Biology'212A'
Cell'Biology'
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Spring,'2016'
Course'Syllabus'
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Sue'Hannaford'
Office:'Th'223C'
Phone:''x2959'(office);'206@963@0260'(cell/home)'
e+mail:''shannaford@pugetsound.edu'
Office/hours:''Monday'9@10;'Friday'11@12;'many'others'available'by'appointment.'
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INTRODUCTION'TO'CELL'BIOLOGY'
All'living'creatures'are'made'up'on'one'of'more'cells'–'small,'membrane@bound'structures'filled'
with'fluid'and'packed'with'the'biochemical'machinery'needed'to'produce'energy'and'to'signal'
other'cells,'as'well'as'with'genetic'information.''We'study'cells'to'learn'how'they'are'made'from'
molecules'and'how'they'cooperate'to'make'an'organism.''Both'levels'are'of'profound'interest.''
Failure'of'either'the'chemical'machinery'in'the'cell'or'of'the'ability'to'communicate'with'other'
cells'can'lead'to'death.''Similarly,'damage'of'the'genetic'material'can'destroy'the'ability'of'a'cell'
to'replicate.'Thus,'the'study'of'cell'biology'is'relevant'not'only'for'providing'background'
necessary'for'your'professional'development'in'the'biological'sciences'but'also'for'
understanding'everyday'concerns'such'as'obesity,'cancer,'and'aging.''
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COURSE'OBJECTIVES:'
This'course'builds'on'what'you'have'already'learned'in'the'first@year'biology'and'chemistry'
courses.''The'course'will:'
• Introduce'you'to'basic'principles'of'cell'biology.''It'is'helpful'to'remember'the'five'core'
concepts'of'biology:'
(1)'Structure'and'function'@@'structure'reflects'function'(from'molecules'to'organisms);'
we'will'examine'the'organization'of'cells,'their'constituent'parts'(especially'proteins),'
and'how'cells'are'organized'into'tissues;'
(2)''Pathways'and'transformation'of'matter'@@'biological'systems'grow'and'change'by'
processes'based'on'chemical'reactions'and'are'governed'by'thermodynamics;'we'will'
study'chemical'reactions'occurring'within'cells;'
(3)'Information'flow,'exchange,'and'storage/++/organisms'interact'with'their'
environment'through'the'context@dependent'expression'of'the'genetic'information'that'
they'inherit;'
(4)'Systems'–'we'understand'complex'biological'processes'when'we'put'together'
information'from'multiple'functional'scales,'integrating'and'analyzing'complex'data'sets'
from'multiple'experimental'sources;'
(5)/Evolution:'evolutionary'change'ultimately'requires'change'at'the'cellular'level;'an'
evolutionary'lens'helps'us'to'understand'why'cells'are'the'way'they'are'and'why'they'
are'not'perfect.''
• Increase'your'familiarity'with'the'processes'of'performing'and'presenting'scientific'
research.'
• Introduce'you'to'many'of'the'methods'used'to'study'cell'biology,'both'through'the'
lecture'and'laboratory'components.'
• Further'develop'your'powers'of'reasoning'and'analysis.'
'
'
1
REQUIRED'TEXTS:'
1.''Cell/and/Molecular/Biology,'Concepts/and/Experiments,'7th'ed.,'2013,'Karp'
2.''Biology/212/Laboratory/Manual,'Spring'2015,'Staff'
3.''Bound'lab'notebook'with'duplicate'pages'
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RECOMMENDED'TEXT:''/
A/Student/Handbook/for/Writing/in/Biology/4th,'2013,'Knisley'OR''
A/Short/Guide/for/Writing/about/Biology/8th/ed.,'2012,'Pechenik'
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COURSE'MECHANICS''
The'course'consists'of'three'lectures'and'one'4@hour'laboratory'period'per'week.''Reading'
assignments'and'exams'are'listed'on'the'schedule.''I'expect'you'to'prepare'for'lecture'by'
skimming'the'appropriate'material'before'class.''Pay'particular'attention'to'the'figures'(look'at'
the'cartoons'rather'than'photographs'at'this'point)'because'these'often'present'the'“big'
picture.”''You'should'then'read'the'text'more'carefully'after'each'lecture.''Likewise,'you'must'
prepare'for'the'labs'carefully'reading'the'handouts'and'preparing'the'appropriate'pre@lab'write@
up'in'your'notebook.''
