Important to know for final

Question 1

Why are cells small?

Answer 1

• as cell size increases, surface area/volume decreases

- if surface area drops, difficult to take up nutrients and rid wastes

Question 2

Robert Hooke (1665)

Answer 2

described cells in cork (empty and dead cells)

Question 3

Basic properties of cells

Answer 3

• reproduce themselves
• acquire and use energy
• perform chemical reactions, metabolism
• dynamic, capable of movement
• respond to stimuli in environment
• self-regulate

Question 4

Anton van Leeuwenhoek (1665-1675)

Answer 4

animalcule-living cells

Question 5

Theodor Schwann (1839)

Answer 5

tenets of cell theory

1) all organisms composed of one or more cells
2) cells are structural units of life

Question 6

Rudolf Virchow (1855)

Answer 6

tenets of cell theory

3) cells arise from preexisting cells

Question 7

Prokaryotes vs eukaryotes

Answer 7

Differences
Prokaryotes:
-single-celled organisms
-small in size
-DNA free in cytoplasm
-Bacteria and Archaea (extremophiles)
-binary fission
-lack nucleus
Eukaryotes:
-protists, fungi, plants, animals
-membrane-bound nucleus
-more DNA than prokaryotes
-larger in size
-have organelles
-divide by mitosis/meiosis
-more complex cytoskeleton and motility machinery
-segregate activities in compartments 
-DNA compacted into nucleus

Similarities

• plasma membrane
• genetic code
• mechanisms for decoding
• metabolic pathways
• use of ATP
• mechanism for photosynthesis

Question 8

Viruses

Answer 8

• non-living
• can’t reproduce on their own
• bits of nucleic acids with protein coat
• genetic code encapsulated
• hijack host
• can’t respond to stimuli
• precursors to living organisms

Question 9

Viroids

Answer 9

• circular RNA
• no protein coat
• infect plants
• precursor of virus formation

Question 10

Prions

Answer 10

• proteinaceous infectious particles
• no DNA
• biological molecules

Question 11

Macromolecule: Lipids

Answer 11

• insoluble in H20, soluble in nonpolar organic liquids
• small, organic molecule
• hydrophobic
• source of energy and store energy=fats and oils
• hormones and chemical messengers=steroids and prostaglandins
• vitamins
• structural elements of membranes=phospholipids
• fatty acids=amphipathic, form micelles in water, hydrophobic, hydrocarbon chains with carboxyl group

Question 12

Which microscope is used to see organelles in cells?

Answer 12

electron microscope

Question 13

Macromolecule: Carbohydrates

Answer 13

• simple sugar = monosaccharide, source of energy and carbon
• polysaccharide = energy-storing (glycogen in animals and starch in plants)
• monomer=glucose
• face outward into extracellular space of the membrane
• glycoproteins in membrane: cell interactions
• glycolipids: targets for infectious diseases and determine blood type

Question 14

Cellulose

Answer 14

• rigid structural polysaccharide (carbohydrate)
• monomer=glucose
• insoluble
• cell wall of plants
• we can’t digest them
• termites and cows can digest due to symbiotic bacteria and protozoa
• cellulase enzyme can break down cellulose

Question 15

Macromolecule: Nucleic acid

Answer 15

• polymer of nucleotides
• nitrogenous base, pentose sugar, phosphate group, attached by sugar-phosphate group
• store genetic information
• signalling molecule
• energy transfer for metabolism

Question 16

Ribonucleic acid (RNA)

Answer 16

-has oxygen
-chain of ribonucleotides
-sugar is ribose
4 nitrogenous bases (adenine, guanine, cytosine, uracil)
-single stranded
-3D structure
-information storage
-catalysts

Question 17

Deoxyribonucleic acid (DNA)

Answer 17

• chain of deoxyribonucleotides
• sugar is deoxyribose
• oxygen is missing
• 4 nitrogenous bases (adenine, guanine, cytosine, thymine)
• double stranded helix
• bonded together by hydrogen bonds pairing (A-T, G-C)
• the template for RNA production during transcription

Question 18

Macromolecule: Proteins

Answer 18

• one or more polypeptide chains
• monomer=amino acid
• held together by peptide bonds
• functions: enzymes, structural elements, contractile elements, control activity of genes, transport material across membranes, carriers, hormones, antibodies
• R group amino acid side chain *gives variety in amino acids
• structure: primary=sequence of amino acids in polypeptide chain, secondary=beta sheets and alpha helices, tertiary=beta sheets and alpha helices are connected by bonds (hydrogen, hydrophobic, disulfide, covalent), quaternary=when tertiary structures come together
• some remain in cytoplasm, move to mitochondrion, ER or enter endomembrane system

Question 19

Stages of the cycle and checkpoints

Answer 19

M phase:

• entry by maturation promoting factor
• mitosis (nuclear division) -cytokinesis (cytoplasmic division)

Interphase:
-entry by the spindle checkpoint (waits for chomosomes to line up at metaphase plate)
-Go (permanent arrest stage, no further development)
-G1 (growth phase)
-entry by the DNA damage checkpoint
-S phase (DNA replication)
G2 (final growth to get cell prepared for mitosis)
-exit by DNA damage checkpoint

Question 20

Maturation Promoting Factor (MPF)

Answer 20

• entry into mitosis requires this protein complex
• has cyclin b and Cdk 1
• activates lamin proteins and causes nuclear envelope to break
• alters DNA-bound proteins (histones) and DNA condenses
• activates proteins of mitotic spindle
• activity turned off by activating ubiquintin ligase, attaches ubiquintin, tagged for destruction, terminates MPF, causes proteolysis of cyclins
• ensures the cell’s DNA is replicated, big enough, enough stuff to enter the M phase

Question 21

Cyclin b

Answer 21

• regulates Cdk1 activity
• levels rise and fall (cycle) throughout cycle
• forms complex with Cdk1
• activity turned off by activating ubiquintin ligase, attaches ubiquintin, tagged for destruction, terminates MPF, causes proteolysis of cyclins

Question 22

Cdk1 (cyclin dependent kinase)

Answer 22

-kinase: protein that adds a phosphate to cyclin b and its activity is modified

Question 23

Histones

Answer 23

• altered by Maturation Promoting Factor by causing DNA to condense
• DNA binds around nucleosomes composed of a group of 4 histones
• positively charged
• highly conserved proteins
• are modified to make DNA more or less accessible by replacing with modified histones and chemical modifications: *acetylated=looser DNA binding, increases gene expression
• methylated=tighter DNA binding, supresses gene expression
• deacetylase=removes acetyl groups and DNA winds tightly, gene activity silenced

Question 24

Cancer

Answer 24

• DNA damage checkpoint causes Ataxia-telangiectasia and makes them susceptible to cancer
• uncontrolled cell divisions (proliferation)
• normal cells form a monolayer, cancer cells pile up
• properties:
  1) ignore inhibitory growth signals (ignore cell contact which usually stops normal cells from dividing)
  2) growth in absence of stimulatory growth signals (normal cells require signals to proceed through cell cycle-checkpoints)
  3) capable of continuous division (telomerase keeps restoring cancer cells’ telomeres)
  4) aneuploidy=abnormal chromosome number (cancer cells are more tolerant up to a point)
• causes: damage to DNA (mutagens) like radiation and chemicals (carcinogens); stimulation of the rate of mitosis by certain hormones (in breasts and prostate gland), chronic tissue injury (stem cells needed to repair damage), agents that cause inflammation (oxidizing agents) and certain viruses (cervical cancer=human papilloma virus, hepatitis virus=liver cancer, herpes=Epstein-Barr virus, human T-cell leukemia viruses or HTLV-1 and HTLV-2) *for viruses only if unlucky will the cell develop into a tumour, most do not
• mutations in p53 gene in tumour cells
• due to translocations (chronic myelogenous leukemia), placing the control of gene to another gene’s promoter
• tumour cells have presence of telomerase or reactivation which elongates telomeres and allows immortality
• can escape death by chemotherapy from mutations in the ABC transporter which is supposed to detoxify cells
• due to dogs having lots of GPCRs and odorant receptors, they can sniff out cancers that produce unusual amounts of metabolites
• can be caused by mutations in the epidermal growth factor receptor (EFGR) which is overexpression or overactivity (lung cancer)
• reduces risk of developing cancer with eating carotenoid rich diets
• cancer cells take in toxin of chemotherapy and keep trying to divide, but cell divisions end up with too many or too little chromosomes due to microtubules not properly attaching, which eventually the cancer cells die off; normal cells stop cell division and try to get rid of toxins
• intermediate filaments are useful in cancer diagnosis to find where tumour originated (keratin have subtypes unique to different epithelial cells, antibodies bind a keratin subtype in colon cancer cells)
• integrins promotes anchoring of the cell to the ECM by starting a signal cascade; cells can’t survive if not anchored to extracellular matrix=anchorage dependence, but lost when a cell is cancerous due to not relying on signal from integrin
• too much stimulation of the heregulin receptors can cause the cell growth to have too much stimulation (tight junctions seal is broken), causing mutations and cells divide too quickly

Question 25

Components of a checkpoint for DNA damage

Answer 25

1) sensor-is DNA damaged, ATM?ATR proteins
2) transducer-create a signal, Cdc25, p53, MPF protein
3) effector-change key enzyme action or protein, phosphorylated histones, lamins, ubiquintin, p21

Question 26

Astral microtubules

Answer 26

• radiate from centrosome
• form aster
• help position mitotic apparatus
• determine cleavage plane
• shortening help pull centrosomes apart

Question 27

Microtubule organizing center (MTOC)

Answer 27

• duplication of centrosomes during S-phase
• two centrioles arranged perpendicularly
• where microtubules are nucleated and start growth
• microtubules grow outward from the MTOC (minus end in the MTOC)
• two types: basal bodies associated with cilia and centrosomes
• embedded in nuclear membrane

Question 28

Kinetochore microtubules

Answer 28

• attach to chromosomes at kinetochore

- pull chromosomes to different poles

Question 29

Polar microtubules

Answer 29

• interdigitate with opposing pair
• support framework
• help push centrosomes apart

Question 30

Microtubules

*on exam

Answer 30

• biggest in size
• minus end points toward centrosome and away from kinetochore, low rate of assembly=alpha tubulin subunit
• plus end points away from centrosome, high rate of assembly=beta tubulin subunit
• attachment occurs at kinetochore
• rapid fluctuations in length by polymerization (gain) and depolarization (loss) of tubulin subunits at + end
• hollow, rigid cylindrical tubes
• greatest amount of strength and durability
• made from tubulin dimer with alpha and beta tubulin subunits, which polymerizes to form protofilaments (form cylinder) that are asymmetric and all with same polarity
• asymmetrical and polarized
• initial polymerization is spontaneous but slow and requires the gamma tubulin subunit which will dissociate from the microtubule after polymerization
• when gamma tubulin subunit is attached, there is no gain of subunits at the minus end, only at the PLUS end
• depolymerization can be spontaneous but slow as well
• constantly being polymerized and depolymerized
• rates of assembly and disassembly (growth) depends on tubulin concentration in the environment
• assembly and disassembly allows for cell movement
• instability controlled by the hydrolysis of GTP bound by tubulin
• **as long as the tubbulin has GTP, it can attach, but if GDP is only present, it won’t be able to attach
• **after a bit of time, suddenly all the GTP have been hydrolyzed to GDP, and now the filament can’t grow anymore and will collapse
• some drugs stabilize and some destabilize microtubules
• microtubule orientations can be variable in different parts of the cell
• two subunits are added at the same time, whereas only one subunit is added at a time on microfilaments

Question 31

Kinesins

Answer 31

• motor protein
• walk toward + end of microtubule
• help move vesicles along a microtubule
• smallest of motor proteins (dyneins are bigger)
• pair of globular heads generate the force
• stalk and fan-shaped tail binds the cargo and determines what will bind
• movements are mediated by ATP hydrolysis (1 ATP per step, 1 dimer at a time (ex-stays on alpha subunits and skips beta subunits)
• moves along single microtubule protofilament
• go toward the plasma membrane from the golgi
• cargo is bound by scaffolding proteins which is required in order for movement to occur
• walking steps:
  1) binding of cargo
  2) only one head of kinesin with ADP bound will bind to microtubule
  3) ATP replaces ADP on bound head and causes the neck to pivot
  4) second head binds, replaces ADP with ATP, bends neck
  5) ATP is hydrolyzed to allow trailing head to release microtubule

Question 32

Dyneins

Answer 32

• motor protein
• walk toward minus end toward centrosome
• head is the moving end of protein
• help move vesicles along a microtubule
• ubiquitous eukaryotic motor protein
• bigger motor protein than kinesin
• head generates force
• 2 identical heavy chains
• cargo attached by dynactin
• functions:
  1) chromsome movement in mitosis
  2) positioning of golgi
  3) momevnt of vesicles and organelles through cytoplasm
  4) axonal retrograde movement of organelles
  5) in fibroblasts and endothelial cells, move endosomes, lysosomes, golgi-derived vesicles toward cell center

Question 33

How is the contractile ring or cleavage furrow in an animal cell formed during cytokinesis?

