucial to smooth operation
  • the output or product of a process is what regulates the process
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48
Q

negative feedback loop

A

the response reduces the initial stimulus

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49
Q

positive feedback loop

A

the response increases the initial stimulus

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50
Q

which feedback loop is most common

A

negative feedback loop

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51
Q

3 types of organism interactions

A
  • mutually beneficial
  • one species benefits, the other doesn’t
  • both are harmed
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52
Q

relationship between organisms and their environment

A

organisms help their environments and the environment helps the organisms

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53
Q

climate change

A

a directional change to the global climate that lasts for 3 decades or more

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54
Q

evolution

A

a process of biological change in which species accumulate differences from their ancestors as they adapt to different environments over time

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55
Q

the order of naming organisms

A
  1. genus (which the species belongs to)

2. unique to the species within the genus

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56
Q

what are the 3 domains of life

A

bacteria
archaea
eukarya

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57
Q

domain bacteria

A

most diverse and widespread prokaryotes

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58
Q

domain archaea

A

live in the earth’s most extreme environments (prokaryotes)

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59
Q

kingdoms in domain eukarya

A
  • plantae
  • fungi
  • animalia
  • protists
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60
Q

kingdom plantae

A

multicellular eukaryotes that carry out photosynthesis (usually live on land)

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61
Q

kingdom fungi

A

characterized by the nutritional mode, which absorbs nutrients from outside of their bodies

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62
Q

kingdom animalia

A

multicellular eukaryotes that ingest other organisms

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63
Q

protists

A

mostly unicellular eukaryotes and simpler, multicellular relatives

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64
Q

what is used to distinguish most of the kingdoms in domain eukarya

A

nutrition

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65
Q

what are the 2 main points in Charles darwin’s “On the Origin of Species by Means of Natural Selection”

A
  • species adapt to different environments over time, and accumulate differences from their ancestors (descent with modification)
  • natural selection is a primary cause of descent with modification
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66
Q

what are darwin’s 3 observations of nature

A
  • individuals in a population vary in their traits, many of which seem to be heritable
  • a population can produce far more offspring than can survive to produce offspring of their own (more individuals than the environment can support=competition)
  • species are generally suited to their environments (adapted to circumstances)
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67
Q

what individuals are more likely to survive and reproduce

A

individuals with inherited traits that are better suited to the local environment, opposed to those who are less well-suited

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68
Q

corralation between time and suitable traits

A

over generations, a higher and higher proportion of individuals in a population will have the advantageous trait

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69
Q

darwins proposal of descendant species

A

-one population of organisms became fragmented into several populations
-b/c they were isolated in different environments
-1 species radiated into multiple species and adapted to the different environments
(galapagos finches)

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70
Q

genomics

A

large scale analysis of the DNA sequences of a species

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71
Q

bioinformatics

A

using computational tools to deal with huge volumes of sequences data

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72
Q

compound

A

made of atoms, joined by bonds

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73
Q

what does number of protons determine

A

determines and atoms identity

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74
Q

what does electron distribution determine

A

ability to form bonds

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75
Q

what does a compound’s properties depend on

A

its atoms and how they are bonded together

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76
Q

matter

A
  • organisms are composed of it
  • anything that takes up space and has mass
  • matter is made up of elements
  • consists of chemical elements in pure form and in compounds
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77
Q

element

A

a substance that cannot be broken down to other substances by chemical reactions

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78
Q

how many elements occur in nature

A

92

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79
Q

compound

A

a substance consisting of 2 or more different elements combined in a fixed ratio

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80
Q

what percentage of the 92 naturally occuring elements are essential

A

20-25%

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81
Q

essential elements

A

organisms need these to live and to reproduce

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82
Q

what are the top 4 essential elements and the % of living matter that they make up

A 
oxygen
carbon
hydrogen
-nitrogen
96%
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83
Q

what are the top 4 trace elements and the % of living matter that they make up

A 
calcium
phosphorus
potassium
sulfur
4%
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84
Q

Atom

A

smallest unit of matter that still retains the properties of an element

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85
Q

subatomic particles

A

what atoms are composed of…

  • protons (+)
  • electrons (-)
  • neutrons
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86
Q

what 2 subatomic particles are almost identical in mass

A

protons and neutrons (about 1 dalton)

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87
Q

characteristics of the atomic nucleus

A
  • protons and neutrons are tightly packed
  • electons are moving rapidly
  • electrons form a “cloud” of negative charge
  • the attraction between the opposite charges keep the electrons near the nucleus
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88
Q

what is a Dalton

A

named after John Dalton who helped develop the atomic theory, and is used to measure atoms/subatomic particles (amu)

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89
Q

atomic number

A

the number of protons unique to that element (bottom)

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90
Q

mass number

A

total number of protons and neutrons in the nucleus of an atom (top)

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91
Q

how do you find the # of neutrons

A

atomic number - mass number (bottom-top)

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92
Q

atomic mass

A

total mass of the atom

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93
Q

isotopes

A
  • when all atoms of a given element have the same number of protons
  • buttt some of the atoms have more neutrons (and a greater mass)
  • essentially are different forms of the same element
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94
Q

radioactive isotope

A
  • nucleus spontaneously decays => gives off particles of energy
  • isotopes are unstable, nuclei lose subatomic particles
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95
Q

what happens when radioactive decay causes a change in the number of protons in an isotope

A

the atom transforms to that of another element

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96
Q

radioactive tracers

A

used to follow chemical processes of an organism and diagnose problems (but is dangerous)

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97
Q

radiometric dating

A

used to measure radioactive decay of fossils in order to date them

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98
Q

half life

A

when a parent isotope decays into its daughters isotope at a steady rate (time it takes for 50% of the parent isotope to decay)

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99
Q

when 2 atoms approach eachother during a chemical reaction, how do their nuclei behave

A

they do not interact because they do not come close enough to. most of an atom is empty space

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100
Q

what subatomic particle is directly involved in reactions

A

electrons

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101
Q

what is energy and how does it relate to electrons

A

energy is the capacity to do work. electrons of an atom vary in energy levels

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102
Q

what is potential energy and how does it relate to electrons in the nucleus

A
  • energy that matter has because of its location or structure
  • matter tends to move towards the lowest area of potential energy
  • potential energy results from an electrons distance from the nucleus
  • the further away the electrons are from the nucleus, the greater the potential energy (takes for work to keep them further away)
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103
Q

energy levels

A

electrons exist at specific energy levels

  • closer to the nucleus = less energy
  • further away from the nucleus = more energy
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104
Q

what are electron shells

A

electrons live here, each shell has a unique distance and energy level

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105
Q

can electrons move from one shell to another? if so, how?

A

yes, BUT only by absorbing or loosing energy equal to the difference of PE between positions

  • absorbing energy = moving out
  • loosing energy = moving in
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106
Q

how is chemical behavior determined?