'
NOTE: If you have a physical, psychological, medical or learning disability that may impact
your course work, please contact Peggy Perno, Director of the Office of Accessibility and
Accommodations, 105 Howarth, 253.879.3395. She will determine with you what
accommodations are necessary and appropriate. All information and documentation is
confidential.'
CLASS'MEETINGS'
Lectures'meet'in'MWF'at'10'in'Thompson'193;'Labs'run'1@5'PM'(and'many'will'take'the'full'4'
hours)'in'Thompson'313.''Since'most'science'students'are'not'familiar'with'classrooms'in'
McIntyre'please'review'university'emergency'preparedness'and'response'procedures'posted'at'
www.pugetsound.edu/emergency/.'There'is'a'link'on'the'university'home'page.'Familiarize'
yourself'with'hall'exit'doors'and'the'designated'gathering'area'for'your'class'and'laboratory'
buildings.''
If'building'evacuation'becomes'necessary'(e.g.'earthquake),'meet'your'instructor'at'the'
designated'gathering'area'so'she/he'can'account'for'your'presence.'Then'wait'for'further'
instructions.'Do'not'return'to'the'building'or'classroom'until'advised'by'a'university'emergency'
response'representative.'
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If'confronted'by'an'act'of'violence,'be'prepared'to'make'quick'decisions'to'protect'your'safety.'
Flee'the'area'by'running'away'from'the'source'of'danger'if'you'can'safely'do'so.'If'this'is'not'
possible,'shelter'in'place'by'securing'classroom'or'lab'doors'and'windows,'closing'blinds,'and'
turning'off'room'lights.'Lie'on'the'floor'out'of'sight'and'away'from'windows'and'doors.'Place'
cell'phones'or'pagers'on'vibrate'so'that'you'can'receive'messages'quietly.'Wait'for'further'
instructions.'
COURSE'WEB/MOODLE'PAGE:'
The'course'Web/Moodle'page'can'be'accessed'through'the'UPS'Moodle'page'
http://moodle.pugetsound.edu/moodle/.'Our'site'contains'essential'material'for'both'lecture'
and'lab,'including'laboratory'exercises,'exam'study'guides,'worksheets,'and'outside'readings.'I'
post'my'PowerPoint'slides'on'the'site'(under'last'time)'and'it'is'a'good'idea'to'check'the'page'
before'each'lecture'for'any'important'announcements'and'reminders.'You'should'be'
automatically'enrolled'in'the'page.'Please'let'me'know'asap'if'you'have'any'trouble'accessing'
2
documents'from'the'page.'I'will'also'have'you'turn'in'your'formal'laboratory'reports'to'this'
Moodle'site'using'the'Turnitin'feature,'which'allows'you'to'check'your'work'for'inadvertent'
plagiarism.
GRADING'
Grades'will'be'assigned'based'on'the'total'accumulated'points:'
In@class'quizzes'(ICQs)'–'20'points'each'
''60'pts'
Take@home'quizzes'(THQs)'–'20'points'each'
''60'
3'midterm'exams'–'100'points'each'
300'
Laboratory'work''
140'
Formal'laboratory'report'
''80'
Final'exam''
200'
Total'possible'points'
840'points'
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Grades'will'be'assigned'on'a'straight@scale'basis.'
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BEHAVIOR'EXPECTATIONS''
I'expect'you'to'behave'in'an'appropriate'manner'while'attending'this'class.'Use'your'common'
sense'and'here'are'a'few'guidelines:''
•
Be'punctual—be'on'time'for'both'class'and'lab.''
• During'class'and'lab'time'I'expect'you'to'be'working'on'materials'for'this'course'only.''
• Personal/technology;/please'be'respectful'of'others'in'class:''
- Silence'your'phone'before'coming'to'class''
- You'may'use'your'laptop,'tablet,'etc.'in'class'as/long/as/it/is/not/a/distraction/to/others/'
- Refrain'from'using'email'or'text'messaging'during'class''
- You'may'not'touch'or'use'your'phone/laptop/tablet'in'any'way'during'an'exam''
- You'may'not'listen'to'an'iPod,'phone,'or'similar'device'during'class'or'during'an'exam''
• You'may'not/make'audio'recordings'of'our'class'or'lab'sessions'without'prior'consent'
from'me.''
• If'you'leave'the'room'during'an'exam,'your'paper'will'be'collected'and'you'will'not'be'
permitted'to'return'to'the'exam.''
• Lack'of'respect'for'diversity'will'not/be'tolerated'in'the'class.'Diversity'encompasses'age,'
life'experiences,'profession,'race,'religion,'gender,'lifestyle,'social'class,'learning'style,'
ethnicity,'philosophy'of'life,'sexual'orientation,'personality,'mental'and'physical'
challenges,'customs,'and'values,'among'others.''