Answer 33

• actin and myosin II slide past one another, tighten the noose, shorten length
• myosin head rotates and causes sliding of actin

Question 34

What is the evidence for myosin II in citokinesis? Treatments?

Answer 34

• gene knockout, interfere with RNA, use of antibodies
• cells replicate chromosomes but unable to divide, results in one large multinucleated cell able to have rapid gene expression and lots of RNA/protein

Question 35

Antibodies

Answer 35

• tool to inhibit protein functions
• binds with high specificity to antigen
• may disrupt normal function of protein due to steric hindrance (like antibody binding to myosin prevents cells to divide)
• block protein translation in prokaryotes, which kills bacteria

Question 36

Nucleus

Answer 36

• storage and decoding of genetic information (DNA condensed and organized)
• largest organelle
• structure: nuclear matrix (network), nucleolus (rRNA synthesis, granular region, site of ribosome assembly), surrounded by nuclear envelope

Question 37

Euchromatin vs heterochromatin

Answer 37

euchromatin-active chromatin, appears lighter, open, dispersed
heterochromatin-inactive chromatin, darker and located near periphery of nucleus, not transcribed or translated

Question 38

Progeria

Answer 38

• defects in lamin A (nuclear lamina)
• premature aging
• nuclear chromosomes aren’t held in place correctly
• disease that can arise due to alternative splicing
• nuclear lamins form network lining inside nuclear envelope, mutation in intermediate filaments=progeria

Question 39

Nuclear pores

Answer 39

• opening is lined with proteins=nuclear pore complex
• nucleoporin
• octagonal symmetry
• cytoplasmic filaments extend to cytoplasm
• regulate transport of RNA and proteins into and out of nucleus
• very fast transport of small molecules, but large proteins must be assisted

Question 40

Nuclear Localization Signal (NLS)

Answer 40

• specific amino acid sequence marks proteins entering the nucleus through nuclear pores
• positive charge
• turnstile ticket

Question 41

Importins and exportins

Answer 41

• recognize the NLS, binds to alpha subunit and bring proteins in
• work in the opposite direction, but recognize other signals

Question 42

Diffusion

Answer 42

• spontaneous movement of molecules from high concentration to low concentration
• small molecules enter and exit by diffusion
• energy is dissipated when molecules flow down the gradient
• energy is stored until released which permits molecules to move down their concentration gradient

Question 43

Gross level of organization in DNA packaging

Answer 43

1) histones
2) fibres
3) looped domains
4) mitotic chromosomes

Question 44

Nucleosome

Answer 44

-group of 4 histones in DNA organization

Question 45

Chromosomes

Answer 45

• carriers of genetic information
• form dyads during S phase (chromosome duplicate)
• sister chromatids=attached duplicated chromsomes
• translocations (movement to new chromosome), inversions (portion of chromosome flipped), deletions (section removed), insertions (section inserted)
• share all chromsomes with chimps except 2

Question 46

Centromeres

Answer 46

• constricted part of chromosome
• DNA contains alpha-satellite
• attach to kinetochores during M phase
• made of non-transcribed repetitive sequences

Question 47

Telomeres

Answer 47

• non-coding regions at ends of chromosomes
• short repeated sequences
• specialized proteins
• capped end structure protects ends of chromosomes from nucleases
• helps distinguish chromosome ends from broken DNA
• prevent chromosomes from fusing together
• attachment to nuclear scaffold
• problem=when chromosomes replicate, telomeres get shorter
• cause of aging process
• cloned Dolly has shorter telomeres than normal sheep (premature aging)

Question 48

DNA polymerase

Answer 48

• enzyme that replicates DNA strands

- builds in 5’ to 3’ direction

Question 49

Telomerase

Answer 49

• elongates telomere
• RNA containing enzyme that adds more nucleotides to 3’ end of telomere
• absent in normal tissue
• present in tumour cells, one celled organisms, germ cells, stem cells

Question 50

What are the factors in cell aging?

Answer 50

• telomeres shortening
• accumulated errors and mutations
• chronic risk exposures like oxidants and UV
• glycation (sugar binding DNA, proteins and lipids)

Question 51

RNA polymerase I, II, III

Answer 51

RNA polymerase I:
-transcribes rRNAs
RNA polymerase II:
-complex of proteins
-transcribes genes
-makes hnRNA in nucleus (before mRNA) the primary transcript, has a half-life 
RNA polymerase III:
-transcribes tRNA
-5S rRNA

Question 52

transcription factors

Answer 52

• DNA binding proteins that regulate transcription

- have DNA binding domain, activation domain, and site to bind a second subunit to form a dimer

Question 53

Components of the promoter for gene expression

Answer 53

1) core promoter-on/off regulation of the gene, binds general transcription factors
2) proximal promoter: regulate frequency of transcription, binds general transcription factors
3) distal promoter: response elements, binds specific transcription factors
4) enhancers: activate gene expression, binds specific transcriptional activators, one enhancer can activate multiple genes

Question 54

Which controls if removed can either increase or suppress gene expression?

a) TATA box or proximal promoter
b) distal promoter

Answer 54

a) still some transcription activity, even though the on/off switch has been taken out
b) removing the suppressor makes transcription activity go over and above, gene expression happens whether you want it or not

Question 55

How do transcription factors affect gene transcription/expression?

Answer 55

by altering histone-binding and making the gene accessible to RNA polymerase

Question 56

Coactivators

Answer 56

• link transcription factors to general transcription factors and chromatin re-modeling enzymes
• enhances RNA polymerase activity
• pre-initiation complex work

Question 57

Structure of mRNA

Answer 57

• 5’UTR cap = start
• 5’ untranslated region near cap
• 3’UTR untranslated to coding region = end
• poly-A-tail

Question 58

Spliceosome

Answer 58

• removes introns from the hnRNA
• complex of snRNA, hnRNA and proteins=snurps (snRNPs)
• formed in nucleus during transcription
• does the mRNA splicing
• matching, cutting, ligation of hnRNA

Question 59

snRNPs (snurps) vs snoRNPs (snorps)

Answer 59

snurps

• when small nuclear RNAs (snRNAs) bind to U proteins
• move introns

snorps

• in nucleus only
• removal of spacers and base modifications
• cut, methylate nucleotides, convert some to pseudouridines

Question 60

Ribozyme

Answer 60

• catalytic RNA
• splicing reaction in protozoa, mitochondria, chloroplasts
• part of the intron
• catalytic function of snRNPs is in this RNA portion (snRNA)
• synthesizes proteins

Question 61

5’ methylguanosine cap of hnRNA

Answer 61

• stabilizes 5’ end to protect from exonucleases
• aids in transport out of nucleus
• starts translation process

Question 62

poly A tail of mRNA

Answer 62

• gradually removed by poly A ribonuclease
• when only a small fragment left, mRNA is degraded by exonuclease at both ends
• determines half-life
• if shortened on mRNA, it can no longer be translated

Question 63

Alternative splicing

Answer 63

• different combinations of exons gives proteins with different activities and function
• provides control of gene expression
• increases the number of proteins made at least 2-fold
• sound pitches, sex-determination genes
• skips over weak splice sites (weak exons)

Question 64

Alzheimer’s disease

Answer 64

• disease that can arise from a defective tau protein
• defective MAPs result in Alzheimer’s disease (abnormally high phosphorylation of MAPs or tau proteins that are implicated in this fatal neurodegenerative disease where hyperphosphorylated tau proteins stick together into neurofibrillary tangles in neurons so microtubules disintegrate)
• fruit flies with mutations in tau proteins exhibit neural, motor and cognitive defects like climbing a wall and courtship training where females reject the dance of the male, releases a pheromone and males don’t learn to stop courting

Question 65

Introns

Answer 65

• gets cut out by spliceosome
• allows for variety of proteins to be derived from one gene
• some have regulatory sequences
• permit exon shuffling

Question 66

transfer RNA (tRNA)

Answer 66

• small
• translate the information encoded in nucleotide of mRNA into amino acid of polypeptide (with help of ribosome)
• adaptor functions: amino acid to tRNA and codon to anticodon
• carriers of amino acids and becomes activated
• bind to mRNA at the codon
• anticodon: three sequential nucleotides in middle of loop that recognizes complementary RNA codon
• anticodon has a wobble position which can bind to non-complementary nucleotides=degenerative code
• transcribed by RNA polymerase III

Question 67

ribosomal RNA (rRNA)

Answer 67

• assembled in nucleolus
• proteins imported from cytoplasm
• structural and catalytic function
• lots of internal base-pairing
• makes ribosomes
• 5S rRNA is NOT made in nucleolus, transcribed by RNA polymerase III, requires no processing, shipped to nucleolus after synthesis, required to make large subunit of ribosome

Question 68

ribosomes

Answer 68

• made of one large (60S) and small (40S) subunit = 80S eukaryotic ribosome
• made up of rRNA and proteins
• structural, ribozyme and catalytic functions
• subunit assembly takes place in nucleolus
• once assembly done, ribosome sent to cytoplasm for translation
• where mRNA strand assembles
• make proteins in cytoplasm
• some free in cytoplasm and some attached to endoplasmic reticulum

Question 69

Transcription, translation locations in the cell?

Answer 69

transcription=nucleus

translation=cytoplasm

Question 70

translation

Answer 70

• synthesis of proteins
• nucleotide code (codons) translated into amino acid sequence
• takes place in cytoplasm
• occurs on circularized mRNA template, many ribosomes attached
• mRNA can no longer be translated if poly A tail is shortened

Question 71

How to turn off genes experimentally?

Answer 71

• create loss-of-function mutant
• use antisense RNA (double stranded RNA) to block translation
• RNA interference
• use antibodies
• gene knockout

Question 72

RNA interference (RNAi)

Answer 72

1) double-stranded RNA (dsRNA) enters cell
2) Dicer cuts dsRNA into short interfering RNA (siRNAs)
3) RNA-induced silencing complex (RISC) binds siRNA and unwinds, one strand kept
4) RISC and single strand looks for mRNA with exact complementary match
5) slicer (protein of RISC) cuts mRNA and is attacked by exonucleases and destroyed
- add double stranded RNA specific for gene and gene is silenced by destroying all mRNAs with exact match to dsRNA
- Dicer and RISC not found in prokaryotes

Question 73

How can short-term gene silencing be achieved? Long-term?

