Chapter 4

102 terms by ceppes 

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Microscope

-tool that enables researchers to study the structure and functions of cells

Micrograph

-image taken with the aid of a microscope

Zacharias Jansen

-invented first compound microscope (microscope with more than 1 lens)

Robert Hooke

-studied cork under a compound microscope
-coined the word cell, meaning small compartment, to describe the units making up cork

Anton can Leeuwenhoek

-refined technique of making lenses
-observed single cell organisms such as bacteria

3 Important Parameters in Microscopy

1) Resolution
2) Contrast
3) Magnification

Resolution

-measure of the clarity of an image
-ability to observe two adjacent objects as distinct from one another
-improved when illumination source has a shorter wavelength

Contrast

-aids in visualizing particular structures by how different they look from adjacent structures
-staining structures with colored dye can make viewing easier and increase contrast
-colorization - colors are added to micrographs with the aid of a computer for educational purposes

Magnification

-ratio between the size of an image produced by a microscope and its actual size

2 Groups of Microscopes

1) Light Microscope
2) Electron Microscope

Light Microscope

-utilizes light for illumination

Electron Microscope

-uses electrons for illumination
-better resolution than light microscopes because electron beam wavelengths are shorter than visible light wavelengths

2 General Electron Microscope Types

1) Transmission Electron Microscopy
2) Scanning Electron Microscopy

Transmission Electron Microscopy (TEM)

-a beam of electrons is transmitted through a biological sample
-provides a cross-sectional view of a cell and its organelles and give the greatest resolution
-expensive and not used to view living cells

Scanning Electron Microscopy (SEM)

-used to view the surface of a sample
-electron beam scans the samples surface, and secondary electrons are emitted from the sample and are detected to create a 3D image of the surface of the sample

4 Factors that determine cell structure

1) matter
2) energy
3) organization
4) information

Matter

-composed of atoms, molecules, and macromolecules
-each type of cell synthesizes unique sets of molecules and macromolecules that contribute to cell structure

Energy

-needed to produce molecules and macromolecules and to carry out cellular functions

Protein-protein interaction

-build complicated cell structures
-facilitate processes in which proteins interact in a consistent series of steps

Information

-cell structure requires instruction found in genetic material which there is a copy of in every living cell
-genes within each species genomes contain information to create cells with particular function and structure
-passed from cell to cell, and from parent to offspring

2 Categories of Life

1) prokaryotes
2) eukaryotes

Prokaryotes

-simple structure
-prokaryotic cells lack a membrane-enclosed nucleus

2 Categories of Prokaryotes

1) Bacteria - very small, very abundant
2) Archaea - very small, less abundant, occupy extreme environments

Plasma membrane

-double layer of phospholipids and embedded proteins
-forms barrier between cell and external environment

Cytoplasm

-region of the cell contained within plasma membrane
-includes organelles and cytosol

Nucleoid region

-where genetic material (DNA) is located

Ribosomes

-involved in polypeptide synthesis

Cell wall

-found outside of plasma membrane of nearly all species of prokaryotes
-protect the plasma membrane and cytoplasm
-commonly contains peptides and carbohydrates
-relatively porous and allows most nutrients in environment to reach the plasma membrane

Glycocalyx

-outer viscous covering surrounding bacterium that is secreted by many bacteria
-traps water and protects bacteria from drying out

Capsule

-gelatinous glycocalyx that help bacteria that invade animals' bodies to avoid being destroyed by the animal's immune system

Pili

-appendages that allow prokaryotes to attach to surfaces and to each other

Flagella

-appendages that provide prokaryotes with a way to move, also called motility

Eukaryotes

-include protists, fungi, plants, and animals
-cells possess a true nucleus where most of the DNA is housed
-exhibit compartmentalism

Organelle

-membrane-bound compartment with its own unique structure and function

Compartmentalism

-having many membrane-bound organelles that separate the cell into different regions
-allows cells to carry out specialized chemical reactions in different places

Proteome

-all the types and relative amounts of proteins that are made in a particular cell at a particular time and under specific conditions

Cytosol

-region of a eukaryotic cell that is outside the membrane-bound organelles but inside the plasma membrane
-the site of many chemical reaction that produce the materials that are necessary for life

Metabolism

-the sum of the chemical reactions by which cells produce the materials that utilize the energy that are necessary to sustain life
-involves a series of steps called metabolic pathway
-each step in a metabolic pathway is catalyzed by a specific enzyme

Enzyme

-a protein that accelerates the rate of a chemical reaction

Catabolism

-the breakdown of a molecule into smaller components
-needed by the cell to utilize energy and to generate molecules needed to construct cellular macromolecules

Anabolism

-the synthesis of cellular molecules and macromolecules
-ex: linking of amino acids to form proteins

Cytoskeleton

-network of three types of protein filaments:
1) microtubules
2) intermediate filaments
3) actin filaments
-found primarily in cytosol and also in nucleus

Microtubules

-long, hollow cylindrical structures composed of subunits α and ß protein tubulin
-assembly of tubulin to form microtubule results in a polar structure with a plus and minus end
-grow at the plus end; can shorten at plus or minus end
-oscillate between growing and shortening phases by dynamic instability
-growth starts at centrosomes in animal cells
-in plants, nuclear membrane functions are microtubule-organizing center
-important for cell shape and organization

Centrosome

-aka microtubule-organizing center
-contains centrioles
-found in animal cells
-where microtubule growth typically begins

Intermediate Filaments

-found in cells of many animal species
-bind to each other to form a twisted structure
-function as tension-bearing fibers that help maintain cell shape and rigidity
-stable in size

