lecture 1 5

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What Is Life?

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•••••••••

Characteristics of Living Things- Summary

OrganizationEvolution of populationsDNAReproductionGrowth/developmentResponse to environmentMetabolismHomeostasisContain one or more cells

Cell

-Basic unit of life

- Smallest unit with thecapacity to live andreproduce, independentlyor as part of a multi-cellular organism

Living things contain one or more Cells

How do we know this?

To STUDY and UNDERSTAND cells,we had to SEE them…

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When were ‘cells’ first observed?

a.Early 1400sb.Late 1500sc. Mid 1600sd.Early 1800se.Early 1900s

A Very Brief History of Cytology (Cell Biology)Late 1500s (1595)• Zacharias Jansen invents the first

microscope

Mid 1600s• Leeuwenhoek greatly improves

microscopes

1665• “Micrographia”by Robert Hooke

– Credited with coining the term‘cell’ to describe the compartmentshe viewed in cork slices

• Hooke did not understand what hisobservations meant

Origin of the term 'cell‘. Robert Hooke is credited as theoriginator of the term ‘cell’, which he used in hisdescription of the structure of cork. This illustration is takenfrom his book on microscopy, referred to as 'Micrographia'.

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http://upload.wikimedia.org/wikipedia/commons/f/fe/RobertHookeMicrographia1665.jpg

• Lack of detail

2) Their way of thinking• 17th Century was an “Age of Observation”• Descriptive science

… “Ooohh! Look at this!!!”• Not really interested in “WHY???”

• More than 150 years later…

A Very Brief History of Cytology (Cell Biology)

• After 1665…Not much happened in Cell Biology!

• Scientists were limited by:1) Optical instruments

• Limited resolving power of microscopes

Rembrant. The Anatomy Lesson of Dr. Nicolaes Tulp. 1632

• 1830’s: Advances in Optics– Lens quality improved– Development of the Compound Microscope

• Improved both Magnification & Resolution

• 1831: Robert Brown describes the ‘Nucleus’– Scottish botanist, observed plant cells and plantfertilization

– Noticed that every plant cell had a ‘rounded structure’• Called it a ‘nucleus’…Latin for “kernel”• Further implied the role of the nucleus in fertilization anddevelopment of the plant embryo

– FYI: Pollen grains suspended in water also led Brown to the discoveryof ‘Brownian motion’

• Schleiden & Schwann…



1838• ‘Cell Theory’ put forth by Schleiden & Schwann

– German scientists and colleagues– Schleiden was was a botanist

• Observed cell division in plants

– Schwann was a physiologist• Observed cell division in animal tissues

FYI: Legend has it:• Shared their observations over dinner one evening• Schwann published these findings, omitting Schleiden as author• Thus, Schwann ‘scooped’ Schleiden!


Cell Theory - Schwann (1839)

1) The cell is the unit of structure, physiology, and organizationin living things.

2) The cell retains a dual existence as a distinct entity and abuilding block in the construction of organisms.

3) Cells form by free-cell formation, similar to the formation ofcrystals

Cell Theory - Interpreted

1) All organisms consist of one or more cells.

2) Cell is the basic unit of structure for allorganisms.

3) Cells form by spontaneous generation.

WHAT’S WRONG WITH THIS THEORY?12

Cell Theory - Interpreted


2) Cell is the basic unit of structure for allorganisms.

3) Cells form by spontaneous generation.

13

“Omnis cellula e cellula”

1855 - Virchow- Revised Schwann’s postulate- Based on:

- Brown’s discovery of the nucleus

- Louis Pasteur’s discoveries of ‘germs’, refutingspontaneous generation

All cells arise from only preexistingcells

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RudolphVirchow

Cell Theory - Revised


2) Cell is the basic unit of structure for allorganisms. -Schlieden &Schwan (1839)

3) Cells form by spontaneous generation.-Schwan (1839)

3) All cells arise only from preexisting cells.-Virchow (1855) 15

Founders of Cell Biology

• All provided important contribution thathelped create a foundation for Cell Biology

RobertBrown RudolphVirchow LouisPasteur

Welcome to the World of the Cell!!!

Cells are just as diverse as Organisms…

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Plant Cells: Protist Cells: Bacterial Cells:

Human Cells:

FYI: Estimated that the ‘average’ human body has ~30+ trillion cells!Source: Bianconi et al. (2013) Annals of Human Biology.40, 463-471

Images from Figure1-1

Phylogenetic Organization of Cells

There are ____different ‘Domains’ of livingorganisms recognized in the contemporary

phylogenetic tree of life.

a)b)c)d)e)

twothreefourfiveten

• Tree of Life is continually being redrawn– Earlier classification systems based largely on morphologicalcharacteristics

• Scala naturae (350 BC)– Classification scheme outlined in Aristotle’s History of Animals

» All matter organized as decreed by God» Definition of terms still used today: Vertebrates/Invertebrates

• 2 kingdoms (1700s)– Classification pioneered by Carl Linneaus & his bionomial taxonomy– Everything was either a Plant or an Animal

» Bacteria were considered plants

• 5 kingdoms (1960’s)– Monera (prokaryotes), Protista, Plantae, Fungi, Animalia

» FYI: Original paper published in Science:Whittaker R.H. (1969). Science 163:150–160.http://www.sciencemag.org/content/163/3863/150.full.pdf?ijkey=e364e760bafd3ddb27f995f0c1e9b08fdf28eb0f&keytype2=tf_ipsecsha

Tree of Life

http://www.sciencemag.org/content/163/3863/150.full.pdf?ijkey=e364e760bafd3ddb27f995f0c1e9b08fdf28eb0f&keytype2=tf_ipsecsha

• Current Phylogeny = 3 Domain systemBacteria = Prokaryotes

Archaea = Prokaryotes, many extremophiles

Eukarya = Eukaryotes• Group includes Protists, Plants, Fungi, Animals

• Pioneered by Carle Woese & George Fox in the late 1970’s• Formally recognized in the 1990’s

• Redrawing of phylogenetic relationships based on analysisof rRNA sequences• Why do you suppose rRNA was used for this purpose?

Tree of Life

Redrawing of phylogenetic relationships based onanalysis of rRNA sequences

• All cells require rRNAWhy? Component of ribosomes

• rRNA sequences change slowlywith time– Reflects evolutionary history of life– Can be used to establishevolutionary relationships betweenall species

• Using such data, phylogeneticrelationships were redrawn…

3 Domains of Life‘Hypothetical’ Phylogenetic Tree of Life

*Note: Origins of LUCA and Eukarya lineage are hypotheticalReviews - Nature 440: 623-630; BioEssays 29: 74-84

LastUniversalCommonAncestor

~3.5 BYA

Fig 26.21 24from Campbell et al., 9th ed.

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3 Domains of Life

• rRNA analysis revealed twoseparate groups ofprokaryotes:

- Bacteria- Archaea

• Also suggests thateukaryotes and archaea aremore closely related toeach other than to bacteria

What are Protists?

a) Diverse grouping of eukaryoticorganisms

b) A type of prokaryote

c) A single-celled organismd) A type of delicious pastrye) None of the above.

Protists

• Many diverse lineagesof various eukaryoticorganisms

• Can be unicellular– e.g. dinoflagellates

Red tide dinoflagellate

• Can be multicellular– e.g. some algae species kelp

What is a ‘prokaryote’?What is a ‘eukaryote’?

