Kaplan Biology Chapter 1: The Cell

Cell Theory

A scientific theory which describes the properties of cells as the basic unit of structure in all organisms and also the basic unit of reproduction with 3 basic tenets:

- All living things are composed of cells

- The cell is the basic functional unit of life

- Cells arise only from preexisting cells

4th Recently Developed Tenet of Cell Theory

- Cells carry genetic information in the form of deoxyribonucleic acid (DNA). This genetic material is passed on from parent to daughter cell

Eukaryotic Cells

Cells that contain a true nucleus enclosed in a membrane, including membrane bound organelles.

DNA is tightly wrapped around histone proteins in chromosomes in the nucleus.

Larger and more complex than bacterial cells

Membrane Bound Organelles

Structures within the cells that allow for the compartmentalization of functions

"Organs of the cell"

Major difference between Eukaryotic and Prokaryotic Cells

Cytosol

The soluble portion of the cytoplasm, allows for the diffusion of molecules throughout the cell

Includes small particles, such as ribosomes, but not the organelles covered with membranes.

Deoxyribonucleic Acids - DNA

A nucleic acid molecule, usually a double stranded helix, in which each polynucleotide strand consists of nucleotide monomers with a deoxyribose sugar and the nitrogenous bases A T C G; capable of being replicated and determining the inherited structure of cell's proteins.

Mitosis

A process of nuclear division in eukaryotic cells conventionally divided into five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis conserves chromosome number by equally allocating replicated chromosomes to each of the daughter nuclei.

Nucleus

Control center of the cell contains all the genetic material, DNA and RNA necessary, for replication of the cell

Responsible for growth and reproduction

Most Heavily tested organelle on the MCAT

Nuclear Membrane /Envelope

Double membrane that maintains a nuclear environment separates and distinct from the cytoplasm; present in eukaryotes

Nuclear Pores

Pores in the nuclear membrane that allow for selective two way exchange of material between the cytoplasm and the nucleus

Genes

Coding regions/segments of DNA that code for specific traits

Histones

Globular protein that assists in DNA packaging in eukaryotes. Histones form octamers around which DNA is wound to form a nucleosome.

Rich in amino acids lysine and arginine

Chromosomes

Single piece of coiled DNA and associated proteins found in linear forms in the nucleus of eukaryotic cells and circular forms in the cytoplasm of prokaryotic cells

Contains genes that encode for traits. Each species has a characteristic number of chromosomes.

Nucleolus

Subsection of the nucleus where ribosomal RNA - rRNA is synthesized

Roughly 25% of the nucleus, seen as a dark spot

Ribosomal RNA - rRNA

The most abundant type of RNA, which together with proteins, forms the structure of ribosomes.

Ribosomes coordinate the sequential coupling of tRNA molecules to mRNA codons. Helps make proteins

Synthesized in the nucleolus

Mitochondria

The power plants of the cell, site of cellular respiration; uses oxygen to break down organic molecules and synthesize ATP

Composed of outer membrane and inner membrane

Outer Membrane (mitochondria)

Serves as the barrier between cytosol and the inner environment

Cristae

Infoldings of the inner membrane of a mitochondrion that houses the "electron transport chain" and the enzyme catalyzing the synthesis of ATP.

Folding "increases the surface area" available for reactions

Intermembrane Space

Space between the inner and outer membrane

A "large amount of H+ is concentrated here" for the "electron transport chain"

H+ are pushed out during ETC

Creates a proton motive force

Mitochondrial Matrix

The interior of a mitochondrion (the region bounded by the inner membrane).

Mitochondrial Cytoplasmic/Extranuclear Inheritance

Transmission of genetic material independent of the nucleus

Mitochondrial DNA is passed on outside of the nucleus

Mitochondria evolved from anaerobic prokaryotes engulfing anaerobic prokaryotes

Circular, double stranded DNA

Apoptosis

Programmed cell death - controlled and intentional (important distinction from autolysis)

initiated by the release of enzymes from the electron transport chain from the mitochondria

Lysosomes

- Membrane-bound structures containing hydrolytic enzymes that are capable of breaking down different substrates, including substances ingested by endocytosis and cellular waste products

- works in conjunction with endosomes

- sequesters its enzymes to prevent damage to cell

Autolysis

- Release of enzymes in the lysosomes that results in cell death - these enzymes can be released into the extracellular environment

- Enzymes directly lead to the degradation of cellular components

- It occurs due to injury or infection

- It generally not happening in healthy tissues.