A

by the distribution of electrons in the electron shells (mostly the outer shell)

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107
Q

periods on the periodic table

A

elements are arranged in 3 rows, and they correspond to the number of electron shells in their atoms

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108
Q

1st shell

A

this is the lowest electron shell (2 electrons)

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109
Q

3rd shell

A

highest electron shell (up to 18)

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110
Q

how many electrons does the 2nd shell hold

A

8

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111
Q

valence electrons

A

electrons in the outermost shell

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112
Q

valence shell

A

the outermost electron shell

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113
Q

electron orbitals (definition)

A

the 3D space where an electron is found 90% of the time

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114
Q

what is the reactivity of an atom dependant on

A

unpaired electrons

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115
Q

atoms with incomplete valence shells…

A

can interact with certain other atoms so that it can complete its valence shell

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116
Q

methods of completing a valence shell (2)

A

sharing or transfering valence electrons

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117
Q

strongest kinds of bonds (for covalent and ionic)

A
  • covalent=in molecules

- ionic=dry ionic compounds

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118
Q

covalent bonds

A

the sharing of a pair of electrons by 2 or more atoms

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119
Q

double bonds

A

when atoms form a molecule and share TWO pairs of valence electrons

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120
Q

bonding capacity

A

when an atom has a full valence shell of electrons (usually equal to the number of electrons needed to complete it)

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121
Q

electronegativity

A

attraction for a particular atom for the electrons of a covalent bond

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122
Q

the more electronegative an atom is . . .

A

the stronger is pulls on shared electrons towards itself

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123
Q

when is electronegativity the same in both atoms?

A

non polar covalent bonds, because they share electrons

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124
Q

polar covalent bonds

A

when bonds are not shared equally and one atom is more electronegative

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125
Q

polar covalent bonds

A

when bonds are not shared equally and one atom is more electronegative

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126
Q

ionic bonds

A

when 2 atoms are so unequal in the attraction for their valence electrons that the more electronegative one strips an electron away from its partner

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127
Q

ions

A

the 2 resulting, oppositely charged atoms after an ionic bond

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128
Q

cation

A

+ ion

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129
Q

anion

A
  • ion
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130
Q

cation+anion

A

attracted to eachother, form ionic bonds

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131
Q

what are the advantages of weak bonds (ones that arent covalent between molecules)

A

they can effect eachother, but then seperate

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132
Q

important weak interactions

A

hydrogen bonds, vanderwaals interactions, ionic bonds in water

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133
Q

hydrogen bonds

A
  • an H+ ion covalently bonds to an electronegative atom
  • partial + charge of H+ attracts a negative charge and a noncovalent attraction occurs
  • usually takes place between oxygen or nitrogen in living cells
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134
Q

van der waals interactions

A

when electrons are not evenly distributed => can accumulate by chance in one part of a molecule

  • ever-changing regions of postive/negative charge that allows atoms+molecules to stick to one another
  • only occurs when atoms/molecules are very close together
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135
Q

how are molecules aranged when there are 2 or more of them

A

they are always linear

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136
Q

how are shapes of molecules determined

A

by the positions of the atom’s orbitals

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137
Q

what happens to the atoms when a covalent bond is formed

A

the orbitals in the valence shell undergo rearrangement

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138
Q

what happens when molecules with atoms in both s and p orbitals form covalent bonds

A

4 new hybrid orbitals shaped like teardrops extend from the nucleus (tetrahedron with a triangle base)

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139
Q

why is molecular shaoe important

A

it determines how biological molecules recognize and respond to one another

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140
Q

chemical reactions

A

the making and breaking of chemical bonds => changes in composition of matter

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141
Q

reactants

A

starting materials

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142
Q

products

A

resulting materials

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143
Q

how far out can the point of equilibrium be

A

some are so far out that reactions almost go to completion

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144
Q

is water polar or nonpolar

A

polar

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145
Q

what types of charges do O and H have

A
  • o has a partial negative charge

- H has a partial positive charge

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146
Q

how is water bonded and why

A

water forms hydrogen bonds because the weak attractions between oppositely charged O and H

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147
Q

how does water bond in the liquid form

A

hydrogen bonds are constantly breaking and reforming, which allows molecules to slip closer together

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148
Q

how does water bond in the solid form

A
  • hydrgen bonds are stable
  • water molecules are further apart
  • ice is less dense than liquid and floats
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149
Q

what does floating ice do to the water below

A

insulates it, promoting aquatic life

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150
Q

what are polar covalent bonds

A

b/c oxygen is more electronegative than hydrogen, electrons of the covalent bond spend more time closer to the oxygen

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151
Q

why is water a polar molecule

A

b/c the electrons are unequally shared and the molecule is V shaped
-overall charge is unevenly distributed

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152
Q

properties of water

A

properties arise from the attraction between oppositely charged atoms of different water molecules

  • held together by hydrogen bonds
  • in liquid form, bonds are very fragile
  • bonds break and reform VERY often
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153
Q

What are the 4 emergent properties of water

A
  • cohesion
  • high surface tension
  • cohesion and the transport of water against gravity in plants
  • adhesion
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154
Q

cohesion of water molecules

A

hydrogen bonds hold water together collectively

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155
Q

high surface tension

A

hydrogen is bonded to one another and to the water below but not to the air above
-the asymmetry gives high surface tension

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156
Q

cohesion and the transport of water against gravity in plants

A

water goes from the roots to the leaves through a network of water conducting cells

  • water evaporates from the leaf, leaves the veins to tug molecules further down because of the hydrogen bonds
  • an upward pull is transmitted through the water conducting cells to the roots
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157
Q

adhesion

A

the clinging of one substance to another
-because of the H+ bonds in water, adhesion of water to the molecules of a cell wall helps counter the downward pull of gravity in cohesion transport

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158
Q

photosynthesis, reactants and products

A

process that is the foundation of life

reactants: 6CO2 + 6H2O
products: C6H12O6 + 6O2

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159
Q

are all chemical reactions reversible?

