Ch 1 - The Cell

Question 1

4 Tenants of Cell theory (3 in original, 4th added after molecular biology advances)

Answer 1

• All living things are composed of cells
• The cell is the basic functional unit of life
• Cells arise only from preexisting cells
• Cells carry genetic information in the form of DNA, which is passed on from parent to daughter cell

Question 2

Viruses contain genetic material, but which cell theory tenants do they violate?

Answer 2

Cells arise only from preexisting cells
Cells carry genetic information in the form of DNA, which is passed on from parent to daughter cell

Question 3

Eukaryotic characteristics

Answer 3

unicellular or multicellular
contain true nucleus contained in a membrane
Most organelles are membrane bound allowing for compartmentalization of functions
Membranes consists of a phospholipid bilayer - Hydrophilic outside surfaces, hydrophobic inside
Semifluid cytosol allows for diffusion of molecules throughout the cell
Nucleus encloses DNA which is organized into chromosomes
Reproduce by mitosis

Question 4

Nucleus:

Answer 4

contains all genetic material necessary for cell replication. It is surrounded by the nuclear membrane or nuclear envelope, a double membrane

Question 5

Nuclear pores:

Answer 5

in the nuclear membrane allow for two-way exchange of material between nucleus and cytoplasm

Question 6

Genes:

Answer 6

coding regions on DNA. Linear DNA is wound around organizing proteins known as histones, then further wound into linear strands called chromosomes. Location of DNA in the nucleus allows for separation of DNA transcription and RNA translation

Question 7

Nucleolus:

Answer 7

is a subsection in the nucleus where rRNA is synthesized

Question 8

Mitochondria:

Answer 8

important for metabolic functions
Have 2 membranes, outer and inner membranes. Outer serves as a barrier between cytosol and inside of mitochondria. Inner is arranged into numerous infoldings called cristae, and contain components (molecules & enzymes) of ETC. Intermembrane space is space between inner and outer. Space inside the inner membrane is the mitochondrial matrix.
Mitochondria are different from other organelles in they replicate independently of the nucleus via binary fission. Examples of cytoplasmic or extranuclear inheritance – transmission of genetic material independent of the nucleus.
Capable of killing the cell by release of ETC enzymes which starts apoptosis

Question 9

Lysosomes:

Answer 9

Membrane-bound structures containing hydrolytic enzymes that break down different substrates.
Often function in tandem with endosomes, which transport, package, and sort material. Endosomes can transport material to the trans-golgi, cell membrane, or lysosomal pathway for degradation.
Lysosome membranes prevent enzymes from damaging the cell, however release of the enzymes is known as autolysis and results in apoptosis.

Question 10

Endoplasmic reticulum (ER):

Answer 10

series of interconnected membranes connected to the nuclear envelope. Continuous membrane bilayer is folded into numerous invaginations creating complex structures with a central lumen (hollow inside).
2 varieties
Rough ER (RER) is studded with ribosomes, which allow for translation of proteins into its lumen
Smooth ER (SER) lacks ribosomes and is primarily used for lipid synthesis (such as phospholipids) and detoxification of certain drugs/poisons. SER transports proteins from the RER to the golgi apparatus.

Question 11

Golgi apparatus (GA):

Answer 11

Made up of stacked membrane bound sacs. Materials from the ER are transferred to the GA in vesicles. Once inside the GA, the products may be modified by addition of carbohydrate, phosphate, or sulfate groups. The GA can also modify products through signal sequences, which direct delivery of a product to specific cellular locations. Secreted products being transported outside the cells are contained in vesicles and merge with cell membrane and released via exocytosis

Question 12

Peroxisomes:

Answer 12

Contain hydrogen peroxide
One main function of peroxisomes is the breakdown of long fatty acid chains via β-oxidation.
Peroxisomes participate in the synthesis of phospholipids and contain some of the enzymes involved in the pentose phosphate pathway.