Answer 73

short term:
-make dsRNA in vitro
-liposomes
-inject
-shoot
-feed
long term: 
-genetic transformation

Question 74

Medical applications of RNAi

Answer 74

• anticancer therapy: siRNAs injected to reduce liver tumour size
• antiviral therapy: cells treated with siRNA specific for gene to prevent HIV

Question 75

How to add function of gene expression in a transgenic eukaryote?

Answer 75

• combine gene with gene promoter (glue DNA fragments)
• insert recombinant DNA into gene shuttle like a transposon
• introduce into new host by injection, gene gun, electric shock, lipid capsules, viruses

Question 76

Gain-of-function mutants

Answer 76

• add gene to see change in phenotype
• must be dominant gene
• turning on different transcription factors that turn on tissue specific proteins
• alternative splicing

Question 77

Loss-of-function mutants

Answer 77

• remove or turn off gene to see change in phenotype
• RNA interference technology (add double stranded RNA specific for gene and gene is silenced by destroying all mRNAs with exact match to dsRNA)
• differences in miRNAs (RNA blocked)

Question 78

Transposons

Answer 78

• mobile DNA fragments that move around genome and cause mutations
• our genome loaded with them
• can be used for loss of function mutants (RNA interference)

Question 79

microRNAs (miRNAs)

Answer 79

• naturally occurring dsRNAs
  1) pre-miRNAs processed by Dicer into miRNAs
  2) RISC complex unwinds miRNA and guides target mRNA
• miRNA do not bind to target with 100% complementary
• bind to 3’UTR
• translation blocked and turn off gene expression
• single miRNA can bind to more than one gene
• expressed as tissue-specific manner

Question 80

Vesicles

Answer 80

• budding and fusing carriers that transport molecules between compartments
• transport proteins in endomembrane system
• travel along microtubules
• anchored on microtubules by proteins like dynactin
• propelled by motor proteins like dynein and kinesin
• covered by protein coat
• have receptors like integral membrane proteins that bind ligands with high specificity and high affinity

Question 81

endoplasmic reticulum (ER)

Answer 81

• network of membranous tubules in cytoplasm
• involved in production of phospholipids, proteins
• rough and smooth ER

Question 82

Rough ER

Answer 82

• studded with ribosomes
• continuous with nuclear envelope
• synthesis of proteins to be compartmentalized and destined in lysosomes, integral membrane proteins, proteins in lumen of endomembrane system, endoplasmic reticulum, golgi, plant vacuoles and secretory vesicles
• synthesis of integralproteins
• membrane biosynthesis, some lipid biosynthesis
• glycosylation of proteins

Question 83

Smooth ER

Answer 83

• no ribosomes
• site of synthesis of specialized enzymes
• in specialized cells: skeletal muscle, kidney tubules, endocrine glands, secretory cells
• synthesis of steroids
• synthesis of detoxification enzymes
• enzymes involved in glucose release
• release of Ca2+ ions used in muscle contraction
• lipid biosynthesis

Question 84

Chaperones

Answer 84

• ensures tertiary structure of proteins is properly folded
• proteins that bind to alter folding of new proteins
• associate with proteins in cytoplasm or ER
• facilitate folding by unfolding incorrect structures
• if unable to refold, proteins are exported out of ER and destroyed by proteasome

Question 85

Proteases

Answer 85

-enzyme that cuts protein to make it functional or nonfunctional

Question 86

Glycosylation

Answer 86

• most proteins destined for secretion, extracellular matrix, endomembrane system and plasma membrane=glycoproteins
• in golgi=step-wise glycosylation of proteins
• adding sugars to a protein
• N-linked glycoproteins: occurs in rough ER
• O-linked glycoproteins: only occurs in Golgi
• makes proteins more hydrophilic
• allows to bind to extracellular matrix
• reduces susceptibility to proteases
• provides structural complexity
• provides more specificity in interactions with other proteins
• abundance of glycosylated proteins found on cell’s surface for cell-cell interaction

Question 87

Proteins made within the cytoplasm, not rough ER

Answer 87

• cytosolic proteins
• peripheral proteins of inner cell membrane
• sent to nucleus
• destined for chloroplasts, mitochondria, peroxisomes

Question 88

Signal peptide or signal sequence

Answer 88

• hydrophobic
• required on proteins destined for rough ER
• recognized by signal recognition particle (SRP)
• signal peptide binds to interior of translocon to allow translated protein into rough ER
• removed by signal peptidase enzyme

Question 89

Translocon

Answer 89

• protein channel or translocator
• allows ribosome to bind, then signal peptide to bind to interior, and allow translated protein to enter rough ER
• allows lateral movement of hydrophobic segment of an integral protein into the lipid bilayer

Question 90

Integral membrane proteins (trans-membrane proteins)

Answer 90

• proteins embedded in the membrane that spans the entire membrane
• has hydrophobic section with stop transfer or nonpolar amino acids in alpha-helical conformation
• do not end up in ER lumen
• hydrophobic segment stops in translocon
• orientation is guided by how the transmembrane sequences are oriented within translocon
• roles: communication between cells, organelles and cytoplasm, ion transport, nutrient transport (aqueous channel through lipid bilayer), connections for cytoskeleton
• receptors on vesicles that bind ligands at high specificity and high affinity

Question 91

Proteasome

Answer 91

• destroy proteins that were unable to be properly refolded by chaperones
• protein-degrading machine
• not a membrane bound compartment
• in cytoplasm and nucleoplasm
• in both prokaryotes and eukaryotes
• functions:
  1) housekeeping (clearing out protein from cytoplasm and nucleoplasm at end of their lifespan)
  2) remove improperly folded proteins
  3) remove ubiquin-tagged proteins with MULTIPLE ubiquintin chains on cytosol proteins
• barrel-like structure of globular proteins

Question 92

Unfolded protein response

Answer 92

• too many unfolded proteins are produced at once, which is monitored by ER sensors
• Bip (keeps sensors inactive) releases sensors to help fold proteins and to tells cell to make more chaperones, and to prevent protein synthesis

Question 93

BiP

Answer 93

• keeps sensors of unfolded protein response inactive
• once too many unfolded proteins are found in ER, BiP releases sensors, helps fold proteins and tells cell to make more chaperones, and prevent protein synthesis
• misfolded proteins are bound to BiP which transports them into cytoplasm by reverse translocation through a translocon to be destroyed by proteasomes

Question 94

Heat shock proteins (HSPs)

Answer 94

• chaperones
• recognize unfolded proteins due to heat shock, cold, anoxia
• use ATP hydrolysis to unfold misfolded polypeptides and gives chance to refold properly
• recognize misfolded proteins by looking for hydrophobic regions on surface that are exposed that shouldn’t be
• exposure to a gradual increase in heat gives the cell a chance to make more HSPs and not be killed by extreme heat and cardiac failure

Question 95

Prions

Answer 95

• abnormal forms of proteins
• causes kuru, scrapie, mad cow disease
• anti-chaperones that change shape of proteins into the wrong configuration (normal prion protein in brain = alpha helices, into mutant prion = beta sheets)
• don’t get removed due to their shape that protects them from being processed by the cell’s machinery that removes misfolded proteins

Question 96

N-end rule

Answer 96

• protein half-life

- N-terminal amino acid

Question 97

Ubiquintin and Ubiquintin ligase

Answer 97

• ubiquintin=small, conserved protein
• ubiquintin ligase=recognize proteins destined for destruction and adds ubiquintin units
• single ubiquintin destined for endosomes
• multiple ubiquintin chains destined for proteasomes

Question 98

Endosomes

Answer 98

• single ubiquintin destined for endosomes
• network of cytoplasmic tubules and vesicles that receives material taken up by receptor-mediated endocytosis
• early endosomes located near peripheral of cell
• late endosomes located in interior and receive material from early endosomes and golgi, can develop into lysosomes

Question 99

Membrane lipid bilayer

Answer 99

• asymmetrical composition in the lipid bilayer
• hydrophobic tails (fat soluble) and hydophilic polar heads (water soluble)=amphipathic
• lipid composition made in smooth ER by integral membrane proteins
• made by inserting new lipids into existing membrane
• made primarily of phosphoglycerides
• new lipids added on CYTOSOLIC side, NOT LUMEN
• asymmetry due to flippases, enzymatic modifications of polar head groups, preferential incorporation and phospholipid-transfer proteins=increases membrane durability and withstand physical stresses
• functions: compartmentalization, site for biochemical activities, selectively permeable membrane, transporting solutes, responding to external signals, intracellular interaction, energy transduction
• permeable to: lipids, steroids, O2, CO2
• less permeable to: H20
• impermeable to: water soluble compounds like K+, Na+, Ca2+, Cl-, glucose, RNA
• structure: lipids, proteins, carbohydrates
• fluid mosaic model: lipids in fluid state, rotating and moving laterally, proteins are discontinuous and dynamic

Question 100

Lipid movement

Answer 100

• 1) move laterally on one surface of lipid bilayer
  2) flip from one surface to another by flippases
  3) transfer to new locations by vesicles
  4) single lipids can be carried from one organelle to another

Question 101

Golgi

Answer 101

• stacks of cisternae
• cell’s shipping department
• cis region: sugars and proteins are phosphorylated
• medial region: enzymes remove carbohydrates added in ER and then add new ones
• trans region: where lysosomes are sorted, rich in acid phosphatase
• glycosylation of proteins (adding sugars)
• anterograde movement (forward): rough ER, cis golgi network, cis cisternae, medial cisternae, trans cisternae, trans golgi network, secretory vesicles and lysosomes
• retrograde movement (backward): secretory vesicles and lysosomes, trans golgi network, trans cisternae, medial cisternae, cis cisternae, cis golgi network, rough ER

Question 102

Lysosomes

Answer 102

• are sorted in trans region of golgi
• rich in acid phosphatases (hydrolytic enzyme)
• cell’s digestive organelle
• surrounded by membrane
• hydrolytic enzymes (lysozyme) break down organic substances like cell wall, nucleic acids, proteins…
• proteins destined for lysosomes are tagged with phosphorylated mannose residue, MPRs collect enzymes into budding vesicles
• clathrin protein coat on this vesicle
• internal acidic pH
• membrane contains proton pump (H+ATPase) to maintain acidity
• acidic and glycosylated integral proteins line interior to protect membrane from enzymes
• functions:
  1) heterophagy (degradation of foreign material brought into cell by phagocytosis)
  2) autophagy (digestion of intracellular components that are damaged
  3) autolysis (cellular self-destruction by rupturing itself and killing cell with its contents)
  4) extracellular digestion (discharge enzymes in environment)

Question 103

Dynactin

Answer 103

• helps bind dynein to a vesicle to anchor and move it along a microtubule
• cargo attached by dynactin

Question 104

COP I-coated vesicle, COP II-coated vesicle, clathrin-coated vesicle

Answer 104

COP II-anterograde (forward) movement
COP I-retrograde (backward) movement
Clathrin-trans golgi network to other destinations like lysosomes and endocytosis

Question 105

SNARES

Answer 105

• allows for docking of vesicles on target cell
• proteins that each have different locations or targets
• direct vesicle traffic from a membrane to specific target
• t-SNAREs: target snares located on receiving membrane
• v-SNAREs: located on vesicle, type determined by type of COP

Question 106

Rab proteins

Answer 106

• tether the vesicles to the target membrane to then be fused
• GTP-binding proteins
• extended fibrous proteins
• scaffolding protein that binds cargo to microtubules potofilament

Question 107

Endocytosis

Answer 107

• cellular uptake of particles and macromolecules
• mechanisms: pinocytosis (bulk phase endocytosis that brings up extracellular fluid), receptor mediated endocytosis (specific uptake of ligands)

Question 108

Phagocytosis

Answer 108

• uptake of material and delivery to lysosome
• enclosed in phagosome which is acidic, contains lysozyme to degrade cell wall, oxidases that produce hydrogen peroxide to kill bacteria

Question 109

How does the membrane adjust to changes in temperature?