A

theoretically, all chemical reactions are reversible

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160
Q

the greater the concerntration of reactant molecules…

A

the more frequently they collide and react to form products

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161
Q

what happens as products in chemical reactions accumulate

A

collisions resulting in reverse reaction become more frequent

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162
Q

chemical equillibrium

A

when reactions/reverse reactions offset eachther

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163
Q

how does water moderate air temp

A

by absorbing heat from air that is warmer and releasing stored heat to air that is cooler

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164
Q

kinetic energy and the relationship with molecules

A

the faster molecules move, the greater their kinetic energy

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165
Q

thermal energy

A

the kinetic energy associated with the random movement of atoms/molecules. passes from warmer to cooler until the 2 reach the same temp

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166
Q

temperature

A

represents the average kinetic energy of the molecules in a body of matter

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167
Q

difference between thermal energy and temperature

A

thermal energy reflects the TOTAL kinetic energy, temperature reflects AVERAGE kinetic energy

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168
Q

heat

A

when thermal energy is transfered from one body of matter to another

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169
Q

calorie

A

amount of heat it takes to raise the temp of 1g of H2O by 1* C
-also the amnt of heat that 1g of H2O releases when it cools by 1*C

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170
Q

kilocalorie

A

1kg=1*C (same as calorie but in kgs)

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171
Q

joule (cals and joules conversion)

A

equals .239 cals

1 cal=4.184 J

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172
Q

Waters specific heat

A

the amount of heat that must be absorbed or lost for 1 g of that substance to change its temp by 1 degree
-H2O changes its temp less often because much of the heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster

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173
Q

what happens when the temp of water drops slightly

A

H bonds form and release energy in the form of heat

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174
Q

evaporative cooling

A

stabilizes the temp of H2O

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175
Q

how does evaporative cooling work

A
  • molecules moving fast enough to overcome attraction can depart the liquid and enter the air as gas
  • some evaporation occurs at any temperature, but when liquid is heated the average KE of molecules increases and the liquid evaporates more rapidly
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176
Q

heat of vaporization

A

the quanitity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas

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177
Q

heat of vaporization of water

A

1g of H2O @ 25*C needs 580 cals of heat

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178
Q

why does H2O have a high heat of vaporization

A

due to the strength of hydrogen bonds

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179
Q

why does ice float on liquid water

A

water expands when it solidifies instead of contracting/becoming denser

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180
Q

solution

A

a mixture (homogenous) of 2 or more substances

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181
Q

solvent

A

dissolving agent

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182
Q

solute

A

the substance that is dissolved

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183
Q

aqueous solution

A

solute is dissolved in water

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184
Q

why is water a versitile solvent

A

because of its polarity

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185
Q

hydration shell

A

a sphere of water molecules around each dissolved ion

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186
Q

what can be dissolved in water

A

anything, as long as the molecules have an ionic and polar region

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187
Q

hydrophilic

A

likes water

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188
Q

hydrophobic

A

scared of water, nonpolar, nonionic

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189
Q

are hydrophilic substances dissolvable

A

not always ex) cotton towels

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190
Q

how are hydrophobic substances bonded

A

nonpolar covalent bonds

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191
Q

molarity

A

of moles of solute per liter of solution (and unit of concentration for aqueous solutions

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192
Q

mole

A

number of molecules in a substance

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193
Q

buffer

A

an acid-base pair that combines reversibly with hydrogen ions, allowing it to resist pH changes

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194
Q

ocean acidification

A

fossil fuels are burned => increase CO2 => CO2 dissolves in ocean

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195
Q

carbon chemistry

A

specializes in the study of carbon

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196
Q

electrons in carbon

A 
2 in first shell
4 in second shell
4 empty electron spots in second shell
valence number = 4
total electrons = 6
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197
Q

what are carbon’s bonding patterns

A

carbon shares electrons with other atoms to complete its outer shell (very little tendency to gain or lose electrons/form ionic bonds)

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198
Q

hydrocarbons

A

organic molecules consisting of only carbon and hydrogens

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199
Q

isomers

A

compounds that have the same molecular formula but different structure and therefore have different properties

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200
Q

what are the 3 classes of isomers

A
  • structural isomers
  • geometric isomers
  • enantiomers
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201
Q

structural isomers

A

differ in the arrangements of their atoms

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202
Q

geometric isomers

A

cis-trans

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203
Q

entantiomers

A

mirrored

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204
Q

functional groups

A

components of organic molecules that are most commonly involved in chem reactions (bonded to carbon skeleton)

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205
Q

6 functional groups

A 
hydroxyl
carbonyl
carboxyl
amino
sulfhydryl
phosphate
methyl
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206
Q

hydroxyl

A
  • OH
  • ex)alcohols
  • polar (O is electroneg)
  • water is attracted to these
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207
Q

carbonyl

A

=O (double bond)

  • aldehyde (on end of carbon skeleton)
  • ketone (in middle of carbon skeleton)
  • polar
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208
Q

carboxyl

A
  • COOH
  • carboxylic acids
  • have acidic properties because H+ tends to dissociate
  • covalent bond between H and O are VERY polar
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209
Q

amino

A
  • NH2
  • amines
  • act as bases
  • commonly attract H+ ions, giving it a + charge
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210
Q

sulfhydryl

A
  • SH
  • thiols
  • stabilizes the structure of proteins
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211
Q

phosphate

A
  • PO4-

- important for the transfer of energy between organic compounds

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212
Q

methyl

A
  • CH3
  • methylated compounds
  • nonpolar
  • adding a methyl group to DNA affects gene expression
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213
Q

what makes carbon the basis for all biological molecules

A
  • can form 4 bonds (with other atoms/groups of atoms)

- can bond to other carbons (carbon skeleton)

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214
Q

what does ccarbon commonly bond with

A
  • hydrogen
  • oxygen
  • nitrogen
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215
Q

organic chemistry

A
  • carbon containing compounds = organic

- study of these

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216
Q

what kind of bonds do carbons form

A

a covalent bond

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217
Q

what kind of molecules does carbon form and why

A
  • large, complex molecules

- b/c molecules can branch out from a carbon in as many as 4 directions

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218
Q

what shape will carbon be in 4, singular&covalent bonds

A

tetrahedron

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219
Q

what shape will carbon be in for 2, double bonds

A

both carbons will be in the same plane (molecule is flat)

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220
Q

shapes of carbon skeletons

A
  • vary in length
  • straight
  • branched
  • closed ring
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221
Q

what constitutes carbon’s molecular complexity in living matter

A

-some have double bonds that vary in number and location => variation in carbon chains

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222
Q

hydrocarbons

A

organic molecules consisting of only carbon and hydrogen

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223
Q

how are hydrocarbons bonded

A

covalently

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224
Q

characteristics of hydrocarbons

A
  • hydrophobic

- do not dissolve in water

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225
Q

characteristics of a cis-trans isomer

A
  • atoms differ in spacial arrangement due to the inflexibility of double bonds
  • single bonds allow atoms to rotate freely without changing the compound
  • double bonds to not rotate
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226
Q

characteristics of an enantiomer

A
  • 4 groups can be arranged in space around asymmetric carbon in 2 different ways, which forms mirror images
  • only 1 is usually biologically active (only that 1 form can bond to specific molecules)
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227
Q

why are phosphate groups key to molecular function

A
  • because ATP!