Figure 4-3

Figure 4-5

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Ave. Size of Eukaryotic Cell~10 – 100 um diameter

Prokaryotic Cells vs. Eukaryotic CellsAve. Size of Prokaryotic Cell

~1-5 um diameter

• Plant and animal cells- Share many of the same subcellular structure- We’ll point out a few major differences

Prokaryotes vs. Eukaryotes• Prokaryotic cells (Bacteria & Archaea domains)

– “pro” (before) + “karyon” (nucleus)– Lack internal complexity seen in Eukaryotes– Average size ~1-5 μm diameter

• Eukaryotic cells (Eukarya domain)

–

–

–

–

“eu” (true) + “karyon” (nucleus)NucleusExtensive membrane-bound organellesAverage size ~10-100 μm diameter

Regardless of their diversity,all cells share some common features…

Basic Features of All Cells:

1) Surrounded by Lipid-BasedPlasma Membrane

2) Metabolic Machinery

3) DNA as Hereditary Information

4) Ribosomes as Protein-Synthesizing Machinery

•

Inner Life of a Cellhttp://multimedia.mcb.harvard.edu/media.html

http://multimedia.mcb.harvard.edu/media.html

Cells are teeny-tiny!

http://learn.genetics.utah.edu/content/begin/cells/scale/

http://learn.genetics.utah.edu/content/begin/cells/scale/

Fig 1A-135

Sizes of Cells and Subcellular Structures“The World of the Micrometer”

Micrometer (µm) is the most useful unit forexpressing the size of cells and larger organelles

Fig 1A-236

= 70-80 Å

= 20 Å

Sizes of More Subcellular Structures“The World of the Nanometer”

Nanometer (nm)-or-

Angstrom (Å) arethe units used toexpress size ofmolecules andsmaller subcellularstructures

= 70 Å

Prefixes for SI/Metric Units

u

37* = important for Cell Biology

***

Base Unit*******

38

Other Common Units

Angstrom (Å) = 0.1 nm or 10-10 m• Commonly used to express dimension of molecules

20 Å

Ex. DNA helix diameter= 2 nm Convert to Å

2 nm x 1 Å/0.1 nm= 20 Å

39

Other Common Units

Dalton (Da) = unified atomic mass unit= 1/12 12C= 1.66x10-24 g

• Commonly used to express size of proteins

Ex. Hemoglobin (Human)= 68000 Da

– OR –= 68 kilodaltons (kD)

40

Units Worksheet

- Posted on Blackboard (along with KEY) under‘Course Documents’

- This is for your own practice.

- This will not be handed in for assessment, butyou are responsible for this material

41

Cell = Basic Unit of Life

- Smallest unit with thecapacity to live andreproduce, independentlyor as part of a multi-cellular organism

0 1 2 3 4 5 6 7

Cell Size

Cell Division Pattern inSaccharomyces cerevisiae

growth mitosis

Time

Q: Why don’t the yeast cells just keep growing and growing?Why aren’t we just one giant cell?

Limits to cell size

0 1 2 3 4 5 6 7

Time

Cell Size growth mitosis

44

What limits cell size?

1) Resource Availability (e.g. nutrients, space)

Let’s assume resources are plentiful. Cell size isthen primarily limited by…

2) *Surface Area to Volume ratio

This in turn affects…

3) Rate of molecule diffusion within cell

4) Maintenance of adequate localconcentrations of molecules within cell

45

Cell 1 Cell 2MulticellularOrganism 1

Surface Area to Volume ratio– limits cells size

To demonstrate this concept…Which has a greater surface area to volume ratio?(provide calculations to support your answer)

a) Cell 1: 1µm x 1µm x 1µmb) Cell 2: 5µm x 5µm x 5µmc) Multicellular Organism 1: 125(1µm x 1µm x 1µm)

Limits to Cell Size:Surface to Volume Ratios

*Similar to Figure 4-1

Limits to cell size

0 1 2 3 4 5 6 7

Time

Cell Size growth mitosis

4

Cell 1 Cell 2MulticellularOrganism 1

Surface Area to Volume ratio– limits cells size

To demonstrate this concept…Which has a greater surface area to volume ratio?(provide calculations to support your answer)

a) Cell 1: 1µm x 1µm x 1µmb) Cell 2: 5µm x 5µm x 5µmc) Multicellular Organism 1: 125(1µm x 1µm x 1µm)d) More than one of the above

Limits to Cell Size:Surface to Volume Ratios


Surface Area to Volume ratio- limits cells size

SA (x2) = plasma membraneV (x3) = cell contents

SA to V ratio is critical to cell metabolism

…As cells increase in size…• V (x3) grows proportionately more than SA (x2)

…leads to…

• Lower SA to V ratio…leads to…

• Problematic exchange of substances between cell& environment

…affects...

• Localized [molecule]• Diffusion rate of molecules in cell

Affects RATES of chemical reactions…Slow is not good!

How do cells cope with SA:Vconstraints?

8

0 1 2 3 4 5 6 7

Time

Cell Size mitosis

Strategies to cope with SA:V constraints

Cells divide

Strategies to cope with SA:V constraintsGrowth Stops- Cell enters G0phase

• Withdraw from cell cycle• No growth/proliferation

- Cell may become:• Quiescent

- Phase is reversiblei.e. some cells can re-enter Cell cycle

to begin divisione.g. some stem cells

• Terminally differentiated- Non-reversible

e.g. cardiac muscle cells

Fig 19-32

11

Figure 4-2

Strategies to Increase Surface Area

Membrane Folding: e.g. brush border cells of intestinal epithelium

12Figure 11-4


Membrane Folding – also seen in some prokaryotese.g. Anabaena azollae (type of Cyanobacteria)


Membrane Folding – not limited to the plasma membrane ineukaryotes

e.g. thylakoid membrane in chloroplaste.g. endoplasmic reticulum

Other Strategies Cells use to Copewith SA:V Constraints?

15

200

5

0.125

Which has the greatest surface area to volume ratio?

a) Cell 1: 1µm x 1µm x 1µm

b) Cell 2: 5µm x 5µm x 5µm

c) Organism 3: 125(1µmxµm1xµm1)

d) Cell 4: 0.125µm x 5µm x 200µm

e) More than one of the above

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Muscle fiber

Neuron


Long, thin cells – greater surface area:volume

What about egg cells? Do egg cells breakthe SA:V rule?

Figure 1. Comparisonof egg sizes. Ostrich egg (right), comparedto chicken egg (lower left) and quail eggs (upper left).Photo by Rainer Zenz.

• Although some egg cells canbe quite large…– Ostrich eggs are severalcentimeters long!

• …Metabolically inactive

• …Mostly lipids (fats), storagematerials

• …Actual viable ‘cell’component is very small

Do egg cells break the SA:V rule?

• Transportation of ‘cargo’ by specialized carrierproteins

Strategies to cope with SA:V constraints:Active Transport

• May involve:

• Cytoskeleton- Motor proteins +filamentous tracks

• Carrier Proteins- Transport acrossmembranes

• ACTIVE process = Expenditure of E by the cell

Strategies to cope with SA:V constraints:Cytoplasmic Streaming

• Bulk movement of cytoplasm– Involves microfilaments

• Active process (E expenditure)

http://bio1151.nicerweb.com/med/Vid/Campbell7e/CytoplasmicStream-V.swf

http://bio1151.nicerweb.com/med/Vid/Campbell7e/CytoplasmicStream-V.swf

- Volume stays the same- Surface Area increases


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• SA:V sets an upper limiton cell size

• The only way to get largeris for cells to cooperate

• Driving force behindevolution ofmulticellularity?

Strategies to cope with SA:V constraints:Multicellularity

Question to ponder:What factors make it possible for eukaryotic cells to be somuch larger than prokaryotic cells?

Ave. Size of Prokaryotic Cell~1-5 um diameter

Ave. Size of Eukaryotic Cell~10 – 100 um diameter

22

“Tour of the Cell”

‘Typical’ Prokaryotic cell

• Ave. Size of Prokaryotic Cell = ~1-5 um diameter

• Relatively ‘Simple’ Organization:

Motility structure(e.g. flagella)

Electron micrograph of cross sectionthroughE. coli.