Endoplasmic Reticulum - ER

Series of interconnected membranes that are actually contiguous with the nuclear envelope

Folded numerous times to create complex structures in the lumen

Smooth ER and Rough ER

Rough Endoplasmic Reticulum - RER

Membranes studded with ribosomes, which permit the translation of proteins destined for secretion directly into the lumen

Smooth Endoplasmic Reticulum - SER

Membranes that lack ribosomes and primarily for the synthesis of phospholipids and detoxication of drugs and poisons in the cell

Transports proteins from the RER to the Golgi Apparatus

Golgi Apparatus

Series of stacked membrane bound sacs that modify cellular products via the addition of groups like carbohydrates, phosphates, and sulfates. Can also modify with signal sequences, which direct delivery of the product

Direct delivery of the products to specific cellular location via vesicles (EX: outside the cell, to lysosome, to plasma membrane)

Essentially the shipping center of the cell

Can send products outside the cell via secretory vesicles, exocytosis

Exocytosis

A process in which a cell releases substances to the extracellular environment by fusing a vesicular membrane with the plasma membrane, separating the membrane at the point of fusion and allowing the substance to be released.

What does "Form Follows Function" in relation to cells

Not all cells have the same relative distribution of organelles

- Ex: cells that require a lot of energy for location (sperm cells) have high concentration of mitochondria; cells involved in secretion (pancreatic islet cells) have high concentrations of RER and Golgi apparatuses

Peroxisomes

Contain hydrogen peroxide

Primary functions of breaking down long chains of fatty acids via Beta Oxidation

Participate in the synthesis of phospholipids and contain enzymes involved in the pentose phosphate pathway

Cytoskeleton

Provides structure to the cell and helps maintain its shape

Provides a conduit of transport of materials around the cell

Composed of:

Microfilaments

Microtubules

Intermediate Filaments

Microfilaments

Polymerized rods composed of actin

Organized into bundles/networks

Resistant to compression and fracture so they provide protection for the cell

Plays a role in cytokinesis

Actin

Protein that polymerizes to form microfilaments

Use ATP to generate a force for movement by interacting with Myosin - example for muscle contraction

Cytokinesis

Division of materials amongst the daughter cells

Cleavage Furrow

Microfilament structure that organizes as a ring at the site of divisions between each daughter cells

Actin filaments then contract and the ring becomes smaller pinching off the connection between daughter cells

Microtubules

Hollow polymers of "tubulin" proteins that provide primary pathways along the cell which motor proteins carry vesicles like kinesin and dynein

Kinesin

binds ATP, is an ATPase, uses tubulin as stepping stone, moves towards positive end

Dynein

binds ATP (ATPase), uses tubulin as a stepping stone, moves toward negative end directed

Cilia

Structure composed of "microtubules" that project from the cell

Involved in the movement of materials along the cell surface

Ex : Respiratory system - movement of mucus

Flagella

Structure composed of "microtubules" that are involved in the movement of the cell itself

Ex : sperm cells

Often form the 9+2 structure in Eukaryotic cells

9+2 Structure

The structure is found in both eukaryotic cilia and flagella

9 pairs microtubules form an outer ring structure with 2 microtubules running down the center.

Only found in eukaryotic organelles of motility

Centrioles

Found in the centrosome, organizing center for microtubules

Structured as 9 triplets of microtubules with a hollow center

Migrate to opposite poles of the dividing cell and attach to the chromosomes via Kinetochores

Pull the sister chromatids apart

Kinetochores

Anchor on the Sister Chromatid that attaches to the fiber that pulls the sister chromatids apart.

Intermediate filaments

Diverse group filamentous proteins

- keratin, desmin, vimentin, and lamins

Many involved in cell-cell adhesion or maintenance of cytoskeleton integrity

Withstand tension to make cell structure more rigid

Anchor other organelles

Tissue Formation

Formation of tissues allows for the division of labor

Different cells in a tissue carry out different functions

4 Types:

- Epithelial

- Connective

- Muscle

- Nervous

Epithelial Tissue

Covers the body and lines its cavities providing a means for protection against pathogen invasion and desiccation

In certain organs, involved in absorption, secretion, and sensation

Tightly joined together and to an underlying layer of connective tissue

Often polarized, one side of the cell faces the lumen, the other sided faces interacts with blood vessels and structural cells

Basement Membrane

Underlying layer of connective tissue that composes the floor of epithelial tissue

Parenchyma

Functional parts of the organ that are largely composed of highly diverse epithelial cells that perform a wide array of functions

Ex tissues of the bronchioles, alveoli, ducts, and sacs, that perform respiration, nephrons, hepatocytes, acid producing cells in the stomach

Simple Epithelia

Single layer of cells. Characteristics: absorbs, secretes, filtrates, very thin

Stratified Epithelia

Two or more layers of cells; shape can change in different layers.