- ATP is made up of an adenosine attached to a string of 3 phosphate groups

228
Q

monomer

A

1 building block of a polymer

-small repeating molecules

229
Q

polymer

A

more than 1 monomer joined together to make a large molecule

-long molecules consisting of many identical or similar building blocks linked by covalent bonds

230
Q

polymers and their monomers (biological molecules)

A
  • proteins/amino acids
  • carbohydrates/monosaccharides
  • lipids/fatty acids+glycerol
  • nucleic acid/nucleic acids
231
Q

dehydration reactions

A

removes a water to form a new bond

232
Q

hydrolysis

A

adds a water to break a covalent bond

  • chemical reactions responsible for the disassembly of polymers
  • reverse if dehydration reactions
233
Q

carbohydrates

A

main source of energy in living organisms

234
Q

types of saccharides (4)

A
  • monosaccharides
  • disaccharides
  • trisaccharides
  • polysaccharides
235
Q

what is the general structural formula of monosaccharides

A

(CH2O)n

236
Q

pentose

A

5 carbon sugar

237
Q

ribose

A

RNA (has extra oxygen from the hydroxyl group at its 2nd carbon)

238
Q

deoxyribose

A

DNA (only hydrogen at the 2nd carbon)

239
Q

how are disaccharides bonded

A

glycosidic linkage (covalent bond)

240
Q

structure of disaccharides

A

2 glucose molecules and a loose H2O molecule

241
Q

what are the 3 important disaccharides

A
  • maltose
  • sucrose
  • lactose
242
Q

maltose

A

glucose+glucose

243
Q

sucrose

A

glucose+fructose

244
Q

lactose

A

glucose+galactose

245
Q

starch

A

energy storage form of glucose in plants

246
Q

cellulose

A

major component of plant cell walls

247
Q

lipids

A

3 fatty acids and 1 glycerol

248
Q

lipids

A

3 fatty acids and 1 glycerol

249
Q

saturated fatty acid

A

only single bonds

250
Q

unsaturated fatty acids

A

1 double or triple bond in the chain

251
Q

polyunsaturated fatty acid

A

more than 1 double or triple bond in an ester linkage

252
Q

biologically relevant lipids

A

phospholipids and steroids

253
Q

in a condensation/dehydration reaction, how do the molecules contribute to the loss of a water molecule

A
  • one molecule contributes the -OH group

- one molecule contributes the -H group

254
Q

carbohydrates

A

main source of energy: sugars (saccharides)

255
Q

what are the 3 types of saccharides

A

mono
di
poly

256
Q

about monosaccharides

A
  • simple sugar

- general structure (CH2O)n

257
Q

hexose

A

monosac

6 carbon sugars

258
Q

pentose

A

monosac

5 carbon sugar

259
Q

glucose

A

C6H12O6

aldose sugar

260
Q

fructose

A

C6H12O6

ketose sugar

261
Q

disaccharides

A

two simple sugars joined together

262
Q

glycosidic linkages

A

a covalent bond formed between 2 monosaccharides by a dehydration reaction

263
Q

sucrose

A

(disac)

glucose+fructose

264
Q

maltose

A

(disac)

glucose+glucose

265
Q

lactose

A

glucose+galactose

266
Q

polysaccharides

A

more than 2 simple sugars joined together

267
Q

what are the biologically important polysaccharides

A
  • starch
  • glycogen
  • cellulose
  • chitin
268
Q

starch

A

storage form of glucose in animals
alpha glucose=(-OH group of C1 is down)
1-4 linkages

269
Q

glycogen

A

storage form of glucose in plants
alpha glucose=(-OH group of C1 is down)
1-4 and 1-6 linkages

270
Q

cellulose

A

major components of plant cell walls
polymers of beta glucose (-OH group on C1 is up)
1-4 linkages

271
Q

chitin

A

component of arthropod exoskeleton (invertabrates), and the cell wall of some fungi
beta-glucose (-OH group on C1 is up) with nitrogen appendages

272
Q

fatty acids

A

the building blocks of lipids: long chains of carbon atoms with associated hydrogen

273
Q

saturated fatty acids

A

chains of carbons with single bonds

274
Q

unsaturated fatty acids

A

chains of carbons with one double or triple bonds (makes a kink in the chain)

275
Q

polyunsaturated fatty acids

A

chains of carbons with more than one double or triple bonds

276
Q

long chains of hydrocarbons and their relationship with water

A

no affinity for water

277
Q

basic structure of lipids

A
  • 3 fatty acid chains bonded by an ester linkage (long carbon skeleton of 16-18 carbons in length
  • 1 glycerol (3 carbon alcohol)
278
Q

structure of phospholipids

A
  • 2 fatty acid chains and a phosphate group joined to a glycerol
  • amphipathic (both hydrophilic and hydrophobic parts)
279
Q

what is the charge and polarity of the phosphate group in phospholipids

A

negative charge, polar

280
Q

what is the charge and polarity of fatty acid groups

A

uncharged and nonpolar

281
Q

micelles

A

aggregate of phospholipids that form when they are put into an aqueous solution

282
Q

phosphate heads

A

exposed to water

283
Q

carbon tails

A

are shielded from the water

284
Q

importance of phospholipids

A

they form cell membranes/lipid bilayers

285
Q

steroids

A

lipids characterized by a carbon skeleton consisting of 4 fused rings

  • different steroids have different functional groups attached to the rings
  • vertebrate sex hormones
286
Q

cholesterol

A

common component of animal cell membranes, precursor from which other steroids are synthesized

287
Q

proteins

A

made of amino acids joined together by peptide bonds

288
Q

how many amino acids are there that make up proteins

A

20

289
Q

amino acid structure

A
  • amine group
  • carboxyl group
  • R group (gives each amino acid different chemical properties, like polar/nonpolar/acid/base)
290
Q

what are 2 amino acids bonded together called, and how are they bonded

A

dipeptide, bonded by peptide bonds

291
Q

what is it called when many amino acids are bonded together

A

polypeptide

292
Q

primary structure

A

a linear sequence of amino acids

293
Q

secondary structure

A
  • alpha helix

- beta pleated sheets

294
Q

primary structure

A

a linear sequence of amino acids

295
Q

secondary structure

A
  • alpha helix

- beta pleated sheets

296
Q

alpha helix

A

forms dur to hydrogen bonding every 4th amino acid in primary structure

297
Q

beta pleated sheet

A

due to hydrogen bonding between 2 sections of the primary structure that are aligned parallel to eachother

298
Q

tertiary structure

A

irregular contortions from bonding between R-groups of the various amino acids

299
Q

hydrophobic interactions

A

amino acids with non-polar R-groups tend to cluster in the center of the protein

300
Q

how do hydrogen bonds form in tertiary structure

A

between polar side chains

301
Q

how do ionic bonds form in tertiary structure

A

between positive (base) and negative (acid) charged R-groups

302
Q

what force is betwee R-groups in tertiary reactions

A

vanderwaals forces

303
Q

disulfide bridges

A

covalent bonds between sulfur groups in the R-group of amino acid cystein

304
Q

quaternary structure

A

overall protein structure that results from the aggregation of polypeptide units

305
Q

collagen

A

3 polypeptides that aggregate to form a triple helix

306
Q

hemoglobin

A

consists of 2 kinds of polypeptide chains, with 2 of each kind per hemoglobin molecule