Answer 109

1) phosphoglycerides: double bond or kink (unsaturated) increases fluidity
2) sphingolipids: decreases fluidity by packing closer together due to one fatty acid chain, more rigid than phosphoglycerides
3) cholesterol: at high temp=decreases fluidity, low temp=increases fluidity
4) longer chains: decreases fluidity

Question 110

Peripheral proteins

Answer 110

• outside lipid bilayer of membrane
• non-covalent bonds
• on either extracellular or cytoplasmic surface
• attached to hydrophilic head groups of phospholipids or hydrophilic portion of integral proteins
• on cytoplasmic surface, function in transmembrane signal transduction

Question 111

Lipid-anchored proteins

Answer 111

• inside or outside of membrane

- covalently linked to lipid

Question 112

Osmosis

Answer 112

• diffusion of water across selectively permeable membrane driven by difference in concentrations
• membrane must be permeable to water but not to dissolved ions and small organic solutes
• water goes from low SOLUTE concentration to high SOLUTE concentration
• causes changes in volume and pressure

Question 113

Cells in hypertonic vs hypotonic

Answer 113

hypertonic environment: high salt concentration outside cell causes water to flow out of cell = cell shrinks
hypotonic environment: low salt concentration outside the cell causes water to flow into cell = cell swells and mus burst
-cells return to normal after some time due to channels regulating the concentrations inside the cell

Question 114

Osmosis and the cell wall of plants

Answer 114

• water flows in due to plants being hypertonic to their environment = turgor pressure
• cell wall is rigid and prevents pressure from exploding the cell
• plasmolysis occurs if in hypertonic environment

Question 115

Osmosis and animal cells

Answer 115

• free living protozoa like amoeba
• use contractile vacuole due to hypotonic environment where water flows into cell
• uses vacuole to expel water by exocytosis
• uses lots of energy to pump ions into vacuole and even more energy to recover the ions

Question 116

Diffusion and electrical gradients

Answer 116

-voltage potential created when membrane selectively permeable for charged ions
-only if channel is present that ions can move down concentration gradient
-high concentrations inside cell: K+ (flows out of cell)
high concentrations outside cell: Ca++, Na+ (flows into cell)

Question 117

Facilitated diffusion

Answer 117

• transmembrane (integral) proteins create pore where ions and small hydrophilic molecules can pass by diffusion
• protein channels opened or closed = gated
• ligand-gated ion channels: ligand binds to receptor but is not transported through channel, it opens and closes gate
• mechanically-gated ion channels: sound waves bend cilia in ear and open up ion channels=nerve impulses
• voltage-gated ion channels: channels open and close in response to impulses across plasma membrane of neuron and muscle cells

Question 118

Active transport

Answer 118

Active transport: transmembrane (integral) proteins or transporters use ATP to force ions or small molecules through membrane against their concentration gradients
Passive transport: do not use ATP, and move down their concentration gradient, carriers and channels, can be gated

Question 119

Aquaporins

Answer 119

• diffusion through pores for movement of water
• transmembrane protein
• passive, so don’t need energy
• water moves down concentration gradient
• more aquaporins at the cell surface means more water uptake for kidney cells

Question 120

Glucose transporter

Answer 120

• carrier mediated passive transport

- insulin regulates translocation of glucose transporter

Question 121

Direct vs indirect active transport

Answer 121

direct active transport: transporter binds ATP directly and uses energy of hydrolysis
indirect active transport: transporter uses energy of gradients created from direct active transport, cotransport

Question 122

Na+/K+ ATPase (sodium-potassium pump)

Answer 122

• pump out 3 Na+ and pump in 2K+ against concentration gradients
• creates resting potential of the cell to prepare for nerve and muscle impulses and contractions
• more sodium outside cell allows for osmotic balance
• provides energy to indirect pumps
• one third of all energy generated by animal cells used to run this pump

Question 123

Ca2+ATPase

Answer 123

• in resting striated muscles, high concentration of Ca2+ in sarcoplasmic reticulum (ER)
• contraction= Ca2+ pumped back into smooth ER or sarcoplasmic reticulum
• located in plasma membrane of all eukaryotic cells

Question 124

ATPase pumps *direct active transport

Answer 124

1) P-type trasnporter: gets phosphorylated, (Ca2+ pump of smooth ER)
2) V-type transporter: pump on vacuoles of plants for H+, and for animals on lysosomes, vesicles in kidney
3) ABC type: ion transporters, transmembrane proteins, have ATP-binding domain, helps move noxious chemicals across membranes to detoxify cells
* cancer cells deal with chemotherapy and escape death by mutations in this transporter

Question 125

Symport vs antiport pumps

Answer 125

symport: driving ion and pumped molecule go in same direction (Na+/glucose cotransporter used to absorb water into intestinal or gut cells during diarrhea or cholera=water loss)
antiport: driving ion diffuses through pump and other ion goes in opposite direction (Na+/Ca2+ exchanger in skeletal muscles)

Question 126

Chloride transporter

Answer 126

• causes cystic fibrosis disease when lungs become thick with mucous and cause impaired breathing
• mucous needs to be wet, not gel like for cilia to beat in lungs
• Cl- flow in the disease is not enough so mucous becomes gel-like

Question 127

Types of signaling:

1) autocrine
2) paracrine
3) endocrine
4) synaptic
5) cell contact

Answer 127

1) signal bind to receptors on cells that secreted them
2) bind to receptors of nearby cells
3) hormones are secreted into the blood (steroid hormones)
4) signal passed through synapse between transmitting cell and receiving cell
5) cells have adjacent plasma membranes

Question 128

Lipophilic vs lipophobic signals

Answer 128

lipophilic: signal can cross the plasma membrane
lipophobic: signal can’t cross the plasma membrane, water soluble

Question 129

Transduction

Answer 129

• propagation of signal through the cell across the membrane or transferred to other molecules
• occurs by direct phosphorylation or by G proteins

Question 130

Amplification

Answer 130

• process where signal is multiplied and increased
• intracellular signal is amplified by second messengers
• permits initial signaling molecule like a hormone to be in limited concentrations but still effective
• one hormone activates numerous enzymes
• *coordination of several different pathways simultaneously
• one receptor turns on several G-proteins which can then activate several effectors

Question 131

Steroid hormones

Answer 131

• endocrine signals
• small and fat soluble
• lipophilic
• made from cholesterol
• travel through bloodstream bound to carrier proteins
• cortisol
• easily enter cell by high affinity receptors present in cytoplasm or nucleus
• increases gene expression
• slow and long term response

Question 132

GPCR (G-Protein Coupled Receptors) and G proteins

Answer 132

• GTP-binding protein
• in nematodes, mutations of G-protein can cause abnormal changes in movement
• integral proteins
• alpha helix structure
• turn on effector molecule to make second messenger
• when ligand binds, there is a conformational change in GPCR shape and allows G protein to interact
• to stop signaling, it hydrolyzes GTP to inactivate itself
• activate adenylyl cyclase when bound by glucagon and epinephrine
• our sense of smell is based on GPCRs on olfactory sensory neurons (affinity for more than one odorant)
• dogs can sniff out cancers which produce unusual metabolites due to lots of GPCRs and odorant receptors
• insects use GPCRs to detect pheromones (males seeking females or ants following chemical trail to food sources)
• receptor of epinephrine and glucagon

Question 133

Cholera or diarrhea

Answer 133

• Na+/glucose cotransporter used to absorb water into intestinal or gut cells during diarrhea or cholera=water loss
• cAMP induces chloride channel remains open and water loss occurs due to cholera toxin binding to G-protein and can no longer hydrolyze GTP, so adenylyl cyclase remains active all the time

Question 134

Epinephrine

Answer 134

• from adrenal gland
• increases blood glucose during stress = adrenaline hormone
• when bound to GPCR, activates adenylyl cycase, which then forms cAMP, binds to PKA, cascade of phosphorylation, glycogen production stops and gluconeogenesis increases by activation of PEPCK gene
• induce lipid second messengers (DAG and IP3) through G-proteins

Question 135

Glucose

Answer 135

• primary energy source

- stored as insoluble polymer, glycogen

Question 136

Glucagon

Answer 136

• released from pancreas
• increases blood glucose
• when bound to GPCR, activates adenylyl cycase which then forms cAMP, binds to PKA, cascade of phosphorylation, glycogen production stops and gluconeogenesis increases by activation of PEPCK gene

Question 137

Glycogen

Answer 137

• storage of glucose as an insoluble polymer
• glycogen to glucose accomplished by hormones
• broken down into glucose-1-phosphate
• produced when glucose levels in the blood is too high

Question 138

PEPCK gene

Answer 138

-increases gluconeogenesis (increase glucose production) when blood glucose levels are low

Question 139

Which is a faster way to yield glucose? Cytoplasmic conversion of glycogen or gluconeogenesis?

Answer 139

cytoplasmic conversion of glycogen

gluconeogenesis takes longer due to having to go through transcription and translation

Question 140

Lipid Second Messengers

Answer 140

-phospholipase C which produces two signal molecules: DAG (stays embedded in membrane, activates PKC and opens Ca2+ channels in smooth ER) and IP3 (highly soluble, enters cytoplasm, Ca2+ released) that activate gluconeogenesis

Question 141

Vasopressin

Answer 141

• antiduretic hormone
• increase ion and water uptake from nephrons of kidney cells and retuns it to bloods, reduces urine volume
• the more aquaporins at the surface of the cell = more water uptake
• binds to GPCR, activates adenylyl cyclase, cAMP, PKA and vesicles with aquaporins move to plasma membrane

Question 142

Adnelyl cyclase

Answer 142

• effector in the cell used to increase glucose production
• activated by GPCRs
• activates cAMP and PKA to begin phosphorylation cascade

Question 143

Receptor Tyrosine Kinases (RTKs)

Answer 143

• receptor is an enzyme/protein
• phosphorylates target proteins at tyrosines
• single transmembrane segment (monomer)
• regulate growth, cell division, survival and death, cell attachments and migrations
• function as dimers when one ligand binds to both monomers or one on each
• can autophosphorylate each other once dimerized and become activated
• insulin receptor
• epidermal growth factor receptor to stimulate cellular growth, proliferation and cellular differentiation (causes changes in gene expression, activate transcription factors, overexpression or overactivity from mutation in EGFR can cause cancers)

Question 144

Insulin

Answer 144

• produced when blood glucose increases after eating
• causes glucose uptake by liver, mucle, fat cells
• acts to decrease blood sugar by producing glycogen or fat
• gluconeogenesis is inhibited

Question 145

Diabetes

Answer 145

• defect in insulin signaling
• high levels of glucose in bloods, loss of glucose in urine, excessive water loss from frequent urination, high blood pressure
• Type 1: no insulin produced by pancreas, autoimmune disorder, heritable
• Type 2: insulin resistance in cells that should take in glucose (loss of sensitivity) due to faulty insulin receptor or intracellular signaling
• to increase sensitivity to insulin: remove off switch or negative regulator for insuling receptor, or protein tyrosine phosphatase (PTP=gene knockout in mice to produce insulin-sensitive mice)removes P from insulin receptor

Question 146

Calcium

Answer 146

• both first and second messenger
• released form internal vesicles in response to calcium channels on cell surface=calcium induced release
• rapid amplification and rapid coordination
• voltage dependent channels: nerves and muscles with receptor-mediated calcium channels
• fertilization: calcium channels open (calcium influx) in oocyte after a sperm has entered to prevent another sperm from entering=activation of cyclins to start cell division

Question 147

Nitric oxide

Answer 147

• inorganic gas
• extracellular messenger and secondary messenger
• autocrine and paracrine hormone
• induces production of cGMP and causes muscles to relax for better blood flow