Question 13

Cytoskeleton provides structure to the cell and helps maintain shape. 3 components of cytoskeleton:

Answer 13

1. Microfilaments
2. Microtubules
3. Intermediate filaments

Question 14

Microfilaments:

Answer 14

made up of solid rods of actin. Actin filaments provide protection for the cell from compression or fx. Actin filaments can also use ATP to generate force for movements by interacting with myosin, such as in muscle contraction.
Also play a role in cytokinesis, the division of materials between daughter cells. During mitosis, the cleavage furrow is formed from microfilaments, which organize as a ring at the site of division between two new daughter cells. The actin filaments in the ring contract to pinch off the connection between daughter cells

Question 15

Microtubules:

Answer 15

hollow polymers of tubulin proteins. Radiate throughout the cell and provide pathways along which motor proteins like kinesin and dynein carry vesicles.
Cilia and flagella are composed of microtubules

Question 16

Cilia and flagella:

Answer 16

composed of microtubules
Cilia are projections from a cell primarily used in the movement of materials along the surface of the cell (such as cilia which line the respiratory tract are involved in the movement of mucus)
Flagella are involved in cell movement, such as movement of sperm through reproductive tract.
Cilia and flagella share same structure, 9 pairs of microtubules forming an outer ring with two microtubules in the center. Known as 9+2 structure, seen only in eukaryote motile organelles.

Question 17

Centrioles:

Answer 17

found in a region of the cell called the centrosome. This is the organizing center for microtubules and are structured as nine triplets of microtubules with a hollow center
Centrioles organize the mitotic spindle during mitosis Microtubules emanating from centrioles attach to chromosomes via kinetochores and pull sister chromatids apart.

Question 18

Intermediate filaments:

Answer 18

Diverse group of filament proteins including keratin, desmin, vimentin, and lamins
Involved in cell-cell adhesion, maintenance of overall integrity of the cytoskeleton, and anchorage of organelles
ID of intermediate filament proteins is specific to cell and tissue type.

Question 19

4 tissue types:

Answer 19

epithelial, connective, muscle, and nervous

Question 20

Epithelial tissues:

Answer 20

cover the body and line cavities providing protection against pathogen invasion and desiccation. In some organs, are involved in absorption, secretion, and sensation. Epithelial cells are joined tightly to each other and to an underlying layer of connective tissue known as the basement membrane.
Highly diverse and perform numerous functions
Most organs epithelial cells constitute the parenchyma, the functional organ parts (nephron of kidneys, hepatocytes of liver, acid producing cells of the stomach)
Epithelial cells are often polarized, meaning one side faces a lumen or outside world, while the other interacts with underlying blood vessels and structural cells.
Simple epithelia have one layer of cells. Stratified epithelia have multiple layers. Pseudostratified epithelia have one layer with different cell heights.
Epithelial cells may be classified as cuboidal (cube-shaped), columnar (long and thin), or squamous (fat and scale-like).
Ex: In small intestine, one side of cell with absorb nutrients from lumen and other side with release nutrients into circulation for body use.

Question 21

Connective tissue:

Answer 21

supports the body and provides a framework for epithelial cells to carry out their function.
main contributors to the stroma or support structure. Most cells produce and secret materials such as collagen and elastin to form the ECM.
Ex: Bone, cartilage, tendons, ligaments, adipose tissue, blood

Question 22

Prokaryote characteristics:

Answer 22

Simplest of all organisms – all bacteria
Prokaryotes contain no membrane bound organelles and their genetic material is organized into a single circular molecule of DNA located in the nucleoid region.
Prokaryotes may live in colonies with other cells and may signal these cells to share information about the environment

Question 23

3 Domains of Life

Answer 23

1. Archaea – prokaryotes
2. Bacteria – prokaryotes
3. Eukarya – eukaryotes

Question 24

Archaea:

Answer 24

single celled organisms visually similar to bacteria. Genes and metabolic pathway more similar to eukaryotes.
Notable for ability to use alternate sources of energy such as photosynthesis and chemosynthesis (energy from inorganic compounds such as ammonia)
Eukarya and Archaea both start translation with the same amino acid, contain similar RNA polymerases, associate DNA with histones
Bacteria and Archaea both have single circular chromosome, divide by binary fission or budding, and share similar overall structure

Question 25

Bacteria:

Answer 25

contain a cell membrane and cytoplasm. Some have flagella or fimbriae (similar to cilia).
Eukarya and Bacteria share similar analogous structures, making it difficult to target only bacteria. However, bacteria flagellum and eukaryotic flagellum are different enough that vaccines can target only bacteria, and bacterial ribosome is significantly smaller than eukaryotic ribosome allowing for antibiotics to target bacteria.
Some bacteria are mutualistic symbiotes with humans. Bacteria in the gut produce Vitamin K and Vitamin B7. Other bacteria are pathogens or parasites which can live intra or extracellularly

