Kaplan Biology Chapter 1: The Cell

What are the 4 basic principles in cell theory?

1. all living things are made up of cells

2. the cell is the basic functional unit of life

3. cells arise only from preexisting cells

4. cells carry genetic info in the form of dna, passed from parent to daughter cell

Viruses are small structures that

• contain genetic info, but unable to reproduce on their own

• replicate by invading other orgs and may use rna

• not considered living orgs

Describe prokaryotic organisms

• always single celled

• no nucleus or mem bround organelles; just contain ribosome, cell wall, cell mem, dna, and flagellum

• genetic info organized into a single circular molecule of dna in nucleoid region

Describe eukaryotic organisms

• can be unicellular or multicellular

• have nuc enclosed in a mem

Within the nuc of a euk cell, genetic material is

• encoded in dna

• nuc is surrounded by the nuclear mem/envelope, helping to maintain a nuclear environment separate from cytoplasm

• nuclear pores in mem allow exchange between these 2 environments

Describe the genetic info, DNA. DNA contains coding regions called

• genes

• linear dna→wound around histones→further wound into chromosomes

• nucleolus is where rRNA is made

Describe parts of mito.

• outer mem is barrier between cytosol and inner environment of mito

• inner mem, arranged into foldings called cristae, contain ETC parts

• space btwn these 2 mems is intermem space

• space inside inner mem is mito matrix

Mito are diff from other parts of the cell in that they are semiautonomous. What does this mean?

• contain some of their own genes and replicate independently of the nuc via binary fission

• this is an example of cytoplasmic/extranuclear inheritance, the transmission of genetic info, independent of the nuc

• mito can also perform apoptosis by releasing enzymes from ETC

Lysosomes are mem bound structures containing enzymes that can

• break down substrates

• these enzymes are released via autolysis

• work with endosomes→these transport cell material traveling to and from mem; locations include transgolgi, cell mem, or lysosomal pathway for degradation

The rough ER has

• ribosomes→help translate proteins destined for secretion

The smooth ER lacks

• ribosomes and is used for lipid synthesis and detoxification of drugs/posions

• also transports proteins from rough ER to golgi app in vesicles→once in GA, can be modified by adding groups, putting signal sequences to help direct delivery to a specific location→then repackaged into vesicles→go to location→if needs to be secreted, vesicle merges with cell mem and contents released via exocytosis

Peroxisomes contain

• hydrogen peroxide

• help break down LCFA via beta oxidation

• also help out in syn of phospholipids and PPP

The cytoskeleton helps cell maintain shape. What are the 3 components of it?

• microfilaments, microtubules, and intermediate filaments

Microfilaments are made up of

• actin→organized into networks resistant to compression and fracture→offers protection for cell

• actin filaments can also use ATP to interact with myosin like in muscle contraction→generate force for movement

• also help form the cleavage furrow during cytokinesis in mitosis

Microtubules are made up of

• hollow tubulin

• provide pathways for motor proteins(kinesin and dynein) to carry vesicles

• microtubules also make up cilia(involved in movement of materials) and flagella(involved in movement of cell itself)

Cilia and flagella are made up of

• 9 pairs of microtubules forming an outer ring, and 2 central microtubules, seen only in eukaryotic organelles of motility

Centrioles are found in the

• centrosome→organizing centers for microtubules and structured as 9 triplets of microtubules with a hollow center

• in mitosis, centrioles go to opp poles of the dividing cell and organize mitotic spindle→microtubules coming out of the centrioles attach to the chromosomes via kinetochores and exert force on the sister chromatids, pulling them apart

Intermediate filaments include

• keratin, desmin, vimentin, and lamins

• involved in cell-cell adhesion or maintaining integrity of the cytoskeleton

• increase rigidity of the cell, and help anchor other organelles

What are the 4 types of tissue?

• epithelial, connective, muscle and nervous

Epithelial tissues help protect against

• pathogen invasion and desiccation

• epithelial cells are joined together and to a layer of connective tissue called basement mem

• these cells constitute the parenchyma(functional parts of the organ) and are often polarized(one side faces lumen and other interacts with blood vessels/structural cells)

Epithelia can be classified according to the number of layers they have and shape of their cells. What are they?

• simple→one layer of cells

• stratified→multiple layers

• pseudostratified→appear to have multiple layers due to diff in cell height, but only one layer in reality

• cuboidal→cube shaped

• columnar→long and thin shaped

• squamous→flat and scale-like

Connective tissue supports the body and provides a framework for the epithelial cells to carry out their functions. Connective tissues are the

• main contributors to the stroma(support structure)

• examples of connective tissue are bone, cartilage, tendons, ligaments, adipose tissue, and blood

• most cells in these tissues produce and secrete collagen and elastin to form the ECM

All bacteria contain a

• cell mem and cytoplasm, and some have flagella or fimbriae(similar to cilia)

What does it mean for bacteria to be either mutualistic symbiotes or pathogens/parasites?