307
Q

what are the 2 classes of proteins

A

structural proteins

functional proteins

308
Q

function of structural proteins

A

cell structure

309
Q

clases of functional proteins

A
  • enzymes
  • transport proteins
  • hormones
  • receptor proteins
  • contractile/motor proteins
  • defense proteins
310
Q

what determines protein conformation

A

a polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a 3D shape maintained by the above interactions
-also depends upon the physical and chemical conditions of the proteins environment (pH, salt concentration, temp)

311
Q

denaturation

A

unraveling of protein structure due to adverse environmental conditions, the protein is said to be inactive

312
Q

Nucleic acids

A

DNA

RNA

313
Q

structure of nucleic acids

A
  • composed of chains of monomers called nucleotides
  • pentose sugar (deoxyribose/ribose)
  • nitrogenous base: pyrimidine (6 membered ring fused to a 5 member ring) (adenine and guanine)
  • phosphate group
314
Q

nucleosides

A

pentose sugar + nitrogenous base

315
Q

nucleotides in DNA

A

GATC

316
Q

nucleotides in RNA

A

GAUC

317
Q

polynucleotide structure

A

anti-parallel double helix (5’/3’ ends)

  • base pairing via hydrogen bonds (DNA=A-T G-C) (RNA= A-U G-C)
    - 2 H bonds between A and T and 3 H-bonds between C and G
318
Q

organelles

A

tiny sacs and compartments bounded by membranes

319
Q

what characteristics do both euks and proks share

A
  • outer plasma membrane
  • internal region of DNA
  • cytoplasm
320
Q

plasma membrane

A

forms boundaries between cell and external environment

  • phospholipid bilayer
  • contains sterols(cholesterol)
  • contains proteins for transport and recognition
321
Q

phospholipid bilayer

A
  • hydrophilic end

- hydrophobic end

322
Q

fluid mosaic model

A

plasma membrane is a fluid structure with a mosaic of various proteins embedded in it
the fluid nature of the membrane allows the proteins and phospholipids to move in the horizontal plane without losing the membrane’s integrity

323
Q

nucleus

A

contains DNA organized into chromosomes, existing in the form of chromatin (a DNA histone complex)

  • membrane
  • nuclear pores
  • nucleoli
  • nucleoplasm
324
Q

membrane in nucleus

A

bound by a double lipid bilayer-nuclear envelope

325
Q

nuclear pores

A

highly selective to protect chromosomes

326
Q

nucleoli

A

synthesis of ribosomes

327
Q

nucleoplasm

A

cytoplasm of nucleus

328
Q

characteristics of cytoplasm

A
  • within plasma membrane but outside of nucleus
  • cytosol (the watery substances supporting organelles
  • contains metabolic machinery (organelles, enzymes, etc)
329
Q

mitochondria

A 
energy center (powerhouse of the cell)
-forms ATP through the electron transport system
330
Q

how many membranes does the mitochondria have

A

2, one outer and one inner that folds and forms cristae

331
Q

why are cristae important

A

they increase the surface area of the membrane to permit increased ATP production

332
Q

what does the double membrane in mitochondria create

A

matrix-space inside the inner membrane

intermembrane space-space between the inner and outer membrane

333
Q

ribosomes

A
  • composed of rRNA and r-proteins

- used to make protein from DNA

334
Q

endoplasmic reticulum

A

circulatory system of the cell

335
Q

smooth ER

A

lipid assembly/modification and transport

  • carbohydrate metabolism
  • detoxification of drugs and poisons
336
Q

rough ER

A

protein assembly/modification and transport

  • bounded by ribiosomes
  • stores proteins
337
Q

golgi apparatus

A

recieves protein from ER (cis end) and further modifies

-packages proteins for transport either within or external to cell (trans end)

338
Q

lysosomes

A
  • contains hydrolytic enzymes that digest macromolecules
  • bind with vesicles containing ingested materials (food, bacteria) and break it down
  • autophagy
339
Q

autophagy

A

recycling of cells own organic materials derived from damaged materials

340
Q

peroxisomes

A
  • contains enzymes that transfer hydrogens from (usually toxic) substances to oxygen creating hydrogen peroxide
  • detoxifies alcohol
  • converts hydrogen peroxide to water because hydrogen peroxide is toxic
341
Q

vacuoles/vesicles

A
  • vesicles are smaller vacuoles

- transport, storage

342
Q

cytoskeleton

A

gives mechanical support to the cell, anchors organelles in the cytoplasm

  • aids in cellular molarity
  • helps to maintain its shape
  • made up of 3 types of fibers
343
Q

what are the 3 types of fibers in the cytoskeleton

A
  • microtubules
  • microfilaments
  • intermediate filaments
344
Q

microtubules

A

shape and support the cell and serve as tracks along which the organelles can move

345
Q

microfilaments/actin

A

bear tension within the cell

-help support the cell’s shape and are involved in cell motility

346
Q

intermediate filaments

A

-specialized for bearing tension and fixing the position of organelles, especially the nucleus

347
Q

centrosomes

A
  • microtubules organizing center for cell division

- composed of 2 centrioles (9 triplet microtubules) arranges in a ring

348
Q

what organisms lack centrosomes

A

-plant and yeast cells lack centrosomes

349
Q

flagella

A
  • composed of microtubules
  • external to plasma membrane
  • provide motility
350
Q

cilia

A
  • composed of microtubules
  • shorter and more numerous than flagella
  • used in movement of protozoa (single celled euks)
351
Q

how do cilia work in humans

A

ciliate cells move mucous and materials past the cell for expulsion

352
Q

pseudopodia

A
  • false feet
  • composed of microfilaments
  • projections of cytoplasm which creates ameboid movement
  • used in human phagocytes to engulf foreign material
353
Q

what are the organelles that are specific to plants

A 
chloroplast
central vacuole
tonoplast
cell wall
protoplast
plasmodesmata
middle lamella
354
Q

chloroplast

A
  • site of photosynthesis

- envelope of 2 phospholipid bilayers (inner and outer), separated by an intermembrane space

355
Q

structures in the chloroplast

A 
stroma
thylakoid membranes
grana
chlorophyl
thylakoid space
356
Q

stroma

A

space between the envelope and the thylakoid membrane

357
Q

thylakoid membranes

A

“pancake stacked” membranes that separate the stroma from the thylakoid space (or lumen)

358
Q

grana

A

the “pancake stacks” that increase surface area

359
Q

chlorophyll

A

resides in the thylakoid membranes

360
Q

thylakoid space

A

space inside the thylakoid membrane

361
Q

central vacuole

A

contains sap; nounded by the tonoplast

362
Q

tonoplast

A

membrane that regulates the traffic of molecules between the sap and the cytosol

363
Q

cell wall

A

external to the plasma membrane

364
Q

primary cell wall

A

all plant cells have; secreted as the cell grows and develops

365
Q

secondary cell wall

A

produced by certain specialized plant cells; closer to the protoplast than the primary wall because it forms after the cell has stopped growing: provides protection and support