Regenerates from below: basal cells divide and cells migrate to the surface.

More durable than simple epithelia and protection is the major role

Pseudostratified Epithelia

Appears like multiple layers due to a difference in cell height, but are really one layer

Ex: Lines respiratory tract

Three main shapes of epithelial cells

Cubiodal - Cube shaped cells

Columnar - long and thin

Squamous - flat and scalelike

Connective Tissue

Supports the body and provides a framework for the epithelial cells to carry out their functions

Contribute to the stroma of organs

Most cells in connective tissue produce and secrete materials such as collagen and elastin to form extracellular matrix

Ex : bones, cartilage, tendons, adipose tissue, and blood

Stroma

the supportive tissue of an organ, tumor, gonad

Consisting of connective tissues and blood vessels.

Prokaryotic Cells

Cells that do not contain membrane-bound organelles or a nucleus

Genetic Material is organized into circular molecule of DNA

Simplest of all cells, includes all bacteria

Nucleoid Regions

Single circular molecule of DNA in the middle of prokaryotic cell

Prokaryotic Domains

Classification and Structure of Prokaryotic Cells

2 Domains:

Archea

Bacteria

Archaea

Single-celled organisms that are visually similar to bacteria, but contain genes and metabolic pathways more similar to eukaryotes

Considered extremophiles but are now noted to be found in a variety of habitats

Notable for ability to use alternative sources of energy (photosynthetic, chemosynthetic - generating energy from inorganic compounds)

Hypothesized that they share a common origin with Eukaryotes

Extremophiles

Archea that are found in isolated harsh environments: extremely high temperatures, high salinity, or no light

Bacteria characteristics

Cells that contain a cell membrane and cytoplasm

Some have Flagella and Fimbrea

Bacteria and eukaryotes share analogous structures

Cell Membrane

A thin, flexible barrier around a cell; regulates what enters and leaves the cell

Fimbriae

Surface appendages that allow a bacterium to stick to a surface.

Mutualistic Symbiotes

Both humans and bacteria benefit from their relationship

Examples include bacteria that produce vitamin K or biotin (vitamin B7) in our intestines

Pathogens / Parasites

Provide no advantage or benefit to the host, but rather cause disease

Can live intracellularly or extracellularly

Cocci

Spherical bacteria

- Ex: Streptococcus pyogenes

Bacilli

Rod shaped bacteria

- Ex: Escherichia coli

Spirilli

Spiral shaped bacteria

- Treponema pallidum (Causes syphilis)

Obligate Aerobes

Bacteria that require oxygen for metabolism

Anaerobes

Bacteria that use fermentation/ another metabolism that does not require oxygen

Obligate Anaerobes

Bacteria that can not survive in the presence of oxygen

Produce oxygen-containing free radicals leading to cell death

Faculative Anaerobes

Bacteria that can toggle metabolic processes using oxygen for aerobic metabolism if present and switching to anaerobic metabolism if not present

Aerotolerant Anaerobes

Bacteria that cannot use oxygen for metabolism but are not harmed by its presence

Prokaryotic Cell Stucture

Contain Cell wall followed by cell membrane: together known as the envelope

Primitive Cytoskeleton (not as complex as euk.)

No nucleus, or membrane-bround organelles (lacking mitochondria)

Contain ribosomes (with no membrane) made up of 30 and 50s subunits (euk have 40S and 60S)

Single-cell organisms: each cell able to perform all functions for life but may live in colonies and signal these cells to share info about environment

Cell wall Prokaryotes (two types)

Forms the outer barrier of the cell, protecting it from the environment

Provides structure and controls the movement of solutes in and out of the bacterium, maintaining concentration gradients

Gram-negative bacteria.

Cell wall is composed of a thin layer of peptidoglycans also containing lipoteichoic acids

Gram Negative Bacteria

Cell wall is a very thin layer of peptidoglycan, adjacent to the plasma membrane separated by a periplasmic space

Also has an outer membrane containing phospholipids, lipopolysaccharides and porins

Lipopolysaccharides trigger the immune response in the body (much more so than to lipoteichoic acid)

Gram staining

A method of differentiating bacteria into Gram-positive and Gram-negative.