- Cell wall: protective layer ofcarbohydrate surrounding plasmamembrane

- Plasma membrane

- DNA (not enclosed) – nucleoidregion

-Some species have plasmids

- May/not have motility structure

Smooth ER

Lysosome

Ribosomes

Golgi apparatus

Nucleolus

ChromatinRough ER

Flagelium

Centrosome(with centrioles)

CYTOSKELETON

Microfilaments

Intermediatefilaments

Microtubules

Microvilli

Peroxisome

ENDOPLASMIC RETICULUM (ER)

Mitochondrion

Nuclear envelope

NUCLEUS

Plasma membrane

Similar to Fig 4-526

Eukaryotic Celle.g. ‘typical’ Animal cell

In plant cells but notanimal cells:ChloroplastsCentral vacuole and tonoplastCell wallPlasmodesmata

Roughendoplasmicreticulum Smooth

endoplasmicreticulum

NUCLEUSNucleolus

Chromatin

Intermediatefilaments

Microtubules

Chloroplast

PlasmodesmataWall of adjacentcell

Golgi apparatus

Ribosomes (small brwon dots)

Central vacuole

Tonoplast

Microfilaments

Centrosome

MitochondrionPeroxisome

Plasma membrane

Cell wall

CYTOSKELETON

Similar to Fig 4-6

27

Eukaryotic Celle.g. typical Plant cell

Nuclear envelope

Before we discuss cells…a few cell/molecular biology

techniques…

Cell Fractionation• Separation of a cell structures/components• Two phases

1. Homogenization• lysing cells open• chemicals, enzymes, or sound waves

2. Centrifugation

Mouse liver

Homogenizetissue

Figure 12A-1

Centrifugation

• Use of centrifugal force to separatemixture(s)– Fixed-angle– Swinging-bucket

• Separation based on density & size– “Pellet” = Substance(s) thatsediment at bottom– “Supernatant” or “Super” =remaining liquid– Sometimes have an “Interface” –region between two phases

Similar to Figure12A-2

Sedimentation coefficient (S)

= Measure of how rapidly a sample sediments whensubjected to centrifugal force

S values ____________ from left to right.

a)Increaseb)Decrease

S values ____________ from left to right.

a)Increaseb)Decrease

• Larger/denser objects sediment more quickly (large S value)• Smaller/ less dense objects sediment less quickly (smaller S value)

Figure 12A-3

Sedimentation coefficient (S)

Tour of the Cell…

Keep in mind as we take our tour…

• Cells are DYNAMIC SYSTEMS!!!

Cells can adjust structures to meetchanging needs

– e.g. adjust # of mitochondria to meet metabolicneeds

Subcellular structures interact with oneanother

– i.e. they are not isolated entities

- Internal contents of cell

- Contains:• Cytosol

~semi-fluid material•Organelles (eukaryotes)• Subcellular structures

e.g. ribosomes

Cytoplasm

*More about this later (Ch. 7)…

38

Plasma Membrane• 4-8nm (40-80 Å) thick layer of lipids + protein

•Boundary between cell and external environment- defines ‘cell’- regulates movement in/out- mediates communication with external environment (e.g. receptors)

•Fluid Mosaic- many components (mosaic)- flexible, dynamic structure; not static

• Region outside of cell (“extra” cellular)

• Made of various proteins/polysaccharides (varies by species)

– e.g. collagen (fibrous protein); e.g. cellulose (polysaccharide)

• Linked to cell via Plasma membrane components– e.g. integrins (intermembrane proteins)

Extracellular Matrix (ECM)

39

Functions of the ECM:Include:

– Support/Structure• e.g. Cell Walls in plants (…more on this in a bit…)

Bone matrixProtection against osmotic pressure changes

– Adhesion/anchorage to surrounding medium• e.g. tissue formation

40

ECM: Plant Cell Walls

– ECM of plant cells

– Made of cellulose fibers embedded in other polysaccharidesand protein

– Functions• mechanical strength• growth/development• protection

41

Cell Wall

Fig 17-24

ECM: Prokaryotic Cell Walls

N- Acetylmuramic acid(NAM)

N- Acetylglucosamine(NAG)

BacteriaPeptidoglycan:

• NAM-NAG polysaccharide• Cross-linked with peptides

(short amino acid chains)

Archaea4 known variations:

a. Sulfated polysaccharidesb. Glycoproteins stabilized by Na+c. S-layers – protein chain maild. Pseudomurein (shown below)

• NAG – NAT polysaccharide• Cross-linked with peptides

N-Acetyltalosaminuronicacid (NAT)

Cell wall

(a) Gram-positive:-Simple cell walls- cell walls have large amount of peptidoglycan- traps violet dye in the cytoplasm- alcohol rinse does not remove the violet dye,which masks the added red dye.- Cells appear violet after counter-stain is added

(b) Gram-negative:-Complex cell walls with less peptidoglycan- Cell wall located in layer between-PM and an outer membrane- outer membrane also has lipopolysaccharides-violet dye is easily rinsed from the cytoplasm,- cells appears pink/red after counter-stain isadded

Cell wallPeptidoglycanlayer

Plasma membrane

Protein

Gram-positivebacteria

20 µm

OutermembranePeptidoglycanlayer

Plasma membrane

Gram stain• Tool to ID bacteria based on cell wall characteristics

Cells stained with violet dye Rinse with alcohol Stain again with counter-stain (usually red dye)

Lipopolysaccharide

Protein

Gram-negativebacteria

• Can be Gram+or Gram- ; also Gram variable

Pathogenic Prokaryotic Species

• Examples of Pathogenic Gram-

• Yersinia pestis (Plague)• Bordetella pertussis (Whooping cough)• Chlamydia tachomatis (STD)

• Examples of Pathogenic Gram+

• Clostridium botulinum (Botulism)• Bacillus anthracis (Anthrax)• Streptococcus pneumoniae (bacterialpneumonia, bacterial meningitis)

• Examples of Pathogenic Gram variable• Mycobacterium tuberculosis (Tuberculosis)• M. leprae (Leprosy)

• Used as a quick diagnostic tool• Examples:

– Classification of new species• Based on CW characteristics• Also preserves shape (e.g. spiral, rods)

– To confirm/rule out bacterial infection• Swabs taken from wounds, joint fluids, CSF, etc.(see recent example on next slide)

– Assessing bacterial contamination of tissue cultures– Environmental/Industrial contamination

• Natural disasters• Milk production

Gram Stain

Predictive value of superficial cultures toanticipate bloodstream infection.

Bouza E1, Rojas L2, Guembe M3, Marín M2, Anaya F4, Luño J4, López JM4,Muñoz P5; on behalf of the COCADI Study Group.

AbstractWe performed a prospective study in patients with tunneled cathetersto assess the validity of Gram stain and superficial culture foranticipating catheter exit-site infection and hemodialysis catheter-related bloodstream infection. The sensitivity and negative predictivevalue were high, and we succeeded in identifying a subpopulation atlow risk of infection.