366
Q

protoplast

A

are spherical naked plant cells produced by the removal of the cell wall with digestive enzymes

367
Q

plasmodesmata

A

cytoplasmic channels that pass through pores in the cell walls allowing the protoplasts of neighboring cells to be connected

368
Q

middle lamella

A

adhesive layer that cements together the cell walls of the adjacent cells

369
Q

prok cell structure

A
  • bacteria and archeae are considered proks
  • unicellular
  • smallest of all organisms (viruses are smaller but acellular)
  • bacteria
370
Q

shapes of bacteria

A
  • coccus
  • bacillus
  • vibro
  • spirillum
  • spirochete
  • pleiomorphic
371
Q

coccus

A

spheres

372
Q

bacillus

A

rods/coccobacillus (in between the 2)

373
Q

vibrio

A

comma shaped

374
Q

spirillum

A

cork skrew with flagella at one end or both ends

375
Q

spirochete

A

cork skrew with internal flagella

376
Q

pleiomorphic

A

bacteria exhibiting many shapes

377
Q

patterns of bacteria

A

cocci and bacilli

378
Q

types of cocci

A
  • diplococci
  • staphylococci
  • streptococi
  • tetrad
  • sarcinae
379
Q

diplococci

A

pairs

380
Q

staphylococci

A

clusters

381
Q

streptococci

A

chains

382
Q

tetrad

A

4 cell cube

383
Q

sarcinae

A

8 cell cube

384
Q

types of bacilli

A

bacillus and palisade

385
Q

bacillus

A

chains

386
Q

palisade

A

bacilli side-by-side

387
Q

cell/plasma membrane function/structure kinda

A

forms boundary between cell and external environment

-contains proteins for transport

388
Q

what does the bacterial cell membrane lack

A

sterols (cholesterol) but they contain sterol-like molecules called hopanoids

389
Q

characteristics of the cell wall

A
  • lies outside the cell membrane
  • porous
  • maintains integrity of cell shape
  • main component is peptidoglycan (murein)
390
Q

cross linking

A

a bond that links 1 polymer chain to another

391
Q

what type of amino acid can not be broken down by common enzymes

A

stereoisomers of common amino acids

392
Q

gram +

A

thick peptidoglycan wall

393
Q

gram -

A

thin peptidoglycan wall

394
Q

characteristics of the outer membrane of prok cells

A
  • gram -
  • attached to the cell wall and lipid bilayer
  • contains lipopolysaccharide (LPS)
  • core polysaccharide
  • o antigen
395
Q

lipid A

A

embedded in the outer membrane

-stabalizes outer membrane structure

396
Q

abt O antigen

A

displays antigen variation

397
Q

periplasmic space

A
  • gap between the cell membrane and the cell wall
  • includes peptidoglycan, enzymes, and proteins which makes up the periplasm
  • serves as a site for transport of nutrients protection
398
Q

protoplasts and spheroplasts

A

-the cell wall protects bacteria from osmotic lysis when they are in a hypotonic solution

399
Q

what does digestion of cell wall in gram + yield

A

protoplasts

400
Q

what does digestion of cell walls in gram - yield

A

spheroplasts

401
Q

cytoplasm

A
  • watery substance in the cell
  • contains metabolic machinery like proteins and DNA
  • determines cell shape
402
Q

nuclear region (nucleoid)

A

contains compacted DNA with some associated protein (not histones) and RNA

403
Q

plasmids

A

extra chromosomal DNA

404
Q

types of plasmids

A
  • conjugative plasmids
  • col plasmids
  • virulence plasmids
  • metabolic plasmids
405
Q

conjugative plasmids

A

F plasmids and R plasmids

406
Q

col plasmids

A

produce bacteriocins

407
Q

virulence plasmids

A

encode virulence factors

408
Q

metabolic plasmids

A

encode degradiative enzyme

409
Q

cytoskeleton

A

homologs of all 3 eukaryotic cytoskeletal components have recently been identified in bacteria (microtubules, microfilaments and intermediate filaments)

410
Q

functions of the cytoskeleton

A
  • participate in cell division

- localize proteins to certain sites within the cell

411
Q

ribosomes

A
  • RNA & protein structures that ain in synthesizing protein
  • euks: 80S
  • proks: 70S
412
Q

what does “S” mean

A

suedberg unit; sedimentation coeficcient measure of sedimentation velocity in a centrifuge

413
Q

inclusion granules

A

storage pools of required metabolites

  • stores glycogen and glucose
  • stores volutin and polyphosphate
414
Q

capsule

A

well organized and not easily washed off

415
Q

slime layer

A

more diffuse and can easily be removed

416
Q

similarities of the capsule and the slime layer

A

both are external to the cell wall and can be called glycocalyx

417
Q

functions of the capsule and the slime layer

A
  • prevents phagocytosis

- aids in adherance to host tissues

418
Q

pili/fambriae

A

-hollow projections

419
Q

what are the 2 types of fili/fambriae

A

conjugation pili and attachment pili

420
Q

conjugation pili

A

transfer of genetic material

421
Q

attachment pili/fambriae

A

attach to surfaces like cells and water

422
Q

flagella

A
  • external to cell wall

- provide motality

423
Q

key base word of flagella

A

trichous

424
Q

flagella prefixes

A
  • mono: 1
  • amphi: 1 at each end
  • lopho: 2 or more at one or both ends
  • peri: all over surface
  • a:none
425
Q

clockwise flagella movement

A

direct movement

426
Q

counter clockwise flagella movement

A

random movement

427
Q

chemo movement

A

move toward (positive) or away (negative) from chemical substances

428
Q

photo movement

A

toward or away from light

429
Q

aero movement

A

toward or away from oxygen

430
Q

osmo movement

A

move toward or away from osmotic pressure

431
Q

vegetative cells

A

cells that are actively metabolizing

432
Q

spore formation

A

occurs under harsh conditions

433
Q

dormant state

A

form within the cell

434
Q

endospores

A

highly resistant to environmental conditions, contains little water, resistant to heat

435
Q

sporulation

A

when conditions are right, the spores will germinate=begin to develop into vegetative cells again

436
Q

cell-cell recognition

A

a cells ability to distinguish one type of neighboring cell from another

437
Q

oligosaccharides

A

are on the external side of the plasma membrane, they vary from cell to cell and species to species

438
Q

what enables oligosacs to function and how do they function?