Gram positive bacteria stain purple because the thick peptidoglycan layer retains the crystal violet stain during the alcohol step

Gram negative bacteria become colorless during the alcohol step and then stain red-pink with safranin, the counterstain

Bacteria Cell Membrane

Composed of phospholipids similar to that of eukaryotes

Used for the electron transport chain and generation of ATP

Peptidoglycan

Found in both gram positive and negative cells

Larger concentration in gram positive cells

Polymer substance made from peptides (chain amino acids) and sugars

May aid a pathogen by providing protection from hosts immune system

Lipoteichoic Acid

Also found in gram-positive cell walls

Provides an unknown function

Human immune system is activated by this substance

Lipopolysaccharides

Found in the outer membranes of gram-negative bacteria

Containing lipid and polysaccharide parts

Can be known as endotoxins

Lipopolysaccharides (LPS), also known as endotoxins, are large, toxic molecules found in the outer membrane of Gram-negative bacteria (such as E. coli and Salmonella). They act as a protective barrier for the bacteria but are potent triggers of the mammalian immune system

Flagella Bacteria

Composed of Basal body, Hook, and Filament

Whiplike structure used for propulsion; bacteria may have one, two, or many

Flagellin

Polymerized protein that forms the long, hollow, helical structures in the filaments of prokaryotic flagellum.

Chemotaxis

Ability of a cell to detect chemical stimuli and move towards or away from them

Basal Body

Complex structure that anchors the flagellum to the cytoplasmic membrane

The motor of the flagellum (rotates at rates up to 300 Hz)

Hook

Connects the filament and the basal body so that as the basal body rotates it exerts torque on the filament

Causing spinning and thus movement of the bacteria

Plasmids

Circular DNA structures that are acquired from external sources

Carry DNA that is not necessary for surival of the prokaryote

Not considered part of the genome, but are often advantageous

Ex : Antibiotic Resistance

Binary Fission

Simple form of asexual reproduction seen in prokaryotes

1. Circular chromosome attaches to inside of inner membrane and replicates (starting at replication origin) while the cell grows in size

2. Chromosome separates to opposite sides of the cell

3. Plasma membrane and cell wall begins to grow inward and invaginate (pinch off)

4. Two daughter cells are produced

(E. coli can replicate every 20 min)

Genetic Recombination

Many bacteria contain plasmids that carry genes that benefit the bacterium (EX antibiotic resistance)

May also carry virulence factors

Helps increase bacterial diversity and thus permits the evolution of a bacterial species over time

Through the methods of :

Transformation

Conjugation

Transduction

Virulence Factors

Traits that increase how pathogenic a bacterium is

Can cause toxin production, attachment to specific cells, and evasion of a hosts immune system

Episomes

Plasmids that are capable of integrating into the genome of the bacterium

Transformation

Results from the integration of the foreign genetic material into the host genome

Genetic material most often comes from other bacteria that have lysed, spilling contents to the environment

Common in Gram-negative rods

Conjugation

Bacterial form of mating

Involves to bacterium forming a conjugation bridge that allows the transfer of material

Transfer is unidirectional (from donor male to recipient female)

helps bacteria evolve

Conjugation Bridge

Structure formed between two bacterial cells that allow for the transfer of genetic material

Made from appendages called sex pili

Donor Male +

Bacterium that donates the genetic material during conjugation

Recipient Female -

Bacterium that recieves the genetic material during conjugation

Conjugative (sex) Pili

Appendages that form the conjugation bridge

Can only be formed if sex factors are present in the bacterium, the donor male, typically as a plasmid, but it's possible to be integrated into the host genome (transformation)

Sex Factors

Plasmids containing the necessary genes that allows for the formation to sex pili

Most common is the Fertility Factor, F, in E. coli

F - Fertility Factor

Allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by "conjugation".

F+ cells contain the F factor and form a single sex pilus that connects to F- cell

The F factor is then replicated via DNA polymerase

F- cell now gains replicated F factor cell becoming F+

Hfr - High Frequency of Recombination

Cells that have undergone genetic recombination via conjugation and then through processes, such as transformation, integrated a sex factor plasmid into the host genome

Donor cell will now attempt to transfer entire copy of genome into recipient during conjugation but bridge usually breaks before full DNA sequence is done