Diagn Microbiol Infect Dis. 2013 Dec 17. pii: S0732-8893(13)00650-0.doi: 10.1016/j.diagmicrobio.2013.12.008. [Epub ahead of print]

Copyright © 2013 Elsevier Inc. All rights reserved.

http://www.ncbi.nlm.nih.gov/pubmed?term=Bouza%20E%5BAuthor%5D&cauthor=true&cauthor_uid=24428979

http://www.ncbi.nlm.nih.gov/pubmed?term=Bouza%20E%5BAuthor%5D&cauthor=true&cauthor_uid=24428979

http://www.ncbi.nlm.nih.gov/pubmed?term=Mu%C3%B1oz%20P%5BAuthor%5D&cauthor=true&cauthor_uid=24428979

http://www.ncbi.nlm.nih.gov/pubmed?term=Mu%C3%B1oz%20P%5BAuthor%5D&cauthor=true&cauthor_uid=24428979

http://www.ncbi.nlm.nih.gov/pubmed/24428979

Prokaryotic Cell Wall-Synthesis Inhibitors

• Certain antibiotics work by inhibiting cell wall biosynthesis• Compromise integrity of the CW

Makes bacteria susceptible to osmotic pressuresWith weakened CWs, they will generally lyse

• Examples:

– Fosfomycin• Interferes with peptidoglycan biosynthesis

- Penicillin• Interferes with peptide synthesisand peptidoglycan cross-linking

Penicillium fungus(DIC image)

Brightfieldimageof Streptomyces fradiae

Continue our “Tour of the Cell”…

• Stores DNA = CONTROL CENTER

• Large organelle~5-6um diameter~10% total cell volume

• Surrounded by Nuclear Envelope (NE)- Double membrane layer- Supported by Nuclear Lamina (…more in a bit…)

- Punctured at intervals by Nuclear Pores (…more in a bit…)

- Regulated openings through nuclearenvelope

- Control movement of substances in/outof nucleus

Nucleus

Nuclear Pores• Regulated openingsthrough Nuclear Envelope

• Openings controlled byNuclear Pore Complex(NPC)

• NPC controls movementof substances in/out ofNucleus

Q: What sorts of moleculesare moving in/out of nucleus?

Diagram source: http://www.goldmanlab.northwestern.edu/index.htm

CLSM of nuclear lamina(green) & DNA (red)from mousenucleusSource:http://medicalphysicsweb.org/cws/article/opinion/34548/1/SIM_1006

Nuclear Lamina• Network of intermediatefilaments (componentsof the cytoskeleton)

• Lie just beneath innerlayer of NuclearEnvelope

• Scaffolding that supportsnuclear structure

• Thought to also play arole in chromatinorganization

http://www.goldmanlab.northwestern.edu/index.htm

http://medicalphysicsweb.org/cws/article/opinion/34548/1/SIM_1006

• Region within the Nucleus

• Clustered regions of ribosomalRNA genes surrounded by specificRNAs & proteins

• Site of ribosomal subunitsynthesis

• Q: How do ribosomal subunits exitthe nucleus?Q: What happens after they

leave the nucleus?

Nucleolus

54

Nucleus

(SEM)

Type of microscopyused?

25 – 30 nm

55

Ribosome• Found in all cell types (pro/eukaryote),and certain

organelles• Not an organelle

The process by which genetic informationcoded in messenger RNA directs the

formation of a polypeptide sequence iscalled____________.

a)b)c)d)e)

TranscriptionTransformationTranslationTransgressionNone of the above

• Sizes of ribosomesdiffer betweenprokaryotes &eukaryotes

Eukaryote

Prokaryotic vs. Eukaryotic Ribosomes• Ribosomes are RNP (ribonucleoprotein) complexes

Q: What is an RNP complex??A: Complex of RNA and protein

Prokaryote

• Exam 1 will take place on Wednesday, 2/5/14, from12:30 pm-1:45pm.

Please go to the following exam location based on thespelling of your last name:A-J: Schmitt; K -Z: Ford Auditorium...*2 pt deduction onexam for going to the wrong room* :(

• Everything through lec 6 will be covered.• Please bring a No. 2 pencil.• You must also show your student ID when handing in your

exam.• Only 4-function calculators are permitted.• See syllabus for more details regarding the exam, approved

calculators, and secure testing.

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due today at 12:30pm• Assignments #3 and #4 are now available.

–due at 12:30pm on 2/3/14–i.e. ONE week from the availability date

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Protocol DescribingFractionation/Centrifugation

Nuclei extraction from brain tissueTotal nuclei were extracted via sucrose gradient ultracentrifugation. In the workpresented here (mouse), each sample was derived from a single forebrain (adultmales, 8–12 weeks of age); (human) 1000 mg of cerebral cortex. All the reagents usedwere pre-chilled and the entire procedure was performed on ice. Fresh or frozensamples were homogenized by douncing 50 times in 5 mL NEB with 0.1% Triton X-100,or alternatively, 0.1% NP-40. Triton X-100 was preferable if nuclei requireimmunotagging (with NeuN, for example), while NP-40 as a milder detergent left morenuclei intact and sufficient when working with nuclei expressing GFP. After douncing,brain homogenates were transferred into 14 mL ultracentrifuge tubes (Beckman, 14 ×95 mm, 344061), and 9 mL of Sucrose Cushion was carefully loaded directly to thebottom of the ultracentrifuge tube. Ultracentrifugation was performed at 24400 rpmfor 2.5 hrs at 4°C (Beckman, L8-70M, SW28 rotor). After centrifugation, a nucleipellet – thin and typically with a light yellow taint – was formed on the bottom ofthe tube. The sticky white tissue debris was restrained in the middle interface of thetwo sucrose layers. Supernatant, including debris, was carefully removed.

Source: Jiang et al. (2008). Isolation of neuronal chromatic from brain tissue. BMCNeuroscience 9, 42.

Type of microscopyused?

25 – 30 nm

4

Ribosome• Found in all cell types (pro/eukaryote),and certain

organelles• Not an organelle

• Sizes of ribosomesdiffer betweenprokaryotes &eukaryotes

Eukaryote

Prokaryotic vs. Eukaryotic Ribosomes• Ribosomes are RNP (ribonucleoprotein) complexes

Q: What is an RNP complex??A: Complex of RNA and protein

Prokaryote

Fig. 17-16Campbell and Reece, 8 ed.

Ribosome

Translation

Fig. 17-14Campbell and Reece, 9 ed.

E P A

MasteringBiology® animation onTranslation

• View ‘Protein Synthesis’ (BioFlix tutorial) inAssignment #4

Overview of Translation in Ch 22

Figure 22-7

binds to the start codon (AUG).

AA1

tRNA carryingfirst amino acid

UACAnticodon

5′

AUGStart codon

mRNA UAGStop codon

3′

Large Ribosomalsubunits

Small5′

INITIATIONAUG

1 During initiation, the componentsof the translational apparatus cometogether with an mRNA, and a tRNAcarrying the first amino acid (AA1)

AA1

© 2012 Pearson Education, Inc.

Overview of Translation

AA1

tRNA carryingfirst amino acid:INITIATOR tRNA

UACAnticodon

5′

AUGStart codon

mRNA UAGStop codon

3′

Large

Small

Ribosomalsubunits

5′INITIATION

AUG

1 During initiation, the componentsof the translational apparatus cometogether with an mRNA, and a tRNAcarrying the first amino acid (AA1)binds to the start codon (AUG).

AA1

AA1 AA2AA3

and are added, one byone, to a growingpolypeptide chain.

AA4 AA5

ELONGATION

2 During elongation,amino acids are broughtto the mRNA by tRNAs

5′

© 2012 Pearson Education, Inc.Figure 22-7


AA1

tRNA carryingfirst amino acid

UACAnticodon

5′

AUGStart codon

mRNA UAGStop codon

3′

Large Ribosomalsubunits

Small5′

INITIATIONAUG

1 During initiation, the componentsof the translational apparatus cometogether with an mRNA, and a tRNAcarrying the first amino acid (AA1)binds to the start codon (AUG).

AA1

AA1 AA2AA3

and are added, one byone, to a growingpolypeptide chain.

AA4 AA5

ELONGATION

2 During elongation,amino acids are broughtto the mRNA by tRNAs

5′

translational apparatus comes apart,releasing a completed polypeptide.