• mutualistic symbiotes: both humans and the bacteria benefit from the relationship; ex include bacteria in the human gut that produce vit K and biotin and also prevent growth of harmful bacteria

• pathogens/parasites: they provide no advantage to the host, but rather cause disease

Most bacteria exist in 1 of 3 shapes. What are they?

• cocci→spherical

• bacilli→rod shaped

• spirilli→spiral shaped

Describe the difference between aerobes and anaerobes for bacteria.

• obligate aerobes: require oxygen for metabolism

• anaerobes: don’t require oxygen and instead use fermentation etc

• obligate anaerobes: can’t survive in an oxygen-containing environment

• facultative anaerobes: uses oxygen for aerobic metabolism if it’s present and switching to anaerobic metabolism if it’s not

• aerotolerant anaerobes: unable to use oxygen for metabolism, but not harmed by its presence in the environment

How do you tell if a cell wall for a bacteria is gram pos or gram neg?

• determined by gram staining: a crystal violet stain→followed by counterstain with safranin

• if envelope(cell mem and cell wall) absorb violet stain→deep purple→gram pos

• if envelope absorbs safranin→pink-red→gram neg

Describe the difference between gram pos and gram neg cell walls?

• gram pos: thick layer of peptidoglycan and lipoteichoic acid

• gram neg: thin layer of peptidoglycan separated from mem by periplasmic space; also have outer mems containing phospholipids and lipopolysaccharides(triggers immune response in humans)

What is chemotaxis?

• ability of a cell to detect chemical stimuli and move toward/away from them

What is flagella composed of?

• filament, basal body, and hook

• filament: hollow, helical structure composed of flagellin

• basal body: anchors flagellum to cyto mem and is also the motor

• hook: connects the filament and basal body so basal body can rotate

Plasmids carry DNA that is not necessary for

• survival of the prokaryote and not part of the genome of the bacterium, but offers an advantage such as antibiotic resistance

Binary fission is a simple form of asexual reproduction seen in

• prokaryotes; does not increase genetic variability

• process: circular chromosome attaches to the cell wall and replicate while cell grows→plasma mem and cell wall begin to grow inward along midline to produce 2 identical daughter cells

• this chromosome is necessary to cell to survive and reproduce; some bacteria have plasmids, which carry genes that give some benefit to the bacterium such as antibiotic resistance

• a subset of plasmids is called episomes and can integrate into the genome of bacteria

Bacterial recombination helps increase bacterial diversity. These processes include

• transformation, conjugation, and transduction

• transformation:foreign genetic info into host genome

• conjugation: transfer of genetic info from one bacterium to another across a conjugation bridge

• transduction: transfer of genetic info from one bacterium to another by a bacteriophage that requires a vector(a virus that carries genetic info from one bacterium to another)

Describe the conjugation process.

1. to form a pilus on donor male, bacteria must have plasmids called sex factors that contain the necessary genes such as the F(fertility) factor→termed F+ cells

2. F+ cell replicates its F factor and donates the copy to the F- cell, converting it to an F+ cell

3. This helps the cell obtaining the new plasmid to then transfer copies to other cells

4. donor male has sex pilus to help form conjugation bridge betwn it and recipient female to transfer genetic info

What is a high frequency of recombination?

• when a donor cell attempts to transfer an entire copy of its genome into the recipient, but the bridge breaks before the full dna sequence can be moved

Describe the bacterial transduction process.

• this is when bacteriophages(viruses that infect bacteria) accidentally put in a segment of host dna during assembly

Transposons are genetic elements

• capable of inserting and removing themselves from the genome

• if one is inserted into a coding region of a gene, that gene can be disrupted

What are the phases in which bacteria grow?