Question 148

Convergence vs crosstalk

Answer 148

convergence: two receptors cause the same secondary signal to be activated
crosstalk: where pathways interconnect to receive different combinations of signals, but cell decides which one is priority to respond to (inhibit cell division to first make glucose when under stress) *override priorities

Question 149

Anabolism vs Catabolism

*on exam

Answer 149

Anabolism: synthesis of complex compounds from simpler ones
Catabolism: break down of complex compounds into simpler ones

Question 150

2 energy sources

Answer 150

1) electromagnetic: light energy

2) chemical: stored energy in molecules with electron orbitals and bonds

Question 151

Glycolysis

*on exam

Answer 151

• all organisms use it
• occurs in cytoplasm
• breaks down glucose
• end products: 2 pyruvate, 2 ATP, 2 NADH
• no oxygen required

Question 152

Citric acid cycle (TCA) / Krebs Cycle

*on exam

Answer 152

• occurs in mitochondria for eukaryotes and cytoplasm for prokaryotes
• oxidative phosphorylation
• breakdown of pyruvate into acetyl CoA and NADH
• end products: 3NADH, FADH2, 2CO2, GTP
• net gain of ATP from TCA amd ETC is 36 ATP

Question 153

Electron transport chain (ETC)

*on exam

Answer 153

• uses NADH and FADH2
• end products: ATP (NADH=3ATP and FADH2=2ATP), H20 (when 02 accepts electrons
• net gain of ATP from TCA and ETC is 36 ATP

Question 154

Mitochondria

*on exam

Answer 154

• function: produce lots of ATP
• 1500 per liver cell or 15-20% of cell volume
• vary in shape and size, as well as number of cristae
• 300,000 mitochondria in oocytes due to lots of cell division without getting any larger
• in sperm: concentrated around base of flagellum (lots of energy needed to swim)
• in renal tubular cells: between baso-lateral membrane invaginations and around periphery with ATPase pumps to create concentration gradients
• structure: outer membrane (nonselective porins), intermembrane space (heavily folded/convoluted), inner membrane (electron transport chain, ATP synthase, greater surface area), matrix (TCA cycle, circular DNA strands coding for 13 polypeptides, ribosomes)
• divide by fission
• highly metabolic organelle that does lots of oxidation and free radical by-products
• has porins which controls what comes in

Question 155

Porins

Answer 155

• integral proteins
• form large, nonselective membrane channels
• in outer membrane of the mitochondrion

Question 156

Mitochondrion similarities to bacteria

*on exam

Answer 156

• double membrane with cardiolipin (membrane composition)
• divide by binary fission from preexisting mitochondria/bacteria
• circular DNA encoding rRNA and tRNA
• endosymbiosis theory: mitochondria in eukaryotes evolved from aerobic bacteria living within their cells, engulfed but not digested

Question 157

How does the cell use the energy stored in NADH and FADH2?

Answer 157

1) electrons transferred to NAD+ to make NADH and FADH2
2) NADH and FADH2 create a proton gradient
3) energy from gradient used by reversible proton pump, ATP synthase, to make ATP
4) oxidation (loss of electron) and reduction (gain of electron)
5) energy from electron transport chain used to pump H+ out and from H+ gradient
6) (separate reaction) H+moves down concentration gradient through ATP synthase

Question 158

How do mitochondrion generate and store the energy used to produce most of the ATP made during aerobic respiration?
*on exam

Answer 158

by generating an ionic (electrochemical) gradient

Question 159

Carriers of the electron transport chain

*on exam

Answer 159

• protons: translocated across membrane from matrix and accumulate in intermembrane space
• electrons: transported along the membrane by protein carriers
• oxygen: terminal electron acceptor of electrons and H+ to produce water
• NADH delivers H+ and electrons to electron transport chain =proton gradient increases and H+ builds up outside inner mitochondrial membrane

Question 160

Hydrogen ion gradient

Answer 160

• used to make ATP
• protons can escape through porins
• electrochemical gradient
• 20% of stored energy due to concentration difference of H+ (low in matrix and high in intermembrane space, enough to cause a 1 pH change so from 7 to 6)
• membrane impermeable to hydrogen ions
• 80% of stored energy is electrogenic (voltage generated gradient) not permeable to counter-ions that protects cytoplasm from pH difference of one pH unit

Question 161

ATP formation

Answer 161

1) energy stored in proton gradient drives phosphorylation of ADP
2) catalyzed by ATP synthase
3) ATP synthase has a F1 headpiece projecting into matrix and F0 basepiece embedded in lipid bilayer (contains H+ channel)
4) controlled movement of H+ through channel induces a conformational shape change and chemical change, driving ATP formation

Question 162

How can nanotechnology use ATP synthase?

Answer 162

• ATPase molecule engineered to be a motorized propeller
• create flow of liquid across a plate
• used to deliver drugs or manufacture miniaturized components of larger instruments

Question 163

Targeting of proteins to the mitochondria

*on exam

Answer 163

1) pre-sequence signal (positively charged alpha helix) recognized by receptor on mitochondria
2) cytosolic chaperone protein unfold protein to enter single file into pore
3) chaperone refolds protein once inside and pre-sequence cut off

Question 164

Thermogenin

Answer 164

-when protons re-enter mitochondrial matrix without contributing to ATP synthesis (proton leak or mitochondrial uncoupling) by this proton channel and results as heat

Question 165

Brown adipose (brown fat)

Answer 165

• where thermogenin is found in tissue

- brown in colour due to high levels of mitochondria

Question 166

Non-shivering thermogenesis

Answer 166

-primary means of heat generation in newborn and hibernating animals

Question 167

How are mitochondria implicated in cellular aging?

Answer 167

• accumulated mtDNA mutation due to being an oxidative organelle, which can cause damage and result in mutations
• old people have more mtDNA mutations than young people
• mutator strain in mice of mtDNA mutations age prematurely and die at half the normal age

Question 168

Why do mitochondria have multiple chromosomes?

Answer 168

1) divide by fission to have multiple chromosomes for daughter
2) highly metabolic organelle that needs lots of protein turn-over
3) extra copies of genes allows for removal of damaged DNA by superoxide molecules (free radicals)

Question 169

Peroxisomes

*on exam

Answer 169

• membrane bound vesicles
• don’t have their own genome
• good at metabolizing molecules like fatty acids
• have oxidative enzymes (urate oxidase and amino acid oxidases) that produce hydrogen peroxide as a toxic by-product that destroys membranes and proteins
• converts hydrogen peroxide to something less toxic
• similarities to mitochondria: oxidative metabolism, import proteins into organelle, form by dividing from pre-existing organelles
• have high concentrations of catalase to remove highly reactive peroxide and free radicals (charged molecules of oxygen) for a prolonged cell function
• ex) fruitflies with extra copies of catalase gene live longer
• ex) nematodes induced to increase catalase activity livelonger
• move along microtubules
• capable of hydrolyzing
• mops up the free radicles of mitochondria

Question 170

Catalase

*on exam

Answer 170

• remove highly reactive peroxide and free radicals for prolonged cell function
• ex) fruitflies with extra copies of catalase gene live longer
• ex) nematodes induced to increase catalase activity live longer

Question 171

Heterotroph vs Autotroph vs Chemoautotroph vs Photoautotroph

*on exam

Answer 171

• heterotroph: gets organic compounds from another organism, earliest forms of life used carbon sources abiotically
• autotroph: use CO2 to make organic molecules
• chemoautotroph: use energy stored in inorganic molecules to convert CO2 into organic compounds, bacteria that live in high temperatures use this
• photoautotroph: use radiant energy to convert CO2 into organic compounds, used by plants, eukaryotic algae, protists, prokaryotes like blue-green bacteria

Question 172

Two fundamental mechanisms in photosynthesis

*on exam

Answer 172

1) light reactions: photochemical reactions
* products: ATP (primary source of chemical energy) and NADPH (primary source of reducing power)
- occurs in thylakoid membranes of chloroplasts
2) dark reactions: thermochemical reactions
- opposite of mitochondrion that breaks down carbohydrates, whereas the chloroplast build up carbohydrates
- ATP and NADPH used to synthesize carbohydrates
- occurs in stroma of chloroplasts
* NADH (in mitochondria) used for catabolism and NADPH (in chloroplasts) used for anabolism

Question 173

Chloroplast

Answer 173

• organelle where photosynthesis takes place
• opposite of mitochondrion that breaks down carbohydrates, whereas the chloroplast build up carbohydrates / NADH (in mitochondria) used for catabolism and NADPH (in chloroplasts) used for anabolism
• 3 types of membranes
  1) smooth outer membrane: freely permeable to molecules
  2) smooth inner membrane: contains transporters (integral membrane proteins that regulate the passage in and out of chloroplast of sugar and proteins synthesized in cytoplasm but used in chloroplast)
  3) thylakoid membranes
• divide separate from the cell cycle by fission where two contractile rings pinch themselves (one inside and one outside) which occurs at the same time as DNA replication
• ATP synthase embedded in thylakoid membrane
• endosymbiotic theory: chloroplast startedas a photosynthetic bacterium that got assimilated by a larger cell
• resemblance to bacteria: circular genome, double membranes, photosynthetic enzymes

Question 174

Mitochondria vs Chloroplasts

*ON EXAM

Answer 174

Mitochondria: has porins that controls what comes in, break down of carbohydrates (catabolism), uses NADH, different electron acceptors
Chloroplasts: freely permeable to molecules, build up carbohydrates (anabolism), uses NADPH, different electron acceptors

Similarities:

• both have ATP synthase to produce ATP
• both divide separate from the cell cycle, by fission where they pinch themselves with contractile rings which occurs at the same time as DNA replication
• binary fission (like bacteria as well)
• both produce reactive oxygen due to being a highly metabolic organelle
• both can produce heat
• proton gradient drives ATP formation
• endosymbiotic theory: grew in symbiosis with a bacteria providing it with its capabilities and receiving safety within as well as nutrients
• circular genome
• double membrane
• generation of chemical energy (electron transport coupled to proton gradient)

Question 175

Thylakoids

Answer 175

• enclose lumen (system of vesicles interconnected)
• grana stacked in arrays
• in light reactions, these three proteins are embedded here
  1) photosystem I: chlorophyll and carotenoid molecules, integral proteins
  2) photosystem II: chlorophyll and carotenoid molecules, electron transport chain
  3) ATP synthase: make ATP like in mitochondria

Question 176

Chloroplast stroma (matrix)

Answer 176

• fluid with enzymes needed to carry out dark reactions: CO2 into organic molecules like glucose and ATP into NADPH energy to build sugars
• has DNA carrying complete chloroplast genome which is transcribed in the nucleus, translated in the cytoplasm and transported in the chloroplast

Question 177

Rubsico

*ON EXAM

Answer 177

• chloroplast-specific protein
• world’s most abundant protein
• does carbon dioxide fixation during Calvin Cycle or Dark Reactions

Question 178

Absorption of light

Answer 178

• energy from sun travels in photons (energy packets)
  1) photon absorbed
  2) compound converted to higher energy state=excited state
  3) returns to ground state in three different ways: energy dissipated as heat, re-emitted as longer wave length or transferred to another molecule (photosynthetic pigment)

Question 179

Photosynthetic pigments

*ON EXAM

Answer 179

• pigments: molecules that contain a chromophore
• chromophore: packet of chlorophyll capable of absorbing light at a particular wavelength
• red and blue absorbed, green is emitted (this is why plants are green)
• overlap of absorbance and action spectra is where photosynthesis is working at optimal efficiency