• You'may'bring'food'and/or'drinks'to'class'as/long/as/the/consumption/of/food/and/or/
drinks/is/not/a/distraction/to/others./'
• ABSOLUTELY'NO'FOOD'OR'DRINK'is'allowed'in'the'laboratory.'Food'and/or'drinks'can'
be'kept'outside'the'lab'door.'Wash'your'hands'prior'to'consuming'food'or'drink.''
• Telephones'located'in'classrooms'and'labs'are'for'staff'use'and'medical/safety'
emergencies'only'(no'personal'calls).''
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EXAMS'
There'will'be'three'mid@term'exams'and'one'final'exam.'IMPORTANT:'To'ensure'that'
you'are'not'rushed'when'you'take'the'mid@terms,'they'will'be'given'in'the'evening'from'6:00'–
8:00'PM'on'the'scheduled'day.'Please'make'arrangement'now'to'reserve'those'times.'Lectures'
on'those'days'will'be'replaced'with'an'extra'office'hour'to'address'last'minute'questions'on'
exam'material.'Exams'will'primarily'cover'lecture'material'but'may'also'contain'questions'
relating'to'the'lecture'and'laboratory'readings.'Make@up'exams'will'not'be'given'but'adequate'
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consideration'may'be'given'and'adjustments'may'be'made'if'there'is'a'medical'or'family'related'
emergency.'Written'documentation'of'the'nature'of'the'emergency'may'be'required'
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LABORATORY'EXERCISES'
The'notebook'
Through'the'course'you'will'be'planning'and'performing'experiments,'collecting'and'analyzing'
data,'and'using'this'information'to'design'further'experiments'and'to'prepare'presentations'of'
your'work'in'the'lab.''To'perform'these'tasks'properly,'you'must'keep'an'accurate'laboratory'
notebook'describing'exactly'how'you'performed'an'experiment'and'exactly'what'results'you'
obtained.''Without'such'a'record'it'is'unlikely'that'you'will'remember'accurately'what'you'did'
and'found,'and'it'is'possible'that'you'or'others'interested'in'the'experiment'will'not'be'able'to'
reproduce'the'original'results,'making'it'impossible'to'use'those'results'as'a'guide'to'further'
experiments.''The'only'way'to'keep'a'good'laboratory'notebook'is'to'record'your'methods'and'
results'in'the'laboratory'while'you'are'performing'an'experiment.''
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Although'you'may'meticulously'plan'for'an'experiment,'unanticipated'events'may'occur'that'
result'in'slight'modifications'to'the'procedure.''These'changes'must'be'recorded'before'they'are'
forgotten.''Your'notebook'doesn’t'have'to'be'a'work'of'art'–'it'just'has'to'be'legible'so'that'you'
or'another'scientist'can'follow'the'directions.''You'may'be'tempted'to'recopy'your'notes'
outside'of'the'lab.''Do'not;'this'is'a'dangerous'practice'since'it'may'introduce'errors.''You'will'
turn'in'your'notebook'at'the'end'of'most'sessions.''It'will'be'evaluated'for'completeness'and'
legibility,'and'you'will'be'given'suggestions'for'improvement,'if'needed.'
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Prelabs'
All'good'scientists'plan'what'they'are'going'to'do'in'the'laboratory'before'beginning'an'
experiment.''To'assist'you'in'using'your'time'in'the'lab'efficiently,'we'require'that'you'prepare'
for'the'labs.''Often'this'preparation'will'entail'making'a'formal'prelab.''These'are'outlines'of'the'
experimental'procedure'that'you'plan'to'follow'for'a'given'experiment.''These'may'take'several'
forms;'some'people'record'the'procedure'as'a'stepwise'process'while'others'make'a'flow'chart'
in'the'notebook.''A'general'rule'of'thumb'is'that'you'should'be'able'to'replicate'your'
experiment'working'only'from'your'lab'notebook.'
'
Whatever'format'your'prelab'takes,'you'should'be'sure'to:'
• Answer'the'questions'posed'at'the'beginning'of'the'lab'exercise.''(Only'some'labs'will'
have'such'questions.)'
• State'the'purpose'or'question'to'be'addressed'in'the'exercise.'
• Prepare'a'list'of'reagents.'
• Outline'the'procedure'in'a'stepwise'manner'or'as'a'flow'chart'before'coming'to'lab.''