TERMINATION

3 During termination, a stop codonin the mRNA is recognized by aprotein release factor, and the

UAGStop codon

Releasefactor

3′

Completedpolypeptide

5′

Recycling oftranslationalcomponents

© 2012 Pearson Education, Inc.Figure 22-7


Please note:If these topics seem totally foreign to you,please review transcription/translation (Ch. 21& 22)

Prokaryotic Protein-Synthesis Inhibitors

• Certain antibiotics work by inhibiting ribosomeactivity

– Spectinomycin• interferes with mRNA interaction with the30S ribosome

• Examples:- Tetracyclin

• irreversibly binds to 30S subunit;• prevents tRNA from entering A site on 70Sribosome

Endomembrane System

Nuclear envelope

ER

Transport Vesicles

Vacuoles(not shown)

Lysosomes

Golgi

PlasmaMembrane

16Similar to Fig 12-1

• System of membranes and internal spaces

• Can be directly connected or connected viatransport vesicles

• Includes:– Nuclear envelope– ER– Golgi– Lysosomes– Vacuoles– Plasma Membrane– Transport Vesicles

Endomembrane System

Smooth ER

Rough ER

ER lumenCisternae

RibosomesTransportvesicle

Smooth ER

Nuclearenvelope

Rough ER

The Endoplasmic Reticulum (ER)• Accounts for ~½ the membranesin eukaryotic cell

200 µm

18

– ~10% total cell volume

• Contiguous with outer nuclearmembrane

• Two distinct regions of ER- Smooth ER, lacks ribosomes- Rough ER, contains ribosomes

Rough ER– Large, flattened sheets

– Ribosomes temporarily boundto cytosolic side= “rough” appearance

– Produces proteins,glycoproteins

– Products are distributedthroughout cell by transportvesicles

• Other endomembranecomponents

• Secreted products19

20

Smooth ER

• Lack ribosome– “smooth” appearance

• Functions:– Lipid synthesis

• e.g. cholesterol, steroids

– Carbohydrate metabolism– Stores Calcium– Detoxifies poison

• Two distinct regions of ER– Smooth ER, lacks ribosomes– Rough ER, contains ribosomes

• Functionally SEPARATEcompartments

e.g. A Secreted Protein would go through the RER would NOT go through the SER

Smooth ER

Rough ER

ER lumenCisternae

RibosomesTransportvesicle

Smooth ER200 µm

Nuclearenvelope

Rough ER

The Endoplasmic Reticulum (ER)

Abundant smooth ER in a hepatocyte. TEM of ahepatocyte of chronic alcoholic.

23

ER Adaptations

• Like most subcellular structures, the ER is dynamic• Cells can adjust relative amounts in response tochanging conditions

The Golgi Apparatus

• The Golgi– System of flattened membranous sacs– Receives many of the transportvesicles produced in the ER- Cis Golgi network (CGN): close to ER- Trans (TGN): other side

• Functions of the Golgi:- Modification of ER products

e.g. glycoproteins

- Manufacture of complex carbohydrates- Sorts and packages molecules for transport to finaldestinations 24

25Figure 12-1

Transport through Endomembrane System

Fig. 17-21 from ‘Biology’by Campbell et al.

Ribosome

mRNA

Signalpeptide

Signal-recognitionparticle (SRP)

Translocationcomplex

SRPreceptorprotein

CYTOSOL

ER LUMEN

ERmembrane

Protein

Recall from Biol 214…

Signalpeptideremoved

Hydrolases are enzymes (biological catalysts)which catalyze the hydrolysis of macromolecules.What exactly does a hydrolase do?

a) Adds a water molecule to a bond, causing it tobreak

b) Adds a water molecule in order to form a bondc) Removes a water water molecule from a bond,

causing it to breakd) Removes a water molecule in order to form a bonde) I have no idea!

27

Lysosome

cis Golgi

trans Golgi

Smooth ER

Nuclear envelop

Plasmamembrane

28

Lysosomes are part ofendomembrane system

- bud off from Golgi

Lysosomes: Digestive Compartments

Lysosome– membranous sac of

hydrolytic enzymes– Function is digestion

Nucleus

Rough ER

29

Intracellular ‘Digestion’ by Lysosomese.g. Phagocytosis

- Ingestion of large particles (>0.5um diamter)

- Breakdown (digestion) of particles carried out by Hydrolasesinside of lysosomes

30

Intracellular ‘Digestion’ by Lysosomese.g. Autophagy

- Process of organelledegradation that takes placeinside the cell“auto” = self “phagy” = to eat

- Used to removeold/damaged cell structures

Homework for next class:Based on what we have discussed,

describe, step by step, the pathway takenby hydrolase enzymes in order to localizethem to the lumen of the lysosome. Startwith transcription of the hydrolase gene.

Hydrolase ?

Lysosome

Vacuoles: Diverse MaintenanceCompartments

• Cells may have one orseveral vacuoles

• Function is cell-specific

Examples:– Central vacuole in plants

(…more in a bit…)

– Food vacuoles (phagosomes)• formed by phagocytosis

– Contractile vacuoles• osmoregulation

Amoeba proteusstained with pH-dependent dye. The dyebecomes dark red in the acidic environment of the foodvacuoles.

32

CentralvacuoleNucleus

Cell wall

Chloroplast5 µm

33

Central Vacuoles– Found in plant cells– Hold reserves of important organic compounds

and water– Maintain fluid balance/ turgor

Central vacuole

Cytosol

Tonoplast

34

Vacuoles in Animal Cellse.g. vacuoles in Paramecium (unicellular protist)

Food Vacuoles

35http://www.linkpublishing.com/video-transport.htm#Paramecium_-_Contractile_Vacuoles

Vacuoles in Animal Cells

Vacuoles in Animal Cells

• Vary in number (depending on cell type)– Few to many

• Much smaller than Central Vacuole found in plants

Energy-converting Organelles

Mitochondrion

Chloroplast

37

Mitochondria and Chloroplasts

• Change energy from one form to another

• Mitochondria– Sites of cellular respiration– Found in most eukaryotes, includingphotosynthetic organisms

• Chloroplasts– Found only in photosynthetic eukaryotes– Sites of photosynthesis

38

Evolution of Chloroplasts & Mitochondria:Endosymbiotic Theory

• Idea championed by Lynn Margullis (Umass) inthe late 1960’s

• Hypothesis:Mitochondria & chloroplasts originated as free-living prokaryotes

• Mitochondria: proteobacteria• Chloroplasts: cyanobacteria

– *Proteobacteria & cyanobacteria are types of Bacteria

Smaller cel taken inside another cell (largerprokaryote)Symbiotic relationship developed Dependency increased over time such that cellsbecame ONE

Evolution of Eukaryotic Cells

What evidence might support theEndosymbiotic Theory for the

Origin of Mitochondria &Chloroplasts?

1)2)3)

4)

5)

6)

Evidence Supporting the Endosymbiotic Theory for theOrigin of Mitochondria & Chloroplasts

Mit/cp Similar size to prokaryotes (~1 um)Replicate by binary fissionDouble membrane– Inner membrane similar to prokaryotes, outer membrane

may have been derived from host ‘phagosome’

70S ribosomes– Sensitive to some antibiotics

Circular genome– Prokaryotic promoters, no histones

Genome sequence similarity– Cp: cyanobacteria;Mit: proteobacteria

7) Reduction of organellar genomes---

Gene transfer to nucleusMany genes needed by mit/cp are nuclear encodedSequence similarity b/w genes in nucleus and cyanobacteria/proteobacteria

Peroxisomes• Similar in shape & size to lysosome

- However, NOT part of endomembrane system

• Main function: Compartmentalizehydrogen peroxide (H2O2)-producingreactions

-RH2 + O2 R + H2O2Note: ‘R’ generically refers to an organic molecule

-H2O2is toxic to cells

-H2O2 is then degraded into H2O + O2 degradation catalyzed by the enzyme catalase

~Figure 4-19

44

45

ChloroplastPeroxisome

Mitochondrion

1 µmFigure 4-20

PeroxisomesOther functions:• Breakdown of long-chain fatty acids

- via β-oxidation pathway (…more on this later…)

• Detoxification of oxidizeable substrates- e.g. alcohols

• Photorespiration inPlants- Strategy to recover

carbon that would beotherwise lost (…moreon this later…)

Cytoskeleton• Network of protein fibers and associated proteins

• Network extends throughout the cytoplasm andunderlie nuclear envelope

• Organizes structures and activities in the cellMicrotubule

0.25 µm Microfilaments 47

Table 15-1

Structure of Cytoskeletal Elements

49

Cytoskeletal-Associated Motor Proteins

Cell Locomotion

50

Neutrophil chasing Bacterium

• http://www.dnatube.com/video/4330/Neutrophil-Chases-Bacteria

http://www.dnatube.com/video/4330/Neutrophil-Chases-Bacteria

signal

52


How does the Eukaryotic cell perceive the bacterium?

signal

53


How is movement towards to bacterium generated?

signal

54


Outline the steps involved in engulfment anddigestion of the bacterium.