Question 180

Carotenoids

*ON EXAM

Answer 180

• involved in photosystem I and II in the light reactions
• orange in colour
• secondary light collectors (absorbs colours that chlorophyll cannot, so increases efficiency of absorbing light
• absorb blue and green, reflect yellow, orange and red
• protects photosynthetic machinery from reactive oxygen species damage and dissipate excess energy as heat
• animals can’t make carotenoids but obtain it from their diet
• uses: ornamental colouring of flamingos, salmon lobsters; is an antioxidant (reduces risk of developing cancer with eating carotenoid rich diets); lycopenes in tomatoes decrease lipid peroxidation and heart attacks and increase fertility in males

Question 181

Photosystem II (PSII)
*on exam

Answer 181

1) P680 (reaction center chlorophyll) absorbs photons/light most strongly at 680nm
2) P680 gives up electrons to primary electron acceptor of higher reducing potential (stronger affinity)
3) P680 replenishes its electrons from H20 by splitting it (removes electrons from H20 which generates a proton gradient)
4) H20 is oxidized and O2 released as a by-product
5) excited electron is passed to primary electron acceptor (02)
6) photosynthesis in thylakoid takes electrons from H20 and passes to P680 to replace electrons passed to primary electron acceptor

Question 182

Photosystem I (PSI)

Answer 182

7) passed to photosystem I by electron transport chain
8) ATP produced to be used in Calvin Cycle
9) P700 chlorophyll uses light to excite the electron to primary acceptor
10) electron sent down another chain to create NADPH or for the Calvin Cycle
11) back to P700 to form ATP

Question 183

Cyclic and non-cyclic photophosphorylation

Answer 183

• noncyclic pathway: electrons taken from chlorophyll not recycled back down to ground state but end up on NADPH
• electrons move in linear path from H20 to NADP+, uses PSI and PSII, formation of ATP, NADPH and O2
• cyclic pathway: only photosystem I used, electrons are excited, passed down the chain, create ATP and then go back to P700 to be used again (oxygen and NADPH are not produced)
• electrons move from P700 to ferredoxin and back to P700, involves PSI only, formation of ATP

Question 184

Z scheme or pathway

Answer 184

• two photosystems I and II act in series
• electron flow:
  1) between H20 and PSII
  2) between PSII and PSI, electron transport chain
  3) between PSI and NADP+
• electrons flow in Z, H+ ions move from stroma to inner compartment of thylakoids
• proton gradient is the end result (high in lumen of thylakoid and low in stroma)

Question 185

Photophosphorylation

Answer 185

• formation of ATP due to electrons moving through PSI and PSII
• proton gradient drives ATP formation
• ATP synthase embedded in thylakoid membrane

Question 186

What are people trying to achieve using artificial photosynthesis?

Answer 186

• replace fossil fuels as energy sources
• convert sunlight, water and CO2 into hydrogen, water and carbohydrates
• hydrogen as a new energy source=clean fuel
• genetically alter cyanobacteria to release H+
• engineered enzymes as solar cells
• use artificial dark reaction in hopes to mop up excess CO2 in atmosphere

Question 187

Light reaction vs dark reaction (calvin cycle)

Answer 187

light reaction:

• occurs in grana of chloroplasts
• depends on light to use PSI and PSII
• photolysis of water and oxygen is liberated
• ATP and NADPH is produced and used to drive dark reaction

dark reaction:

• occurs in stroma of the chloroplast
• does not require light or photosystems
• carbon dioxide absorbed
• glucose produced
• NADP is oxidized

Question 188

Activities contributing to establishment of H+ (proton) gradient across thylakoid membrane
*on exam

Answer 188

• splitting of water in thylakoid lumen
• translocation of protons from stroma to thylakoid lumen by cytochromes
• reduction of NADP+ in stroma

Question 189

Cytoskeleton

Answer 189

• functions
  1) structure and support (scaffolding to give cells their shape, shape associated to function, cytoskeleton can resist mechanical stresses with strength of focal adhesions, cytoskeleton can rearrange itself to change the shape of the cells)
  2) intracellular transport (not static, movement of objects from interior to exterior but not all the way to perimeter, microtubules are the tracks where vesicles and mRNA macromolecules run on, movement of membranous carriers from ER to golgi, movement of neurotransmitter-containing vesicles from synthesis site to axon terminal, transport of peroxisomes on microtubules)
  3) contractility and motility (cilia, flagella and pseudopodia are force generating elements that help single -celled organisms to move, multicellular organisms have independent locomotion like sperm, white blood cells, fibroblasts, growing axon tip)
  4) spatial organization (framework to position organelles and molecules, anchored in place of organelles by interactions of proteins adhering to cytoskeleton like polarized epithelial cells or neurons, arranged in pattern along axis from apical to basal end of the cell)
  5) separating chromosomes and cytokinesis during cell division
• cytoskeleton fibers: microtubules, intermediate filaments, microfilaments
• cytoskeleton defects caused by drugs or mutations which result in the misplacement of organelles and causes reduced organization

Question 190

Intermediate filaments

Answer 190

• tough, ropelike fibers
• made of a variety of related proteins
• medium in size

Question 191

Microfilaments

Answer 191

• solid
• made of actin
• smallest in size

Question 192

Centrosomes

Answer 192

• plants lack centrosomes
• duplication of centrosomes during S-phase in the microtubule organizing centers (MTOC)
• in animals, 2 centrioles that are perpendicular to one another surrounded by a cloud of molecules (pericentriolar material)
• cylindrical structures
• composed of 9 fibrils fused with 3 microtubules
• centrioles involved in recruiting molecules like gamma tubulin subunits for microtubule nucleation
• microtubule plus end grows away from the centrosomes

Question 193

What helps stabilize microtubules?

*on exam

Answer 193

1) MAPs
2) drugs
3) GTP bound to tubulin

Question 194

Microtubule associated proteins (MAPs)

Answer 194

• attached to microtubules
• help support and stabilize microtubules even in the absence of GTP and it will not fall apart
• alter assembly and disassembly rates=regulators
• crosslink adjacent microtubules to ensure they are parallel to one another
• activity controlled by addition and removal of phosphate on amino acid residues by protein kinases and phosphatases
• defective MAPs result in Alzheimer’s disease (abnormally high phosphorylation of MAPs or tau proteins that are implicated in this fatal neurodegenerative disease where hyperphosphorylated tau proteins stick together into neurofibrillary tangles in neurons so microtubules disintegrate)
• fruit flies with mutations in tau proteins exhibit neural, motor and cognitive defects like climbing a wall and courtship training where females reject the dance of the male, releases a pheromone and males don’t learn to stop courting

Question 195

Motor proteins or molecular motors

Answer 195

• move cargo by attaching to microtubules
• control movement by where microtubules are placed or by regulating motors
• movements are a power stroke and a recovery stroke
• kinesins, dyneins, myosins

Question 196

Myosin

Answer 196

• motor protein
• incoming electrical signals of a neuron is at the dendrites
• outgoing electrical signals of a neuron is at the axon
• motility arises from conformational changes in motor domain as ATP is bound and hydrolized, and products are released
• transport in nerve cell axons (neurotransmitter vesicles all must be brought by motor proteins to the axon endings):
  1) vesicles are handed over to the actin network due to microtubules unable to reach the periphery of the cell
  2) axon endings have an extensive actin cytoskeleton
  3) myosin V takes over to transport vesicles along actin filaments to plasma membrane at the synapse
• large family
• move along actin microfilaments while hydrolyzing ATP
• myosin II found in skeletal muscle = conventional myosin, two heavy chans with globular motor domain, a binding site for ATP and domain that interacts with actin
• myosin V has two heavy chains like myosin II but has a longer neck region
• can take longer strides and carry larger cargo
• attached to the trailing ends of actin and pulls the rest of the cell along when using lamellipodia

Question 197

Tug-of-war between kinesins and dyneins

Answer 197

• cell must decide if kinesin or dynein gets priority of ATP (nature of stimulus determines which one will get more ATP to move cargo)
• rapid dispersal of pigment when octopus is under stress (neural transmission caused chromatophores (kinesins) and melanosomes to disperse)

Question 198

Melanosomes

Answer 198

• where pigments (chromatophores) are stored in organelles

- darken entire cell or aggregated to lighten cell

Question 199

Cilia vs Flagella

Answer 199

Cilia:
-shorter and numerous
-like oars or swimming strokes=cell movement is perpendicular to direction of cilia
-in multicellular organisms, used to move fluids
-ciliary escalator= in upper respiratory tract move thin sheets of mucous upward to remove dust and bacteria trapped
Flagella:
-in sperm, mitochondria are concentrated around base of flagellum (lots of energy needed to swim)
-longer and rarely more than two
-tend to be aligned in the direction of movement

Similarities:

• made of microtubules surrounded by plasma membrane
• core is 9+2 arrangement=axoneme (9 peripheral doublet microtubules and 2 central single micotubules, 1 complete and 1 incomplete)
• at base is the basal body or MTOC
• ciliary dynein arms and radial spokes attached to A tubules
• A tubule linked to B tubule by nexin bridge
• microtubule doublets slide past each other
• heads attached to the right and tails attached to the left side
• dynein arms walk along wall of adjacent doublet
• nexin bridges ensures they don’t detach, which allows for stretching or bending so the microtubules don’t just slide past one another
• HYPOTHESIS: dynein arms are regulated by central microtubule and radial spokes, central pair rotates while beating, rotation promotes sequential contacts with each radial spoke, spoke signal to dynein arm on adjacent microtubule

Question 200

Primary cilium

Answer 200

• lacks central pair of microtubules
• no locomotory function
• only one per cell
• antenna that picks up chemical signals and carry other signalling molecules up and down microtubules
• mechanoreceptors (if bent, it sends a signal to the cell to undergo different events)
• in kidney (kidney epithelium), pulse of fluid flow pressure triggers primary cilia to bend and opens calcium channels (calcium current goes to sarcoplasmic reticulum and causes contraction to slow things down)

Question 201

How can motor proteins be harnessed for nanotechnology applications?

Answer 201

• motor proteins fixed to microchips
• heads can still move to shuttle microtubules across chip’s surface
• coated surface with kinesin
• used to sort materials, assembly of different components, concentrating components for enhanced detection (blood sorting)

Question 202

Intermediate filaments

Answer 202

• stretchy and compressible
• strongest tensile strength (stretched 3X normal strength)
• made of fibrous proteins that intertwine to make dense, rope-like fibers
• in cells that endure huge physical stresses like muscles, neurons and epithelial cells
• holds different components of cytoskeleton together by cross-linking proteins like plectin
• more types of intermediate filaments than microfilaments and microtubules
• alpha helix with globular domains at terminals
• structure:
  1) two monomers wrap around each other to form a dimer parallel to each other
  2) dimers bind to form tetramers aligned in opposite orientations and staggered (tetramers are not polar)
  3) tetramers aggregate to form intermediate filaments which continuously assemble and disassemble (subunits can insert in the middle or ends)
• functions:
  1) mechanical support
  2) hair, fingernails, skin made of keratin intermediate filaments
  3) nuclear lamins form network lining inside nuclear envelope, mutation=progeria
  4) neurons filled with neurofilaments
  5) useful in cancer diagnosis to find where tumour originated (keratin have subtypes unique to different epithelial cells, antibodies bind a keratin subtype in colon cancer cells)
  6) hold cells together (keratin intermediate filaments) by forming junctions (desmosomes), attach cells to matrix (hemidesmosomes), or form loops into plaques spreading out into the cytoplasm