You'can'also'note'any'questions'you'have'about'the'procedure'so'that'you'will'
remember'to'ask'them'during'the'lab.''Because'you'often'need'to'modify'the'
procedure,'you'may'find'it'useful'to'write'out'the'procedure'in'the'left'column'o'the'lab'
and'leave'the'right'column'for'notes,'calculations,'and'modifications.''(This'is'only'a'
suggestion.''Use'whatever'format'works'for'you.)'
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LITERATURE'WORKSHOPS'
Whatever'your'career'plans'may'be,'it'is'likely'that'you'will'need'to'be'familiar'with'the'
processes'of'performing'and'presenting'scientific'research.''We'have'dedicated'two'of'the'
laboratory'sessions'to'be'used'for'discussion'of'scientific'papers.''In'these'class'periods'you'will'
work'in'groups'of'3'to'4'students'to'evaluate'papers'relevant'to'cell'biology.''We'will'then'draw'
4
the'whole'class'together'for'a'discussion'of'both'the'content'and'the'presentation'of'the'data.''
'
LATE'POLICY'
'
• All'late'lab'reports'and'worksheets'must'by'turned'into'me'or'my'mailbox'in'the'Biology'
office'(Th.'223a,'please'ask'the'secretary'to'stamp'your'paper'with'the'date'and'time).''
The'TAs'have'been'instructed'not'to'accept'late'labs'because'some'students'have'more'
access'to'the'TA'than'do'other'students.''A'late'penalty'will'be'assessed,'following'the'
guidelines'shown'below:'
• Quizzes'–'no'make@up'quizzes'will'be'given'
• Tests'–'no'make@up'tests'will'be'given'except'in'the'case'of'a'medical'or'family'
emergency.'
• Labs/–'penalty'for'late'labs'will'be'determined'in'consultation'with'your'TA.''In'general,'
a'lab'will'be'assess'a'5%'penalty'per'day'and'will'not'be'accepted'more'than'one'week'
late.'''
• Literature/workshops'–'attendance'and'active'participation'in'the'discussions'are'
required.''In'the'case'of'a'family'or'medical'emergency'you'will'be'asked'to'write'a'short'
paper'presenting'your'ideas'and'questions'about'the'missed'material.'
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5
Tentative(Cell(Lecture(and(Reading∗ (Schedule(
(
MONDAY(
January'18'
'
'
TUESDAY(
19'
'
26'
Biological'molecules'3:''
lipids'(cont.)'
'
'
February'1'
Biological'molecules'6:''
membranes,'nucleic'
acids'
'
pp.'120J147'(cont.);'76J
78'
2'
8'
'
'
9'
∗
FRIDAY(
27'
'
28'
29'
'
Biological'molecules'5:''
proteins'and'
membranes''
'
pp.'50J76'&120J147'
Biological'molecules'4:''
protein'composition'and'
function''
'
pp.'50J76'
'
Protein'synthesis'and'
targeting'3:'
'
'
pp.'316J318'
THURSDAY(
21'
Course'Introduction;'cell'
structure'review;'
biological'molecules'1'–'
saccharides''
'
Read:''course'syllabus;'
text'–'pp.'1J26;'42J47'
Martin'Luther'King'Jr.’s'
Birthday'–'No'class'
25'
'
WEDNESDAY(
20'
'
3'
THQB1(
4'
'
Enzymes'1:''what'are'
enzymes?''Why'are'they'
necessary?'
'
'
pp.'94J102(
11'
LABORATORY(
'
'
'
NO'LABS'
'
'
'
LIGHT'MICROSCOPY'
5'
'
'
'
'
PROTEIN'ANALYSIS'I'
12'
'
'
'
'
PROTEIN'ANALYSIS'I'I'
'
Protein'synthesis'and'
targeting'2:'
'
pp.'keep'reading'270J
285;'&'skim'285J315'
Protein'synthesis'and'
targeting'1:'
'
pp.'270J285'
10'
22'
'
'
Biological'molecules'2:''
saccharides'and'lipids''
'
'
pp.'47J49'
Enzymes'2:''measuring'
rxn'rates;'the'MichaelisJ
Menton'equation'
'
'
pp.'102J107'
Readings from Karp (2013) Cell and Molecular Biology: Concepts and experiments, 7th edn, John Wiley & Sons, pp. 780.
'
15'
'
'
Enzymes'3:''kinetics'
(cont.)'