Archaea

Proteobacteria

Homework:Based on what we have discussed,

describe, step by step, the pathway takenby hydrolase enzymes in order to localizethem to the lumen of the lysosome. Startwith transcription of the hydrolase gene.

Hydrolase ?

Lysosome

Inner Life of a Cell

• Segment describing co-translational import:http://multimedia.mcb.harvard.edu/media.html

http://multimedia.mcb.harvard.edu/media.html

6Figure 12-1

Transport through Endomembrane System

Figure 12-9

Protein Targeting to Lysosomal Lumen

At the RER:- Hydrolase is fully synthesized- Deposited in RER lumen- Carbohydrate ‘tag’ gets added

(mannose)

At the Golgi:- As glycosylated hydrolase

moves through Golgi,mannose ‘tag’ isphosphorylated by Golgi-specific enzymes

Result: Hydrolase with aMannose-6-Phosphate ‘tag’

Vesicle containinghydrolase buds off of RER Fuses to Golgi

Figure 12-9

Protein Targeting to Lysosomal LumenAt the Golgi:Hydrolase with a M-6-P ‘tag’- ‘Tag’ serves as a ‘Recognition

System’…- Phosphate group binds to a

receptor in Trans Golgimembrane

- Receptor specificallyrecognizes the M-6-P ‘tag’

- Binding triggers packaging ofhydrolase into a vesicle

- Vesicle fuses to acidifiedcompartment: endosome

- Low pH causes dissociation ofHydrolase from receptor

Endosome matures into alysosome


• http://www.dnatube.com/video/4330/Neutrophil-Chases-Bacteria

http://www.dnatube.com/video/4330/Neutrophil-Chases-Bacteria

signal

11


How does the Eukaryotic cell perceive the bacterium?

signal

12


How is movement towards to bacterium generated?

signal

13


Outline the steps involved in engulfment anddigestion of the bacterium.

Tuberculosis

• Infectious disease caused by mycobacteriastrains

• WHO estimates 1/3 of the world populationinfected with mycobacteria

• Commonly affects lungs– Aerial transmission (e.g. coughing, sneezing)

CASE STUDY:Examination of white blood cellstaken from a patient with tuberculosisreveals living bacteria in large vesicles.Continued observation over timeshows that the bacteria remain alivefor a long time.

In this case, which white blood cellprocess might be defective?

[EM image of] Mycobacterium tuberculosisphagosome in alveolar macrophage froman individual co-infected with HIV.Arrowhead, phagosome with M.tuberculosis. Arrows, virus-like particlessuspected to be HIV buddinginside themacrophage.Scale bar = 1 μm.Annu. Rev. Cell Dev. Biol. 2004. 20:367–94

Examination of white blood cells taken from a patientwith tuberculosis reveals living bacteria in large

vesicles. Continued observation over time shows thatthe bacteria remain alive for a long time. In this case,what white blood cell process might be responsible?

a) Deficient receptors on the white blood cell fordetecting bacteria

b) Slow white blood cell motilityc) Failure of the phagocytic vesicle and lysosome to

fused) Mitochondrial deficiencye) Chloroplast defect

What are cells made of?

What are cells made of?

~25 of all known elements are needed for lifeOf those, 5 are found in all living things…

H, C, N, O, P

• 5 elements found in all living things• Constitute 99% of an organism’s weight• Incomplete outer e- shells

– donate, accept or share electrons to form ions andmolecules

– i.e. they are REACTIVE

Which element do you think contributes tomost of our body mass?

a)b)c)d)e)

CalciumCarbonHydrogenNitrogenOxygen

Oxygen - 65Nitrogen – 3.3

Carbon – 18.5 Hydrogen – 9.5Calcium - 1.5 Phosphorous - 1.0

Elemental Composition of theHuman Body

• Percent by mass (approximate)

*these six elements make up ~99% of our bodies

Other ~1%:Potassium 0.2Sulfur 0.2Chlorine 0.2Sodium 0.1Magnesium 0.05Cobalt, Copper, Zinc, Iodine < 0.05 eachSelenium, Fluorine, Manganese, Molybdenum, Nickel < 0.01 each Iron 3.9– 6.4 x 10 -5

Why so much Oxygen?

• Cells are mostly water– Average cell ~70% water– Others have less

• Example: bone cell ~20% water

• Most cellular reactions take place insolution (aq)

What makes an element REACTIVE?

Anatomy of an Atom

• Atom = basic unit of matter– Nucleus surrounded by electrons

Nucleus: consists of protons(+ve) and neutrons(except H which has only 1 proton &no neutron)

Electrons:-ve charged particles

Electrons

• Attracted to positively-chargednucleus– have potential energy becauseof attraction to the nucleus

• Can have only certainamounts, or levels, of energy

• E levels are called electronshells– pictured as spherical regionsaround the nucleus

Valence Electrons• Electrons in the last shell• Valence # = Group # (disregarding transitionmetals)

• Important determinant of reactivity– Can be gained or lost in a chemical reaction– Atoms tend to react in ways that result in filled

outer shell

Electronegativity

• Affinity of an atom/molecule for electrons• Electronegativity Scale:

• The greater the EN value, the stronger theaffinity for electrons

Which atom has a greater affinity forelectrons?

a) Oxygenb) Carbonc) Neither. They are equal

Types of Bonds

Covalent bonds – sharing electrons

• Electrons are shared between atoms• Two different types of covalent bonds:

– Polar covalent– Nonpolar covalent


• Polar molecules– Electrons are unequally shared One part of molecule is more negative thanthe another part of the molecule– Molecule thus has negative and positive ‘poles’

• Similar to a battery• e.g. Water molecule

– Hydrophilic (‘water loving’)


• Nonpolar molecules– Electrons are equally shared– No one part of molecule is distinctly negative orpositive

• no ‘poles’

– Hydrophobic ‘water fearing’

Ionic bond

• Formed through electrostatic attractionbetween oppositely charged ions.

• Due to the attraction between:– an atom that has lost 1 or more electron (e.g.cation+)

– and an atom that has gained one or moreelectrons (e.g. anion-)

• Electrons are NOT shared in an ionic bond

Ionic bond

Covalent bonds

Nonpolar Polar

∂+ ∂-

Ionic bond

+

-

Hydrogen bond• Forces between polar molecules

– Specifically involves hydrogen (H) bound to a moreelectronegative atom, such as N, O or F,) and an O, Nor F of another molecule.

• Electrons are not shared– Electrostatic interaction between dipoles

• Example: Interactions between water molecules:

What other type of force, foundin all molecules, is important?