Question 203

Microfilaments

Answer 203

• smallest of the fibers
• no diversity
• composed of actin
• monomers of protein actin polymerize to form long, thin fibers
• polar due to actin monomer
• nucleotide charged (ATP) needed to add subunit
• adds a single subunit unlike microtubule where two subunits are added at the same time
• functions:
  1) form band under plasma membrane providing mechanical strength for the cell
  2) links transmembrane proteins to cytoplasmic proteins
  3) anchors centrosomes at opposite poles during mitosis
  4) pinches dividing animal cells (cytokinesis) with the help of actin and myosin
  5) generate cytoplasmic streaming
  6) generate locomotion in white blood cells and amoeba (actin network granules move quickly which is the goop in the amoeba)
  7) interact with myosin filaments in skeletal muscle fibers to provide force of muscular contraction
  8) form growing extensions of cells undergoing ingestion (phagocytosis)
  9) form extracellular extensions during cell movement

Question 204

Microfilaments vs microtubules

Answer 204

microfilaments: only one subunit is added at a time, ATP needed to add subunit, anchors centrosomes to opposite poles during mitosis
microtubules: two subunits are added at the same time, GTP used to add subunits, pull out centrosomes to poles

Question 205

Myosin V

Answer 205

• myosin V takes over to transport vesicles along actin microfilaments to plasma membrane at the synapse
• myosin V has two heavy chains like myosin II but has a longer neck region
• carries cargo over twisting track of actin
• has large walking strides due to neck region much longer than mysoin II
• walks along one side of the filament

Question 206

Myosin II

Answer 206

• myosin II found in skeletal muscle = conventional myosin, two heavy chans with globular motor domain, a binding site for ATP and domain that interacts with actin
• heads interact with actin microfilaments in a reaction cycle:
  1) ATP binding causes conformational change that causes myosin to release actin
  2) ATP is hydrolyzed and a conformational change (flexing of the neck) results in myosin weakly binding actin at different place on the filament
  3) Pi release results in conformational change that leads to stronger binding and a power stroke
  4) ADP dissociation leaves the myosin tightly bound to actin (absence of ATP is in state of rigor = muscle rigidity)

Question 207

Lamellipodia

Answer 207

• cells capable of movement without cilia or flagella use and extend these
• rich in actin
• growing actin filaments cause lamellipodium growth
• myosin attached at trailing ends of actin pull the rest of the cell along
• formed by actin meshwork through initiation of actin polimerization and addition of actin monomers at cell membrane with the help of proteins (in response to signaling stimuli and serve to cros link actin network)
• enzymes can cause depolarization of actin filaments towards the base of the lamellipodium by destablizing and severing factors, and those being lost can be recycled for another filament

Question 208

Dictyostelium discoideum (soil living amoeba) and how does it use cAMP detection to induce cell movement?

Answer 208

• solitary life when food abundant
• aggregated into a multicellular assembly called pseudoplasmodium/slime moulds when food is limited
• forms fruiting body to produce spores to be carried in the wind and find more food
• amoebae look for each other with chemoreceptors (cAMP receptor) and move toward concentrated sources of cAMP
• cell movement:
  1) cAMP reception at cell membrane activates G-protein
  2) G protein stimulates adenylyl cyclase
  3) cAMP diffuses out of cell into medium
  4) internal cAMP inactivates external cAMP receptor so it doesn’t follow its own trail=oscillatory behaviour (cell fluctuates between being able to detect or not detect cAMP)
  5) different G-protein stimulates phospholipase C
  6) IP3 induces calcium ion release
  7) calcium ions act on cytoskeleton to induce extension of pseudopodia
• forward movement=activation of signals is high at the front and low at the back in the beginning, then becomes high inhibiting signals at the back and low inhibiting signals at the front (cAMP concentrations are high at the front of the amoeba)
• forward movement requires assembly of growing cytoskeleton at the front and disassembly at the back

Question 209

Extracellular matrix (ECM)

Answer 209

• make contact with each other
• in tissues, between tightly packed cells used to hold cells together, cushion or protect cells
• fills out space between cells
• reservoir for growth factors and hormone
• creates environment for molecules and cells to migrate
• every organism uses it
• cell wall in plants, fungi and bacteria=cellulose
• chitin in arthropods (exoskeleton)
• cellulose and chitin most abundant biopolymers on earth
• composed of water, proteins and carbohydrates (GAGs, collagen, elastin, fibronectin, laminin, proteoglycans
• fibroblast cells secrete connective tissue ECM
• osteoblast cells secrete cartilage-forming ECM
• chondroblast cells secrete cartilage-forming ECM
• fibroblasts and epithelial cells make basement membrane ECM (basal lamina)
• functions:
  1) mechanical support
  2) biochemical barrier
  3) medium for extracellular communication, stable positioning of cells in tissues, repositioning of cells by cell migration during cell development and repair
  4) tensile strength for tendons
  5) compressive strength for cartilage
  6) hydraulic protection for cells
  7) elasticity to walls of blood vessels
  8) calcified to form bones, teeth, cell wall of bacteria, shells of molluscs
  9) chitinized to form exoskeleton of insects and arthropods
• all components interact with each other and interact or bind to cells

Question 210

Glyocalyx

Answer 210

• extracellular space of ECM
• carbohydrates attached to cell membrane proteins and lipids forms this cell coat
• cytosolic glycoprotein scaffold
• involved in:
  1) mediating cell-cell interactions
  2) mediating cell-substrate interactions
  3) mechanical protection of the cell
  4) binding regulatory factors on cell surface

Question 211

Basement membrane (basal lamina)

Answer 211

• extracellular matrix located around muscle cells, fat cells, under epithelial tissues, under endothelial lining of blood vessels
• functions:
  1) provide mechanical support for attached cells
  2) generating signals to maintain cell survival
  3) separating adjacent tissues
  4) acting as a barrier to some macromolecules
  5) establishes cell polarity
  6) orient organelles where the nucleus will be down towards the lamina to then secrete things into the lumen

Question 212

Glycosaminoglycans (GAGs)

Answer 212

• major component of ECM
• unbranched polymers of repeated modified disaccharides
• negatively charged due to sulfates, so attracts Na+, which attracts water and causes cell to puff up into a gel
• only 10% of ECM mass but 90% volume
• provide compressive strength
• metabolically cheap bulking agent
• proteoglycans bind to GAGs to increase volume and water drawing capacity
• good for cushioning

Question 213

Proteoglycans

Answer 213

• major component of ECM
• GAGs and proteoglycans swell up and draw in water, serve same purpose, get fluffy, negatively charged due to sulphate
• more carbohydrates than porteins (protein backbone)
• good for cushioning due to spongy texture
• most abundant in cartilage
• bone extracellular matric rich in collagen and proteoglycans but hardened by impregnation of calcium phosphate

Question 214

Collagen

Answer 214

• **most abundant protein of the extracellular matrix
• **represents 25% of all protein in humans (most abundant protein in human body)
• produced by fibroblasts (cells of connective tissue), smooth muscle, epithelial cells
• 20 different types
• fibrous protein constituent of skin, cartilage, bone and connective tissue
• functions:
  1) scaffolding for body
  2) controls cell shape and differentiation
  3) remodeled (broken down and rebuilt) to help broken bones regenerate, heal and direct blood vessels to grow to feed healing areas
• can be shortened and lengthened to allow cells to migrate on collagen tracts to move around
• trimer protein (3 alpha chains that intertwine to for triple helix)
• assemble into fibrils to increase strength
• are cross-linked at hydroxylated residues (need vitamin C to assist in hydroxylation)
• problems with collagen:
  1) scurvy: lacking vitamin C could result in bruising of skin due to lack of collagen
  2) increased cross-linking occurs with age causing decreased elasticity of skin
  3) mutations of type 1 collagen results in osteogenesis imperfecta (thin skin, fragile bones)
  4) mutation in gene results in hyperflexible joints and extensible skin(not hydroxylated enough)
• in tendons, collagen fibers are parallel in line with direction of the tensions exerted
• in eye’s cornea, layers of collagen are perfectly arranged perpendicularly to other layers to give strength but light can still pass

Question 215

Fibronectin

Answer 215

• multifunctional protein in ECM
• dimer with domains that can bind to different components of ECM and cell receptors
• helps guide cells as they move through body
• during embryogenesis, guides movements of cells like neural crest cells to move out and form nervous system or primordial germ cells to migrate to gonads
• looks like a tong

Question 216

Integrin

Answer 216

• cell receptor that binds many components of ECM
• integral membrane protein
• interact with actin network with adaptor proteins
• has two polypeptides, alpha and beta chains
• cytosolic domains bind to adaptor proteins to link cytoskeleton (actin filaments)
• extracellular domains bind ligands in ECM
• promotes anchoring of the cell to the ECM by starting a signal cascade (cells can’t survive if not anchored to extracellular matrix=anchorage dependence, but lost when a cell is cancerous)

Question 217

Focal adhesions

Answer 217

• anchors cells to ECM
• pinpoints or suction cups
• rich in integrin proteins which are anchored to cell’s intracellular skeleton of actin microfilaments by using adapter proteins (vinculin and talin)
• this binding to adapter proteins to integrin results in activation of focal adhesion kinase (FAK) (lets cell know when they made contact to ECM and tells the cell to start changing shape)
• **know this actin network does not adhere directly to integrin but to Adaptor proteins

Question 218

Hemidesomome vs Desmosome

***ON EXAM

Answer 218

Hemidesmosome:

• uses integrins
• an integrin protein
• link cell to ECM more tightly than focal adhesion
• specialized structure composed of dense plaque of protein (often plectin) to which keratin fibers are embedded in cell (keratin linked to outside of cell by integrin which binds to ECM proteins)
• defect in integrin can result in loss of hemidesmosomes=lower layer of epidermis fails to attach to basement membrane and chronic blistering disease called epidermolysis bullosa
• anchors intermediate filaments in a cell to the extracellular matrix

Desmosome:

• uses cadherins
• connects intermediate filaments in one cell to those in the next cell
• strong anchoring attachment
• forms thick plaques of proteins which are anchored to intermediate filaments of cytoskeleton
• disc-shaped adhesions present on cells subjected to mechanical stresses like muscles and epithelia
• uses cadherins on extracellular side
• provides more protein contact between cells
• autoimmune disorder = pemphigus vulgaris attacks cadherin proteins in desmosomes resulting in blistering

Question 219

Cell adhesion molecules (CAMs)

Answer 219

• helps cells recognize each other
• cadherins, immunoglobulin superfamily, selectins, integrins, connexins
• plants don’t have cell adhesion molecules due to being covered by thick cell wall made of cellulose, polysaccharides and glycoporteins; they have plasmodesmata

Question 220

Selections

Answer 220

• cell adhesion molecules
• integral protein
• heterophilic interaction (bind with specific carbohydrates on other cells)
• found on epithelial cells
• used to mediate interactions with leukocytes (white blood cells)
• involved in first adhesions then integrins assist

Question 221

Immunoglobulin

Answer 221

• cell adhesion molecules
• non-attached = antibodies and secreted proteins
• cell bound = Ig-cell adhesion molecules
• homophilic (bind to each other) and heterophilic (bind to others) especially in immunity related cells and activities
• mediate cell adhesion of lymphocytes, vascular and neural cells
• some viruses have protein on surface that looks like IgCAM, it tricks its host cell to bind and deliver RNA into it
• however, can recoat virus by delivering a molecule that blocks it from injecting the RNA

Question 222

Cadherins

Answer 222

• cell adhesion molecule
• an integral glycoprotein
• 5 tandem domains that Ca2+ separates
• real strength is from number of cadherins attached to each other, not from getting closely packed together
• homophilic interaction (attach to each other)
• anchored to actin network through adapter proteins (catenin)
• during embryogenesis, production of cadherins promotes cells of similar type to adhere
• when cells migrate to new tissue, they lose adhesive properties (cadherins endocytosed)
• new cadherins are used as new cell contacts develop