A

the diversity of molecules and their location on the cell’s surface. the oligosacs function as markers that distinguish one cell from another

439
Q

enzymatic activity

A

a protein embedded into the membrane with enzymatic activity

440
Q

what happens when there are several enzymes in a membrane

A

enzymes are ordered as a team that carries out sequential steps of a metabolic pathways, like in the mitochondria

441
Q

signal transduction

A

membrane protein with a b inding site for a chemical messenger such as a hormone

442
Q

what happens upon the protein bonding to a messanger

A

a signal is transmitted to the interior of the cell

443
Q

extracellular matrix (ECM)

A

the substance in which animal tissue cells are embedded

  • consists of proteins and polysaccharides
  • helps to maintain cell shape, anchor cells in a specific location, stabilizes membrane proteins
444
Q

what are the functions of plasma membrane proteins

A
  • cell/cell recognition
  • enzyme activity
  • signal transduction
  • intracellular joining (gap junctions, etc)
  • attachment to cytoskeleton and extracellular matrix
  • transport
445
Q

semi permeable membrane

A

ability of membranes to selectively permit certain substances to cross it over other substances

446
Q

hydrophobic phospholipid tails

A

core of the membrane. is the main barrier for transport across the plasma membrane

447
Q

molecules that can cross the plasma membrane

A 
-hydrophobic molecules: dissolve into the hydrophobic core of the membrane, enabling them to cross it
ex)
-hydrocarbons
-CO2
-O2
448
Q

molecules that cannot cross the plasma membrane

A

-hydrophilic molecules
ex)
-charged ions
-polar molecules

-large, uncharged and polar molecules (too big)
ex)
carbs
proteins

449
Q

transport proteins

A

proteins that span the membrane that permit the transit of ions, polar molecules and larger molecules across the membrane

450
Q

what type of structure do transport proteins usually have

A

hydrophilic channels

451
Q

aquaporins

A

transport proteins that transport water

452
Q

diffusion

A

the tendancy for molecules of any substance to spread out into available space from a high to low concentration (downhill)

453
Q

concentration gradient

A

a gradient of different concentrations of a solute in a solutions

454
Q

dynamic equilibrium

A

occurs when the concentration of solutes is equal access a membrane. There is no net charge in solute movement across the membrane but the solutes are still moving

455
Q

what must NOT happen in order for diffusion to occur

A

NO WORK must be done to make diffusion happen, it is a spontaneous process and delta G is negative

456
Q

passive transport

A

the diffusion of substances across a biological membrane

457
Q

what does the cell NOT do in passive transport

A

the cell does NOT expend energy

458
Q

facilitated diffusion

A

the passive transport of ions and polar molecules that cannot cross the semipermeable membrane on their own

459
Q

what is required in facilitated diffusion

A

a transport protein is required, it just serves as a hydrophilic channel

460
Q

osmosis

A

diffusion of water across a semi-permeable membrane (aka the passive transport of water)

461
Q

hypertonic solution

A

the solution has a higher solute concentration that the animal cell

462
Q

what happens in a hypertonic solution

A

water exits the cell and the cell shrinks

463
Q

hypotonic

A

a solution that has a lower solute concentration than the animal cell

464
Q

what happens in a hypotonic solution

A

the cell gains water and the cell could lyse

465
Q

isotonic

A

both solutions have the same solute concentration

466
Q

how do water molecules move

A

from a hypotonic solution to a hypertonic solution

467
Q

if a cell is placed in a hypertonic solution, what happens to its membrane?

A

plasmolysis: as the plant cell shrivels, the plasma membrane pulls away from the cell wall

468
Q

if a cell is placed in a hypotonic solution, what happens to its membrane

A

turgid-the cell takes up water until it is full and the turgid cells give a plant its structure

469
Q

what happens to the membrane when a cell is placed in an isotonic solution

A

it is flaccid and there is no net movement of water, so the membrane becomes limp and wilts

470
Q

active transport

A

the transport of solutes against their concentration gradients

471
Q

what does active transport require

A

active transport requires energy

472
Q

transport of large molecules

A

exocytosis, endocytosis

473
Q

exocytosis

A

fusion of vesicles derived from the golgi apparatus with the plasma membrane => extrusion of macromolecules
ex) hormones, insulin

474
Q

endocytosis

A

the taking in of macromolecules by forming vesicles derived from the plasma membrane through the process of phagocytosis, pinocytosis, receptor-mediated endocytosis

475
Q

phagocytosis

A

uptake of particles by wrapping pseudopodia around it and packaging it within a vacuole

476
Q

pinocytosis

A

the cell gulps droplets of extracellular fluid in tiny vesicles

477
Q

receptor mediated endocytosis

A

endocytosis of specific molecules that bind to membrane bound receptors

478
Q

steroids

A

4 fused hydrocarbon rings

479
Q

why is cholesterol important

A

b/c it is important in cell membrane structure

480
Q

what is the precursor molecule for all other human steroids

A

cholesterol

481
Q

how are proteins made in euk cells

A

DNA => mRNA => ribosomes +cytoplasm

occurs mostly in the nucleus

482
Q

how are proteins made in prok cells

A

everything occurs in the cytoplasm because theres no membrane bound organelles

483
Q

when do H bonds occur

A

every 4th amino acid, below the polar R-groups,

484
Q

what do H bonds do to the helix structure

A

stabilizes the alpha helix structure

485
Q

folding

A

FOLDING IS NOT RANDOM, it is due to the amino acids in the polypeptide

486
Q

what are the types of bonds that hold tertiary structure together

A
  • hydrophobic interactions
  • hydrogen bonding between R groups
  • ionic bonds below acidic + charges
  • disulfide bridges
487
Q

hydrophobic interactions

A

amino acids with non polar R-groups will cluser inside of the globular protein

488
Q

disulfide bridges

A

covalent bonds below R groups of cystein amino acids

489
Q

4 prime structure

A

multiple 3 prime proteins are bound together to create a large functional protein molecule

490
Q

chaperonin

A

helps 2 prime => 3 prime and 3 prime => 4 prime

491
Q

what are chaperonins made by

A

other chaperonins

492
Q

what are the types of functional proteins in a cell

A
  • enzymes
  • receptor proteins
  • transport proteins
  • structural proteins
  • motor proteins
  • defense proteins
  • hormones
493
Q

what determines protein structure

A

environment and function

494
Q

denaturation

A

process by which protein structure unfolds. this is irreversible, protein is nonfunctional b/c there is no chaperonins or DNA

495
Q

mRNA

A

codes for proteins

496
Q

RNA

A

carries amino acids to ribosomes to make a protein

497
Q

rRNA

A

structural components of the ribosome

498
Q

central dogma

A

DNA => RNA => protein

499
Q

purines

A

adenine and guanine

500
Q

perimadines

A

thymine, cytosine and uricil

501
Q

nucleosides

A

sugar + base w/o phosphate group

502
Q

what type of bond holds nucleotides together

A

phosphodiester

503
Q

characteristics of DNA

A
  • double stranded
  • antiparallel
  • 3’ and 5’ end
  • 2 different strands are oriented in opposite directions
504
Q

a-t

A

2 hydrogen bonds

505
Q

c-g

A

3 hydrogen bonds

506
Q

characteristics of RNA

A
  • single stranded (mRNA)

- tRNA + rRNA have regions of double strandedness

507
Q

characteristics of RNA

A
  • single stranded (mRNA)