'
'
16'
Enzymes'4:''regulation'
of'enzyme'activity'
'
pp.'102J107'(cont.)(
23'
Cellular'metabolism'1:''
glycolysis'
'
'
'
pp.'108J117'
25'
EXAM(1(
6(to(8(PM'
March'1'
Applications'of'transport'
mechanisms:''nerve'cell'
signaling'
'
pp.''164J174'(cont.)'
7'
'
'
24'
'
'
'
2'
'
'
19'
'
'
Transport'mechanisms'
1:''passive'transport'
'
'
'
pp.'147J157'
(
Transport'mechanisms'
2:''active'transport'
'
pp.'157J164'
29'
'
'
(
18'
ICQB1(
pp.'102J107'(cont.)'
22'
'
17'
3'
Nerve'Cell'signaling'
(cont.)'
26'
'
Transport'mechanisms'
3:''ion'channels'and'
membrane'potentials'
'
'
pp.''164J174'
4'
'
'
Nerve'Cell'signaling'
(cont.)'
'
'
'
BIOINFORMATICS''
'
'
'
CENTRIFUGATION''
'
'
'
'
ENZYMES'I'
'
'
pp.''164J174'(cont.)'
9'
10'
'
'
11'
ICQB2(
Cellular'metabolism'2:''
mitochondria'and'
pyruvate'oxidation'and'
the'TCA'cycle'
'
pp.'173J181'
12'
'
'
Cellular'metabolism'3:''
the'tricarboxylic'acid'
cycle'and'the'electron'
transport'chain'
'
'
pp.'178J204'
'
'
'
'
LITERATURE'WORKSHOP'1'
14'
'
'
'
NO'LABS'
SPRING(BREAK(
'
21'
'
Cellular'metabolism'4:''
insJandJouts'of'the'TCA'
cycle,'links'to'
intermediate'
metabolism'
22'
28'
'
'
Cytoskeleton'2:''more'
on'MTs'
'
'
29'
4'
'
'
Cytoskeleton'4:'
microfilaments'
'
pp.'356J364'
5'
11'
'
'
Signal'transduction'
mechanisms'1:''general'
principles'
'
'
pp.''617J621'
12'
23'
THQB2(
24'
Cytoskeleton'1:'
Overview;'Microtubules'
and'MTJ'based'motility'
'
'
pp.''324J345'
'
Photosynthesis'
'
'
Chapter'6'
30'
(
31'
EXAM(2(
6(to(8(pm(
7'
13'
14'
Extracellular'matrix'and'
adhesions'1:''ECM'
'
pp.'235J244'
ICQB3(
'
Signal'transduction'
mechanisms'2:''G'
protein'linked'receptors'
'
pp.'621J636'
April'1'
'
'
Cytoskeleton'3:''
Intermediate'filaments'
'
'
pp.'354J356'
'
'
6'
'
'
'
25'
'
8'
'
'
Extracellular'matrix'and'
adhesions'2:''junctions'
'
pp.'244J282'
15'
'
'
Signal'transduction'
mechanisms'3:''receptor'
tyrosine'kinases''
'
'
pp.'636J656'
'
'
'
ENZYMES'2'
'
'
'
'
ADVANCED'MICROSCOPY''
'
'
'
'
CELL'CULTURE'I'
'
'
'
CELL'CULTURE'II'
18'
'
'
19'
'
'
Immunology'1:''
overview'
'
'
pp.'699J707'
2'
'
'
26'
(comprehensive)(
8(to(10(AM(
'
'
'
'
27'
(
28'
EXAM(3(
6(to(8(pm(
Immunology'3:''
antibodies'and'the'
humoral'response'
'
Chapter'17''
Final(Exam(
pp.'673J681;'(
10'
'
4'
'
'
29'
'
'
Immunology'2:''T'
lymphocytes'''
'
'
Continue'reading'Ch.'17'
(
Immunology'4:''MHC'
complex'proteins'
'
'
Chapter'17'
11(
(
(
22'
'
Cell'biology'of'cancer'3:''
wrap'up'
'
'
'
pp.'687J693'
Cell'biology'of'cancer'2:''
oncogenes'and'tumor'
suppressor'genes'
3'
9'
'
THQB3(
21'
(
Cell'cycle'and'cancer'1:''
overview'
'
'
pp.'664J673'
2'
20'
'
'
5''''''''''''''''''''6'
12'
READING'PERIOD'
13'
(
'
'
'
'
LITERATURE'WORKSHOP'2'
'
'
'
BIOETHICS'AND''LAB'PRACTICAL'
'
'
'
NO'LABS'
'