London Dispersion Forces• Temporary attractive force resulting whenelectrons in two adjacent atoms occupy positionsthat make the atoms form temporary dipoles

• Found in all molecules• Weakest of all forces

Macromolecules of the Cell

Which molecule is organic?

a)b)c)d)e)

CO2

H2OCH3OHO2

More than one answer

Organic molecules

• Hydrocarbon based– i.e Carbon with hydrogen– e.g. carbohydrates, CH3OH

• The presence of Carbon alone does notconstitute an organic molecule– e.g. CO2 = inorganic carbon

*Note: This is the definition of ‘organic chemistry’ that we will use in this class.Other sources may define ‘organic’ differently.

Carbon

••••

What is so Special about Carbon?

Capable of forming four bondsRelatively neutral electronegativityCovalent bondsForms stable molecules

47Triple bondingSingle bonding Double bonding

HUGE variety of organic molecules

Straight chains

RingsBranched Chains

Functional Groups

• Specific groups of atoms added to organicmolecules

• Lend specific chemical characteristics tomolecule in which group occurs

What charge will the followingmolecule have in an aqueous

environment (aq)?

a) Positiveb) Negativec) Neutral 49

Functional Groups

50Figure 2-5

Functional Groups

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

True or False?: In an aqueous environment,a hydroxyl group will be negatively

charged.

a) Trueb) False

-OH functional group IS NOT the sameas a hydroxide ion (OH-)

• In an aqueous environment, -OH (hydroxyl)functional groups are NOT charged.

• -OH (hydroxyl) functional groups DO NOTdeprotonate in an aqueous environment.

Functional Groups

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Functional Groups

Acetyl group (CH3C-)= Specific type of carbonyl

R

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Functional GroupsCarboxyl

Carboxylic acids, or organic acids

Has acidic propertiesbecause the covalent bond betweenoxygen and hydrogen is so polar; forexample,

Acetic acid, which gives vinegar its sourtaste

Acetic acid

Acetate ion

Found in cells in the ionized formwith a charge of 1– and called acarboxylate ion (here, specifically,the acetate ion).

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIESActs as a base; can pick

up an H+ from thesurrounding solution(water, in livingorganisms).

(nonionized) (ionized)

Ionized, with a chargeof 1+, under cellularconditions.

Glycine

Because it also has acarboxyl group, glycine isboth an amine anda carboxylic acid;compounds with bothgroups are called aminoacids.

Functional GroupsAmino

Amines

OOC

OH+

Carboxylic Acid Amine

H2N C CN C

Amide

HExample of Amide: Peptide bond that joins amino acids in apolypeptide as a result of a dehydration reaction

Note: Unlike amines, amides are uncharged insolution (aq).

+ H2O

Functional Groups

Amide

- Formed by reaction between an acid and an amine:

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Functional GroupsSulfhydryl

Thiols

(may be writtenHS—)

Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.

Cross-linking ofCysteinecysteines in hairproteins maintains the

Cysteine is an important curliness or straightness ofsulfur-containing amino acid. hair. Straight hair can be

“permanently” curled byshaping it around curlers, thenbreakingand re-forming thecross-linking bonds.

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Glycerol phosphate

In addition to taking part in manyimportant chemical reactions incells, glycerol phosphate providesthe backbone for phospholipids, themost prevalent molecules in cellmembranes.

Contributes negative charge tothe molecule of which it is a part(2– when at the end of amolecule; 1– when locatedinternally in a chain ofphosphates).

Has the potential to react withwater, releasing energy.

Functional GroupsPhosphate

Organic phosphates

Polymers

Organic Macromolecules foundin Cells

a) Lipids

b) Nucleic Acids (polynucleotides) - Biol 214

c) Carbohydrates (polysaccharides)

d) Proteins (polypeptides)

Monomer subunits

• Carbohydrates– Monosaccharides

• Nucleic Acids– Nucleotides

• Proteins– Amino Acids

62

63

Organic macromolecules aresynthesized by ______________ reactions.

a)b)c)d)e)

condensationhydrogenationhydrolysispolyhydrationtransamination

64

Breakdown of organic macromoleculesoccurs by ______________ reactions.

a)b)c)d)e)


OH H OH H

Synthesis of Polymers occurs by Dehydration Reaction(type of Condensation Reaction)

–H and –OH are removed (~water)subunits join into a polymer.i.e. components are ‘dehydrated’

monomer monomer monomer

polymer

••••

Why does a carboxylic acid (carboxyl)functional group behave differently insolution compared to a hydroxyl?

Has TWO electronegative oxygensThe O’s pull electrons away from the H atomWeakens the bond between O and HH atoms tends to dissociate from the molecule asa hydrogen (H+) ion.

• Because it donates hydrogen ions, this group isconsidered acidic

• Molecules that contain these groups are knownas carboxylic acids.

Functional Groups

3Figure 2-5

Polymers


a) Lipids




Monomer subunits

• Carbohydrates– Monosaccharides

• Nucleic Acids– Nucleotides

• Proteins– Amino Acids

5

6

Organic macromolecules aresynthesized by ______________ reactions.

a)b)c)d)e)


7

Breakdown of organic macromoleculesoccurs by ______________ reactions.

a)b)c)d)e)


OH H OH H

Synthesis of Polymers occurs by Dehydration Reaction(type of Condensation Reaction)

–H and –OH are removed (~water)subunits join into a polymer.i.e. components are ‘dehydrated’


polymer

Imagesource: http://en.wikipedia.org/wiki/Condensation_reaction

amino acid 1 amino acid 2polypeptide

water

Protein Synthesis via Amino Acid PolymerizationExample of Dehydration Reaction

(aka Condendation reation)

Removalof H2O

http://en.wikipedia.org/wiki/Condensation_reaction



http://upload.wikimedia.org/wikipedia/commons/3/3e/2-amino-acidsb.png






Polymer is split into smaller subunits by adding –H and –OH (~water)i.e. polymer is hydrolyzed

Breakdown of Polymers by hydrolysis reaction“hydro” = water “lysis” = break apart


polymer

Why is hydrolysis of macromoleculesnecessary?

• Some macromolecules are too large to getimported into cells

e.g. starch

• Hydrolysis yields smaller subunits that can entercells

e.g. glucose

• Subunits can then be used in the cell e.g. assembled into polymers via dehydrationreactions

Example of Hydrolysis Reaction:Starch Breakdown

Imagesource: http://www.biology-books.com/Standard/standard.html

http://www.biology-books.com/Standard/standard.html



13


a) Lipids

b) Nucleic Acids (polynucleotides)

c) Carbohydrate (polysaccharides)


• Heterogeneous group of molecules– Defined in terms of solubility characteristics(not structural characteristics)

• All lipids are primarily Hydrophobic molecules– Little affinity for water– Readily soluble in nonpolar solvents

• e.g. chloroform or ether

• Some lipids are amphipathic, having polar andnonpolar regions– Primarily hydrophobic

Lipids

• Functions include:- energy storage- membrane structure- signal transduction

• Different from other macromolecules- not formed by the same type of linear polymerization asproteins, nucleic acids, and polysaccharides

• Still regarded as macromolecules due to:• high molecular weight• importance in cellular structures

• particularly membranes

Lipids

Classes of Lipids• Various classes based structure

– Fatty acids– Triacylglycerols

• a.k.a. triglycerides

– Phospholipids– Glycolipids– Steroids*Ignore Terpines

…More on this later (Ch 7)… Figure 3-27


17

a) Lipids




18


a) Lipids

b) Nucleic Acids (polynucleotides)- Biol 214



Carbohydrates• Most abundant organic molecules on Earth!