- tRNA + rRNA have regions of double strandedness

508
Q

functions of cell to cell recognition (plasma membrane proteins)

A
  • used to help cells recognize eachother

- human immune response (recognizing the difference between self and non self)

509
Q

enzymetic activity

A

plasma membrane proteins that have metabolic functions

510
Q

signal transduction

A

enables cells to monitor environment + respond

511
Q

metabolism

A

the totality of an organisms chemical processes

512
Q

catabolic pathways

A

the metabolic pathways responsible for the breakdown of complex molecules into simpler ones

  • energy is released
  • cellular respiration
513
Q

cellular respiration

A

glucose => CO2 + H2O + ATP

514
Q

anabolic pathways

A
  • the metabolic pathways responsible for the build up of complex molecules from simpler ones
  • energy is consumed
  • photosynthesis
515
Q

photosynthesis

A

synthesis of a protein from amino acids

516
Q

bioenergetics

A

study of how organisms manage their energy resources

517
Q

energy

A

the capacity to do work

518
Q

thermodynamics

A

study of energy transformations that occur in a collection of matter

519
Q

the first law of thermodynamics

A

energy can be transferred and transformed, but it can not be created nor destroyed

520
Q

the second law of thermodynamics

A

every energy transfer or transformation increases the entropy of the universe

521
Q

how do organisms process energy

A

an organism takes in organized forms of energy from the surroundings and replaces them with less ordered forms of energy

522
Q

free energy

A

the portion of a system’s energy that can perform work when the temperature is uniform throughout the system (=potential energy of the system)
-the energy that is available to do work

523
Q

what are the 2 components of free energy (g)

A

H: potential + kinetic energy
S: the systems of entropy (randomness)
T: absolute temp in Kelvin units

524
Q

what is the equation for G free energy

A

G= H-TS

525
Q

chemical rections are of 2 types

A
  • spontaneous

- nonspontaneous

526
Q

spontaneous reactions

A

occur spontaneously because the starting materials have either high energy (unstable) or low entropy (not random) or both

  • complex macromolecules
  • catabolic reactions
527
Q

nonspontaneous reactions

A

require energy to occur. they do not occur spontaneously because the starting materials have either low energy (stable) or high entropy (random) or both

  • monomers
  • anabolic reactions
528
Q

free energy in spontaneous reactions

A

the free energy of a system decreases by either giving up energy (usually in the form of heat) or by increasing randomness

529
Q

what must free energy be in order for a spontaneous reaction to occur

A

change in G must be NEGATIVE

530
Q

what happens to free energy when chemical reactions reach equilibrium

A

free energy G = 0

531
Q

exergonic reactions

A

reactions that occur spontaneously, free energy is negative, and free energy is released (catabolic)

532
Q

endergonic reactions

A

reactions that do not occur spontaneously, free energy is positive, and free energy is absorbed for the reaction to occur (anabolic)

533
Q

metabolic disequilibrium

A

because free energy = 0 when the system reaches equilibrium, the system can do no work.

534
Q

what happens when all of the chemical reactions within a cell reach equilibrium

A

the cell would be dead

535
Q

how do cells prevent equilibrium

A

use the products of the chemical reactions as quickly as they are produced

536
Q

energy coupling

A

use of an exergonic process to drive an endergonic one

537
Q

what is responsible for mediating most energy coupling reactions within cells

A

ATP

538
Q

what happens when the bonds between the phosphate groups are broken by hydrolysis

A

yields an inorganic phosphate molecule and ADP

539
Q

what does hydrolysis of the high energy phosphate bonds do (exergonic)

A

releases energy that can be used to drive endergonic reactions

540
Q

how can ATP be regenerated

A

by the process of cellular respiration

541
Q

enzymes

A

catalytic proteins that lower the free energy of activation of chemical reactions

542
Q

catalyst

A

chemical reagent that changes the rate of reaction without being consumed or changed

543
Q

free energy of activation

A

the initial investment of energy for starting a reaction (the energy that is required to break bonds in the reactant molecules)

544
Q

enzymes and their relationship to substrates

A

enzymes are substrate specific (lock and key)

545
Q

active site

A

site on the enzyme in which the substrate interacts (usually through week interaction) and the catalytic reaction occurs

546
Q

stretching and bending of chemical bonds

A

helps break the bonds that must be broken for the enzyme to bind to the substrate

547
Q

environment for active site

A

active site may have a specific microenvironment that may be suitable for the reactions (acidic R groups, basic R groups etc)

548
Q

inducible fit

A

as the substrate enters the active site of the enzyme, it induces the enzyme to change its shape slightly so that the active site fits even more snugly around the substrate

549
Q

factors that affect enzymatic activity

A
  • concentration
  • temp
  • pH
  • cofactors
  • enzyme inhibitors
550
Q

concentration

A

the more enzymes present, the more enzymatic activity (and vice versa)

551
Q

temperature

A

up to a point, the velocity of an enzymatic reaction increases with increasing temp, partly because substrates collide with active sites more frequently when the molecules move rapidly

552
Q

high temp’s affect on enzymatic activity

A

denaturation (loose structure) of proteins

553
Q

low temp’s affect on enzymatic activity

A

reaction rate decreases because there are less collisions

554
Q

pH affect on enzymatic activity

A

6-8 is usually optimal

555
Q

cofactors affect on enzymatic activity

A

non-protein helpers for catalytic activity (vitamins)

556
Q

co-enzymes affect on enzymatic activity

A

organic molecules that serve as co-factors

557
Q

competitive inhibitors

A

enzymatic inhibitors that resemble the substrate. they bind the active site and reversibly inhibit the enzyme

558
Q

noncompetitive inhibitors

A

do not bind to active site, instead bind to another part of the enzyme and causes the enzyme molecule to change its conformation so the substrate can no longer interact with the active site

559
Q

reversible reactions

A

if inhibitors can be removed

560
Q

irreversible reactions

A

suicide inhibitor

561
Q

bioenergetics

A

the study of how organisms manage their energy resources

562
Q

what do biological systems want to do with energy

A

want to decrease the amount of energy lost as heat because heat can not be used to run chemical reactions. they want to harvest NG as ATP

563
Q

what defines whether or not a chem reaction is spontaneous or nonspontaneous

A

the characteristics of the starting materials

564
Q

spontaneous reactions

A
  • catabolic
  • high energy
  • unstable
  • low entropy
  • organized
  • starting materials are polymers
565
Q

nonspontaneous reactions

A
  • anabolic
  • starting materials are monomers
  • low energy
  • stable
  • high entropy
  • random
566
Q

activation energy

A

required in all reactions

initial investment of energy ensuring all reactants are close enough for their bonds to react

567
Q

what do enzymes do to activation energy and why

A

lower it because they serve as “landing pads” to bring substrate molecules together in 1 place and to expose bonds that need to be worked on to create products

General Chemistry 111 (8 decks)

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