Question 223

Tight junctions

Answer 223

• seals gap between epithelial cells
• homophilic interactions
• brings cell membranes super close together almost to the point of fusion
• much more waterproof than other adhesions (not entirely waterproof), and prevent easy flow of solutes
• found at apical end of cells
• produce occludins and claudin proteins which form a line of spot welds on both cells’ membranes
• claudins permeable to certain ions allowing for controlled leakage
• found in epithelia
• mutations in claudins result in tissue failure where skin leaks water and animals die of dehydration
• epithlia of the lung: have a growth stimulant (heregulin) on apical surface and its receptors are on the basolateral surface, tight junctions provide tight seal so there is no stimulation of its receptors as long as the sheet of cells remains intact, but if broken heregulin reaches receptors causing an autocrine stimulation of mitosis leading to healing of the wound; disorder of lung like chronic bronchitis of smokers, asthma and cystic fibrosis increases permeability of the airway epithlium resulting in autocrine stimulation causing proliferation of epithelial cell (small legions=buildup of cells), and too much stimulation can result in cancer

Question 224

Adheren junctions

Answer 224

• connects actin filament bundle in one cell with that in the next cell
• homophilic interactions
• ring-like structure like a belt attaching all neighbouring cells on all sides
• junctions between cells using cadherin molecules
• on intracellular side, cadherins attach to network of cytoskeleton fibers (actin)
• attach to actin via catenin
• maintains tissue integrity at tissue surface
• form discrete patches holding cells together
• loss of functioning adheren junctions could lead to tumour metastasis

Question 225

Gap junctions

Answer 225

• allows the passage of small water-soluble molecules from cell to cell
• homophilic transduction
• protein pipelines allowing direct contact between adjacent cells’ cytoplasm
• integral protein that lines the channel=connexin
• **ring of 6 connexins (proteins) comprise a connexon
• permits flow of small molecules like ions and simple sugars
• flow is passive but channel can be gated
• flow regulated by connexons (to increase flow of ions, increase number of connexons)
• cilia need to be coordinated
• functions:
  1) for adjacent cells to respond in the same way
  2) permit fast signalling for synchrony (heart sinoatrial node)
  3) cAMP and IP3 can be delivered to adjacent cells when hormones trigger a single cell (tissue in harmony)
  4) allows adjacent cells to connect to only those with the right connexon

Question 226

Actin-linked cell-matrix junction

Answer 226

*anchors actin filaments in cell to extracellular matrix

Question 227

Plasmodesmata

Answer 227

• plants don’t have cell adhesion molecules due to being covered by thick cell wall made of cellulose, polysaccharides and glycoporteins
• connect cells with adjacent plant cells
• lined with cell membrane with desmotubule derived from SER (causes cell to swell or shrink, actin and myosin twist and tighten to open and close the gap)
• pore allows molecules to pass through and controlled by dilation
• some viruses can modify these proteins to open wider to allow passage of the virus through the plasmodesmata

Question 228

Identify the mutations required for cancer to develop

Answer 228

1) mutations of genes in control of cell cycle
- oncogenes: products stimulate mitosis even though normal growth signals are absent
- tumour suppressor genes: inhibit mitosis (p53 gene product normally senses DNA damage and halts cell cycle to be repaires or trigger cell death)
2) genes that regulate apoptosis (programmed cell death)
- allows cell to ignore signals telling it to commit suicide
3) genes that maintain telomeres
- normal cells lose portion of telomeres after each division until too short and dies
- cancer cells regain ability to express telomerase and become immortal
4) genes that stimulate angiogenesis
- developing cancer stimulates growth of new blood vessels into itself by the release of angiogenesis stimulants (VEGF, vascular endothelial growth factor)
- these blood vessels or capillaries can also be a means of escape into the bloodstream and into a new location of the body
5) metastasis genes
- enable cells of tumour to separate from primary tumour and migrate to other parts of the body
- mutations in genes whose products normally keep cells of tissue adhered (cadherin that hold epithelial cells together=carcinomas cancer)
- mutations in genes whose products normally keep cells adhering to their substrate (integrin genes)

Question 229

Describe the progression to cancer

Answer 229

1) a single cell in a tissue (adult stem cell) suffers mutation of gene involved in cell cycle
2) cell now has slight growth advantage over other cells in tissue (hyperplasia: fastest growth compared to neighbours)
3) cell develops into a clone, some descendants suffer another mutation in another cell cycle gene = further deregulates cell cycle (dysplasia: irregular forms of cells)
4) rate of mitosis of clone increases, chances of further DNA damage increases (insitucancer: build up of irregular cells)
5) so many mutations have occurred that growth of clone is completely unregulated
6) full blown cancer
* increasing chance of cancer as we age, have been exposed to chemicals for a longer period of time

Question 230

Name the various treatments for cancer and new therapies

Answer 230

Treatments:

1) surgery
2) radiation therapy *does not always kill all cancer cells (damage cells irreparably by radiation, normal cells can repair themselves)
3) chemotherapy *does not always kill all cancer cells (drugs that inhibit division, cancer cells still attempt division and die)

New therapies:

1) antibodies
- breast cancer has excess growth factor receptor Her2, so the antibody specific for Her2 disrupts receptor and allows tumour to regress
- toxins or radioactive compounds attached to anitbodies that then carry the toxin to cancer cells
2) gene therapy
- tumours lack p53, so adding it back could cause tumour regression
- gene silencing technology used to turn off a targeted gene using double stranded RNA (dsRNA)
3) nanoparticles
- sugar coated nano-sized particles taken in by cancer cells that deliver ferrous metal to make a magnetic field to cook the tumour cells
4) immunotherapy
- inducing patient’s own immune system to target cancer cells
- harvest tumour cells, separate into smaller subsets of cells, treat with cytokine to stimulate growth of healthy immuno-responsive cells, select those cultures that kill tumour cells and reintroduce them back into the patient

Question 231

Death by injury

Answer 231

• cells damaged by mechanical damage or exposure to toxic chemicals
• cell and organelles swell and lose the ability to control the passage of ions/ water OR cell contents leak out, leading to inflammation of surrounding tissues

Question 232

Apoptosis (programmed cell death=clean process)

Answer 232

• death by suicide
• cells are induced to commit suicide by going through this process:
  1) cells shrinks
  2) develops bubble-like blebs on their surface
  3) DNA is degraded
  4) mitochondria breaks down
  5) break into small, membrane wrapped fragments
• if phospholipid phosphatidylserine=signal is exposed on surface (normally hidden within plasma membrane), then it is bound to phagocytic cells’ receptors to then be engulfed and secrete cytokines that inhibit inflammation
• defects in apoptosis can lead to diseases like atrophy (tissue wasting=excessive apoptosis), cancer (insufficient apoptosis) or aging (loss in muscle and neural tissue where no new cells are coming to replace the old ones)
• rate of apoptosis is pretty steady in both adults and children
• why commit suicide?
  1) for proper development (resorption of tadpole tail, formation of fingers and toes by removal of tissue between them, menstruation so the sloughing off of inner lining of uterus, and neural innervations in tissues requiring removal of surplus neurons)
  2) for protection against the threat to integrity of the organism (cells infected with viruses killed by cytotoxic T lymphocytes, cells of immune system, cells with DNA damage so increase p53 protein as a potent inducer of apoptosis, and cancer cells)

Question 233

What makes a cell decide to commit suicide?

Answer 233

1) withdrawal of positive signals
- continued survival of many cells requires continuous stimulation from other cells and continued adhesion
- growth factors and various cytokines stimulate mitosis
- with damaged, it doesn’t get the positive signal to keep dividing when in an open space
2) receipt of negative signals
- increased levels of oxidants within the cell
- damage to DNA by oxidants, UV light, X-rays and cytotoxic compounds
- accumulation of misfolded proteins
- death activators (molecules that bind to specific receptors on cell surface and signal cell to begin apoptosis

Question 234

Intrinsic factors vs extrinsic factors that induce apoptosis

Answer 234

Intrinsic factors:

• caspase 9
• signals come from within the cell due to damage to key organelles (mitochondria)
• internal factors that can induce it: p53 (stops cells from dividing if DNA is damaged, also directly activates Bax proteins to punch holes in mitochondria and inducing caspases to begin apoptosis) and viral double stranded RNA or dsRNA (detected by PKR, a protein that first stops cell’s translation machinery by inhibiting eIF and induces caspases)
• process:
  1) detects reactive oxygen, outer membranes of mitochondria display protein Bcl-2 on surface
  2) internal damage to cell from reactive oxygen causes Bcl-2 to activate Bax which punches holes in outer AND inner mitochondrial membrane = cytochrome c leaks out
  3) released cytochrome c binds to apoptosis-promoting proteins (Apaf-1 and procaspase-9)
  4) proteins aggregate to form apoptosomes
  5) ***apoptosomes activates executioner capsases (proteases)
  6) expanding cascade of caspases which digest structural proteins in cytoplasm and degrade DNA
  7) phagocytes recruited to destroy dying cell

Extrinsic factors:

• caspase 8
• death activators binding receptors at cell surface (tumour necrosis factor or TNF)
• death activators come from immune system cells as a natural defense mechanism of virally-infected cells:
  1) transport viral proteins to the cell surface
  2) viral proteins coupled to MHC (major histocompatibility complex) proteins on surface to infected cell
  3) MHC proteins allow binding with immune system cells like natural killer and cytotoxic T cells
  4) cytotoxic T cells signal to infected cell through interaction of FasL protein (a TNF) with infected cell’s Fas protein (cell surface receptor)
  5) Fas induces infected cell to undergo apoptosis, however many viruses encode proteins that can inhibit apoptosis
• process:
  1) TNF receptors (TNFR1) are integral proteins that detect signals like tumour necrosis factor (a death activator)
  2) TNFR1 cytoplasmic domains then bind to other proteins which recruit procaspase 8
  3) activation of caspase 8
  4) caspase 8 initiates a cascade of caspase activation
  5) leads to phagocytosis of the cell

Question 235

Apoptosis-inducing factor (AIF)

Answer 235

-another pathway of apoptosis
-used by neurons and other cells
does not use caspases in initial stages
-a protein located in intermembrane space of mitochondria
-process:
1) cell receives a signal telling it it is time to die either from an extrinsic signal or high levels of reactive oxygen species
2) AIF released from mitochondria (like release of cytochrome c in intrinsic pathway)
3) migrates into nucleus
4) binds to DNA
5) triggers destruction of the DNA and cell death

Question 236

Describe the signs of apoptosis

Answer 236

• cell shrinkage and rounding due to breakdown of cytoskeleton by caspases
• chromatin undergoes condensation
• nuclear membrane becomes broken and DNA inside is fragmented, nucleus also breaks into several pieces
• cell membrane has irregular buds=blebs
• cell breaks apart into several vesicles=apoptotic bodies then phagocytosed
• progresses quickly and products quickly removed, making it difficult to detect or visualize

Question 237

Stem cells

Answer 237

• loss of cells by apoptosis is balanced by production of more cells
• some daughter cells differentiate into certain cell types
• self-renewing (go through numerous cell divisions while maintaining undifferentiated state)
• immortal due to active telomerase
• as embryo develops, tissues form, cells acquire unique characteristics and become irreversibly differentiated
• have potency (capacity to differentiate into specialized cell types)
• as cells move up, they lose potency and can’t produce any more cells and become undividing (intestinal cells)
• totipotent: give rise to any mature cell type
• pluripotent: can’t become whole organism but can still produce a small variety of tissue (started to differentiate), different tissues have different stem cells
• unipotent: can only produce one type of tissue
• once a cell differentiated into a certain cell type it cannot be reversed=in vivo
• medical applications: take stem cells and put them back in the damaged tissue, mature cells can be reprogrammed to become pluripotent, stem cell therapies (replace damaged or lost cells), generate new eggs from stem cells (reverse menopause/sterility), re-grow new structures or organs (use 3D printers to form tissues)