Question 26

Most bacteria exist in 1 of 3 shapes:

Answer 26

Spherical bacteria known as cocci
Rod shaped bacteria known as bacilli
Spiral shaped bacteria known as spirilli

Question 27

Bacterial metabolism:

Answer 27

Bacteria that require O2 for metabolism are termed obligate aerobes. Bacteria that use fermentation or other cellular metabolism and do not require O2 are anaerobes. Anaerobes that cannot survive in an O2 containing environments are obligate anaerobes. Facultative anaerobes can use O2 for aerobic metabolism if O2 is present and switch to anaerobic metabolism if O2 is absent. Aerotolerant anaerobes cannot use O2 for metabolism but are not harmed by the presence of O2.

Question 28

Bacterial Cell wall forms the outer barrier of the cell. Cell membrane is the layer adjacent and is composed of phospholipids. Together the wall and membrane are known as the envelope.
Cell wall provides structure, controls movement of solutes into and out of the bacterium, and can provide protection from a host organisms immune cell. In bacteria, 2 main types of cell wall: gram + and gram -.

Answer 28

The type of cell wall is determined by the Gram staining process: a crystal violet stain followed by a counterstain with safranin. If the envelope absorbs the violet stain, it will appear purple, and cell is gram +. If the envelope does not absorb the violet stain and instead absorbs the safranin, the cell will appear pink-red and is said to be gram -.
Gram + consist of thick layer of peptidoglycan, a polymeric substance made from amino acids and sugars. Also contains lipoteichoic acid, which may activate human immune system.
Gram – are very thin and contain smaller amounts of peptidoglycan. The walls of these bacteria are separated from the membrane by periplasmic space. Also have outer membranes containing phospholipids and lipopolysaccharides, which triggers an immune response in humans stronger than lipoteichoic acid.

Question 29

Prokaryotic Flagella:

Answer 29

are whip-like structures that can be used for propulsion. May have 1 – several flagella. Ability of a cell to detect chemical stimuli and move toward food or away from them is chemotaxis.
Flagella composed of a filament, basal body, and hook.
Filament is hollow helical structure composed of flagellin.
Basal body is a complex structure that anchors the flagellum to the cytoplasmic membrane and is also the motor of the flagellum.
Hook connects the filament and basal body so when the basal body rotates, it exerts torque on the filament which spins and propels the bacterium forward.
Slight differences in gram + and gram – flagellum.

Question 30

Prokaryotes reproduce asexually by binary fission and can acquire and using genetic material from outside the cell

Answer 30

Binary fission is a simple form of asexual reproduction. The circular chromosome attaches to the cell wall and replicates while the cell grows. Eventually the plasma membrane and cell wall grow inward along the midline to produce two identical daughter cells. Can happen rapidly due to limited stages.

Question 31

Many bacteria contain extrachromosomal (extragenomic) material known as plasmids. These carry genes that impart benefit such as antibiotic resistance and virulence factors which increase pathogenicity. Subset of plasmids called episomes can integrate into the genome of the bacterium. This genetic recombination allows for evolution of species and include transformation, conjugation, and transduction

Answer 31

Transformation results in integration of foreign genetic material into the host genome. This foreign material frequently comes from other bacteria that, upon lysing, spill their contents into the vicinity. Many Gram - rods.

Conjugation is the bacterial form of sexual reproduction. 2 cells form a conjugation bridge that facilitates the transfer of genetic material. Transfer is always from the donor male to the recipient female. Bridge made from appendages called sex pili that are found on the donor male. To form the pilus, bacteria must contain specific plasmids known as sex factors which carry the required genes. Best studied sex factor is the F (fertility) factor in E. coli. Bacteria which possess this sex factor are F+, those who don’t are F-, and during conjugation F+ replicates its F factor and transfers copy to the F- converting it into a F+. This method of genetic recombination allows for rapid acquisition of antibiotic resistance or virulence factors throughout a colony as many plasmids are passed through conjugation bridge.
Sex factors are plasmids but can integrate into the host gnome by transformation. In this case, during conjugation, the entre genome replicates and attempts to transfer entire genome copy to recipient; however, bridge usually breaks before the full DNA sequence can be transferred. Cells that have undergone this change are known as high frequency of recombination (Hfr)

Transduction requires a vector – a virus that carries genetic material from one bacterium to another. Bacteriophages (viruses that infect bacteria) can accidentally incorporate a segment of a host’s DNA during assembly. When the bacteriophage infects another bacterium, it can release the trapped DNA into the new host cell. This transferred DNA can then integrate into the genome giving the host new additional genes.