#1: Cellulose – produced by photosynthetic organisms#2: Chitin – fungal cell walls, exoskeletons of arthropods

• Main Functions in cells:• Structural components• Storage = Major E source

• Molecular Structure:• Poly-hydroxyls ~one per carbon

“carbo” “hydrate” = carbon with water• Aldehyde – or – ketone• Often have ‘-ose’ ending

- e.g. glucose, sucrose

1

2

3

4

5

6

galactose

Carbohydrates

Aldehyde – or – Ketone

- terminal carbonyl - carbonyl withinmolecule

Figure 3-20

• Monosaccharides“Mono” = one, “sacchar” = sugar

• Disaccharides“Di” = two, “sacchar” = sugar

• Polysaccharides“Poly” = many, “sacchar” = sugar

Categories of Carbohydrates

- Main E source for cells*central to cell metabolism

- Structural component ofimportant disacharides andpolysaccharides

Important Monosaccharides

• Monosaccharides“Mono” = one, “sacchar” = sugar

- simple sugars- generally have a molecular formula that is some multiple of CH2O

Glucose:- 6 Carbon aldose = aldohexose

C6H12O6

Fructose:- 6 Carbon ketose = ketohexose

• C6H12O6

- Referred to as “fruit sugar”- Metabolic intermediate- Important disaccharide component

• Combines with glucose to form sucrose (table sugar)


Galactose:- 6 Carbon aldose = aldohexose

• C6H12O6

- Important disaccharide component• Combines with glucose to form lactose (milk sugar)• Galactosemia

- genetic disorder- afflicted individuals cannot metabolize galactose- high levels of galactose can lead to metal retardation


Glyceraldehyde & Dihydroxyacetone (DHA):- 3 Carbon sugars = triose

• Glyceraldehyde = trialdose• DHA = ketotriose

- Metabolic intermediates• Intermediates of both glycolysis pathway and

photosynthesis• Reversible interconversion (equilibrium!!!)

FYI: DHA is active ingredient in sunless tanning products• Combines with different amino acids to form melanoidins

(brown polymers)

• Monosaccharides link together to form largerstructures– e.g. two monosaccharides = disaccharide“di” = two, “sacchar” = sugar

• Join together via condensation reaction toform glycosidic bond:

Disaccharides

Important Disaccharides

Maltose- Dissacharide of glucose

(14 glycosidic linkage)

- Breakdown product of starch (glucose polymer)

26

27


Sucrose- Dissacharide of glucose + fructose


- Table sugar- Transport carbohydrate in many photosynthetic organisms


Lactose- Dissacharide of galactose + glucose


- Milk sugar- Important component of mammalian milk

• Lactose Intolerance:– Inability to digest lactose– Caused by missing/defective lactase enzyme

• Lactase = enzyme that cleaves the (14) glycosidicbond between galactose and glucose

– Results in GI disturbances• e.g. upset stomach, diarrhea

• Management options:– Avoid dairy products– Lactase supplements

• Not on empty stomach as low stomach pH willdenature the enzyme

– Treat dairy products with lactase


• “poly” = many, “sacchar” = sugar

• Polysaccharides are polymers ofmonosaccharides or disaccharides

Important Polysaccharides

Important Polysaccharides - Short term E Storage

Glycogen – branched polymer

Similar to Fig 3-24

• α(14) glucose polymers• α(16) branch points (glycogen and amylopectin)

Starch : amylose (linear)or amylopectin (branched)

Important Polysaccharides

32Figure 3-25

- Structural

Cellulose•β(14) glucose polymer

~2000per

microfibril

25nm

α-Glucose and β-Glucose

• Monosaccharides can exist as linear chains or rings• In aqueous environments (aq), ring structures aremore energetically favorable (more stable)

Humans can digest ___________.

a) starch

b) cellulose

c) both starch andcellulose

d) neither starch norcellulose

• Enzymes that digest starch (amylases) by hydrolyzing α linkagescan’t hydrolyze β linkages in cellulose (requires cellulases)

• Cellulose in human food passes through the digestive tract asfiber

• Some microorganisms use enzymes (cellulases) to hydrolyze βlinkages in cellulose• Many herbivores (e.g. cows, termites) have symbiotic

relationships with such microbes

Many animals (including humans) CANdigest starch but NOT cellulose

36

Important Polysaccharides- structural

Chitin• β(14) glucosidic linkages of N-acetylglucose amine (GlcNAc) residues

Figure 3-26

Found in:- Cell walls of fungi

- Exoskeleton of insects and arthropods(crunchy!)

N- Acetylmuramic acid(NAM)

N- Acetylglucosamine(NAG)

37

Found in:- Cell walls of bacteria

Important Polysaccharides: StructuralPeptidoglycan• Repeating dimer of β(14) linked NAG(GlcNAc) and N-acetylmuramic acid (MurNAc)

Figure 3-26

38

Hyaluronic Acid (aka Hyaluronate)• Repeating dimer of glucuronic acid (glucuronate) and NAG, linkedvia alternating β(13) and β(14) glucosidic linkages

• Prevalent in connective tissue and epithelial tissue

Important Polysaccharides - Structural

Hyaluronic Acid (aka Hyaluronate)• Cosmetic applications:

•Injectable filler for wrinkle remover

•Trade Names: Restylane, Juvederm

Before After!!!

Glucose modifications

• Replacement of a hydroxyl groupwith another functional group

• Examples:– NAG = N-acetyl glucose amine

• Amine linked to Acetyl

– Glucuronic acid• Carboxyl group

Infants suffering from galactosemia shouldavoid products with _________.

a)b)c)d)e)

StarchCelluloseSucroseMaltoseLactose

42


a) Lipids

b) Nucleic Acids (polynucleotides)



Proteins

• Polymers of amino acids

• IMMENSELY diversestructures/functions

• Structure ↔ Function

43

44Table 3-1

*

Protein Functions

Amino Acid Structure

Figure 3-1

45

Classes of Amino Acids:Nonpolar

46Figure 3-2

Glycine(Gly or G)

Alanine(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(Ile or Ι)

Methionine(Met or M)

Phenylalanine(Phe or F)

Tryptophan(Trp or W)

Proline(Pro or P)

Nonpolar amino acids arealso referred to as ________________, meaning

they are water-_____________.

a)b)c)d)

hydrophilic; insolublehydrophilic; solublehydrophobic; insolublehydrophobic; soluble

Classes of Amino Acids:Polar, uncharged

Asparagine(Asn or N)

Glutamine(Gln or Q)

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

Tyrosine(Tyr or Y)

aka. Aspartic acid aka. Glutamic acid

Negative

Arginine(Arg or R)

Histidine(His or H)

Aspartate(Asp or D)

Glutamate(Glu or E)

Lysine(Lys or K)

Classes of Amino Acids:Polar, Charged

Positive

When placed into solution (aq), the amino acidsclassified as ‘negatively charged’ behave as _______and the amino acids classified as ‘positively charged’

amino acids behave as ________.

a)b)c)

acids; basesbases; acidsacids; acids

d) bases; bases

Negative

Arginine(Arg or R)

Histidine(His or H)

Aspartate(Asp or D)

Glutamate(Glu or E)

Lysine(Lys or K)

Positive

Acidic

Arginine(Arg or R)

Histidine(His or H)

Aspartate(Asp or D)

Glutamate(Glu or E)

Lysine(Lys or K)

Classes of Amino Acids:Polar, Charged

Basic

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Functional GroupsCarboxyl or Carboxylic Acid

Carboxylic acids, or organic acids

Has acidic propertiesbecause the covalent bond betweenoxygen and hydrogen is so polar; forexample,

Acetic acid, which gives vinegar its sourtaste

Acetic acid

Acetate ion

Found in cells in the ionized formwith a charge of 1– and called acarboxylate ion (here, specifically,the acetate ion).

Please note:

• Students are required to memorize thestructures of the 20 amino acids

• Students DO NOT need to memorize aminoacid abbreviations(Would be helpful for you to know, but you will notbe required to memorize these for our class).

What type of amino acid is shown below?

a)Acidicb)Basicc)Nonpolard)Polar, unchargede)Hydrophobic

Is the amino acid shown below in solution?

a)Yes, it’s in solution.b)No, it’s NOT in solution.c)Impossible to tell.

lecture 1 5

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