• lag phase: bacteria first adapt to the new local conditions

• exponential/log phase: rate of division increases, causing an exponential inc in number of bacteria

• stationary phase: as the number of bacteria grows, resources are reduced, slowing reproduction

• death phase: happens when resources are depleted

Viruses are composed of

• genetic info, a protein coat which is a capsid that is sometimes surrounded by a lipid-containing envelope

• the envelope is very sensitive to heat, detergents, and dessication so enveloped viruses are easier to kill

• within the capsid, there is single stranded rna that can be translated to protein by ribosomes of the host cell

Bc viruses can’t reproduce independently, they are considered

• obligate intracellular parasites

• viruses must express and replicate genetic info within a host cell bc they lack ribosomes to carry out protein synthesis

• once a virus replicates, it will produce viral progeny called virions, which can be released to infect additional cells

Bacteriophages don’t actually enter bacteria. They inject their genetic material, leaving the

• remaining structures outside the infected cell

• bacteriophages contain a capsid, a tail sheath(infects genetic info into bacterium), and tail fibers(help bacteriophage recognize and connect to the correct host cell

Viral genomes may be made of either single or double stranded dna or rna. Single stranded rna viruses may be positive or negative sense. What is this?

• positive sense: genome may be directly translated to functional proteins by the ribosomes of the host cell, like mRNA

• negative sense: acts as a template for synthesis of a complementary strand, which can then be used as a template for protein synthesis; must carry an RNA replicase in the virion to ensure that the complementary strand is synthesized

What are retroviruses?

• enveloped, single stranded rna viruses where the virion usually contains 2 identical rna molecules

• these carry reverse transcriptase→synthesizes dna from rna→dna integrates into host cell genome, where it is replicated and transcribed as if it were the host cell’s own dna

• example is HIV

Describe the life cycle of HIV.

1. virus binds to CD4 and CCR5 proteins on cell surface

2. it then empties its contents into the cell as it fuses

3. reverse transcriptase makes a copy of the viral rna and creates dna

4. this dna is then inserted into the host cell’s dna by integrase

5. when the infected cell divides, it transcribes the viral dna, making long chains of proteins

6. viral rna and proteins move to the cell mem to begin the process of the new virus creation

7. the enzyme protease modifies protein chains as part of the process in creating a mature virus

What is the diff between enveloped viruses like HIV and bacteriophages?

• enveloped viruses fuse with mem and enter the cell intact, while bacteriophages only insert their genetic material, leaving their capsids outside the host cell

Most dna viruses enter the nuc in order to be transcribed into

• mRNA→then goes to cytoplasm→translated into proteins

• genetic info from pos sense rna viruses stay in cyto where directly translated into protein by host cell ribosomes

• neg sense rna viruses require synthesis of a complementary rna strand via rna replicase, where translated to make proteins

• dna formed through reverse transcription in retroviruses also travels to the nucleus, where it can be integrated into the host genome

• this mRNA doubles as the viral genome for new virions; once new virions are assembled from the structural proteins and mRNA genome, the virions can be released to infected other cells

What are the ways in which viral progeny can be released?

• cell death→results in spilling of the viral progeny

• host cell can lyse as a result of being filled with large numbers of virions; disadvantage for virus bc that cell can no longer be used by virus to carry out its life cycle

• virus can leave cell by fusing with its plasma mem known as extrusion→keeps host cell alive and allows for continued use of the host cell by the virus; this is known as a productive cycle

What is the difference between a lytic and lysogenic cycle?

Lytic: bacteriophage maximizes use of host cell’s machinery w/o caring for its survival→once host is swollen with new virions, cell lyses, and other bacteria can be infected→viruses in lytic phase called virulent

Lysogenic: virus integrates into host genome as a provirus/prophage→virus will be replicated as bacterium reproduces→virus may remain integrated into host genome and be dormant for years, but environmental factors may cause provirus to leave the genome and revert to a lytic cycle

Describe prions.

• nonliving proteins that cause disease by triggering misfolding of other proteins, usually thru conversion of a protein from an alpha helical structure to a beta pleated sheet→reduces solubility of the protein, as well as ability of cell to degrade the protein

Describe viroids.

• small pathogens with short circular single-stranded rna that infect plants

• viroids can bind to a large number of rna sequences and can silence genes in the plant genome→prevents synthesis of necessary proteins→results in metabolic disruption and structural damage to the cell

Archaea are often extremophiles,

• living in harsh environments, and often use chemical sources of energy rather than light; they have similarities to both eukaryotes(start translation with methionine, similar rna polymerases, histones) and bacteria(single circular chromosome, divide by binary fission or budding, lack a nuc)

What types of nucleic acid can form the genome of a virus?

• single stranded rna, double stranded dna, and single stranded dna

Mitochondrial dna is

• circular and self replicating

• this is bc mito are thought to have evolved from an anaerobic prokaryote engulfing an aerobic prokaryote and establishing a symbiotic relationship→mito dna is similar to bacterial dna→organized into a single circular chromosome of double stranded dna that can replicate during binary fission

What subunits do prokaryotic ribosomes contain? Eukaryotic ribosomes?

• 30S and 50S

• 40S and 60S