Question 32

Transposons:

Answer 32

genetic elements capable of inserting and removing themselves from the genome. This phenomenon has been seen in prokaryotes and eukaryotes. If a transposon is inserted within a coding region of the gene, that gene may be disrupted.

Question 33

In a new environment, bacteria adapt the new local conditions during the lag phase. As the bacteria adapt, the rate of division increases causing an exponential increase in # of bacteria during the exponential phase or log phase. As the colony grows, resources are limited which slows reproduction during the stationary phase. After the resources are exhausted, the death phase occurs.

Question 34

Viruses characteristics:

Answer 34

genetic material, a protein coat, and sometimes a lipid containing envelope
Genetic information may be circular or linear, single or double stranded DNA or RNA
Protein coat is a capsid, which may bd surrounded by an envelope made of phospholipids or viral proteins. Envelope is sensitive to heat, desiccation, etc.so enveloped viruses are easier to kill.

Question 35

Viruses are obligate intracellular parasites:

Answer 35

Lack ribosomes so must carry out protein synthesis within a host cell. After hijacking a cell, virus will replicate and produce viral progeny called virions, which can be released to infect other cells

Question 36

Bacteriophages:

Answer 36

do not enter bacteria, just inject their genetic material leaving the remaining structures outside the infected cell. Also contain tail sheath and tail fibers. Tail sheath acts as a syringe injecting genetic material into a bacterium. Tail fibers help recognize and connect to correct host cell.

Question 37

Viral genomes:

Answer 37

come in variety of shapes and sizes.
Single stranded RNA viruses may be + sense or – sense. + sense RNA implies genome may be directly translated to functional proteins by host cell ribosomes, like mRNA. – sense RNA acts as a template for synthesis of a complementary strand, which is then used as a template for protein synthesis. – sense RNA must carry an RNA replicase in the virion to ensure complementary strand in made.
Retroviruses are enveloped, single stranded RNA viruses in family Retroviridae. Virion usually contains 2 identical RNA molecules. Carry enzyme reverse transcriptase which synthesizes DNA from single stranded RNA. DNA integrates into host cell genome where it is replicated and transcribed as if it were the hosts cells own DNA. Mechanism allows for host cell to be infected indefinitely, meaning only way to remove infection is to kill infected cell.
Ex: HIV

Question 38

Viruses can only bind to a specific set of cells because they must bind to specific receptors on the host cell. Enveloped viruses fuse with the membrane of the cell, allowing for entry of the virion.
After infection, translation of the viral genetic material must occur for the viruses to reproduce. Most DNA viruses must enter the nucleus to be transcribed into mRNA. Genetic material from + RNA viruses stay in the cytoplasm to be directly translated into proteins by ribosomes. – RNA requires synthesis of a complementary RNA strand via RNA replicase, which is then translated to proteins.
Most proteins are structural capsid proteins and allow for new virions in the cytoplasm. Viral genome must be returned to its original form before packaging.

Question 39

Multiple ways of virion release:

Answer 39

Viral invasion may initiate cell death resulting in spillage of the viral progeny. Host cell may also lyse. Finally, viruses can leave the cell by fusing with the plasma membrane known as extrusion. This allows for the virus to continue using the host cell; a virus in this state is in the productive cycle.

Question 40

In lytic cycle:

Answer 40

bacteriophage maximize the cells machinery and cause lysis. Viruses in the lytic phase are termed virulent.
Viruses may also integrate into the host genome as a provirus or prophage, initiating the lysogenic cycle. Viruses will be replicated as the bacterium reproduces. This allows for transduction. Infection with one strain in this cycle makes bacteria less susceptible to superinfection (simultaneous infection) with other phages.

Question 41

Prions:

Answer 41

infectious proteins and cause disease by triggering misfolding of other proteins usually by conversion from an a-helical structure to a b-pleated sheet. The mis-shaped protein aggregates form and inhibits cell function.
Ex: mad cow disease

Question 42

Viroids:

Answer 42

small pathogens consisting of a short circular single stranded RNA that infects plants. Viroids can bind to a large number of RNA sequences and can silence genes. This results in metabolic disruption and cell damage. Few human viroids exist (ex: hepatitis D).