Actin Filaments

-aka microfilaments because they are the thinnest cytoskeletal filaments
-have plus and minus ends
-grow at plus end by addition of actin monomers to form two strands of actin monomers that spiral around each other
-support plasma membrane and add strength and shape to the cell

Motor Proteins

-category of proteins that use ATP as a source of energy to promote various types of movement
-consist of head, hinge, and tail
-ATP binds to head and is hydrolyzed to ADP and P which causes the hinge to bend which results in movement
-tail is attached to other proteins or cellular molecules

Three types of movement motor proteins promote

1) movement of cargo via the motor protein
2) movement of the filament
3) bending of the filament

Flagella

-longer than cilia
-found singly or in pairs
-movement occurs by a whiplike motion
-contain internal structure called axoneme

Cilia

-shorter than flagella
-cover all parts of the surface of the cell
-contain internal structure called axoneme

Axoneme

-contains microtubules, the motor protein dynein, and linking proteins
-2 single central microtubules, 9 doublet microtubules connected to central microtubules by radial spokes
-microtubules grow from basal bodies

Basal bodies

-anchored to cytoplasmic side of plasma membrane
-microtubules form a triplet structure
-provide site for microtubules to grow

Movement of Flagella and Cilia

-requires ATP hydrolysis
-dynein is activated and exerts a force that bends the microtubules
-dyneins in base are activate first, followed by dyneins closer to the tip
-resulting movement propels the organism

Nucleus

-organelle found in eukaryotic cells that contains most of the cell's genetic material
-internal compartment enclosed by the nuclear envelope
-10 to 20% of cellular volume

Endomembrane system

-includes nuclear envelope that encloses nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and peroxisomes
-some of the membranes have direct connections to one another; others pass materials to each other via vesicles

Vesicles

-small membrane-enclosed spheres that pass materials through organelles of the endomembrane system

Nuclear Pores

-formed where inner and outer nuclear membranes make contact with each other
-provide a passageway for the movement of molecules and macromolecules into and out of the nucleus

Chromosomes

-found inside the nucleus
-composed of genetic material (DNA) and many types of proteins that help to compact the chromosome to fit inside of the nucleus
-the complex formed by DNA and these proteins is called chromatin
-each chromosome is located in a distinct chromosome territory

Nuclear Matrix

-consists of two parts:
1) the nuclear lamina - composed of intermediate filaments and line the inner nuclear membrane
2) intermediate nuclear matrix - connected to the lamina and fills the interior of the nucleus
-serves to organize chromosomes within the nucleus

Nucleolus

-region in nucleus of non-dividing cells
-where assembly of ribosome subunits (RNA molecules) occurs
-ribosomal proteins are produced in cytosol and imported to nucleolus where they assemble with RNA molecules to form ribosomal subunits

Endoplasmic Reticulum (ER)

-network of membranes that form flattened, fluid filled tubules called cisternae
-ER lumen is the internal space of the ER enclosed by the ER membrane

Rough ER

-outer surface is studded with ribosomes
-Functions:
1) sorting proteins
2) insertion of newly made proteins into ER membrane
3) attachment of carbohydrate to proteins and lipids - glycosylation

Smooth ER

-continuous with the rough ER but lacks ribosomes
-functions in diverse metabolic processes
-surface area of smooth ER membrane provides space for enzymes to play metabolic roles
-in liver, detoxifies harmful organic molecules and plays a role in carbohydrate metabolism
-accumulate calcium ions in ER lumen and regulates their release for cellular processes
-enzymes in smooth ER are critical in synthesis and modifications of lipids

Golgi apparatus

-consists of a stack of flattened membranes that enclose a single compartment
-cis Golgi is close to ER membrane, trans Golgi is near plasma membrane, and medial Golgi is in between
-3 overlapping functions:
1) processing
2) protein sorting
3) secretion

Processing in Golgi

-glycosylation continues in the Golgi (mainly in the medial Golgi)
-proteolysis - enzymes called proteases cut proteins into smaller polypeptides

Secretion from Golgi

-Golgi packages different types of of materials into secretory vesicles that later fuse with the plasma membrane and release their contents to outside of the plasma membrane
-secretory pathway - proteins are synthesized into the ER, travel to the Golgi, and are transported to plasma membrane by vesicles for secretion
-exocytosis - last stage when vesicles fuse with the plasma membrane (in reverse it is called endocytosis)

Lysosomes

-small organelles found in animal cells that lyse macromolecules
-contain many acid hydrolases
-can break down carbs, proteins, lipids, and nucleic acids
-digest substances that are brought into cell by endocytosis
-break down cellular molecules and macromolecules to recycle their building blocks to make new molecules and macromolecules (process called autophagy)

Acid Hydrolases

-hydrolytic enzymes that use a molecule of water to break a covalent bond
-function best at an acidic pH

Vacuoles

-prominent in plant, fungal, and some protist cells; less prominent in animal cells
-made from fusion of many smaller membrane vesicles
-different functions in different types of cells

Vacuoles in animal cells

-used to temporarily store materials or transport substances
-sometimes called storage vesicles

Vacuoles in plant cells

-plant cells have a large central vacuole that occupies 80% of cell volume
-membrane of central vacuole is called tonoplast
2 major purposes of central vacuole:
1) stores large amounts of water, enzymes, and inorganic ions
2) performs a space-filling function; large size of vacuole exerts pressure on cell wall called turgor pressure. if plant is dehydrated and pressure is lost it will wilt. turgor pressure is necessary for plant and cell structure and growth.

Vacuoles in protists

-maintain cell volume: water filled contractile vacuoles expand as water enters the cell, and once it reaches a certain size the contract and expel the water outside of the cell
-degradation: some protists engulf food into phagocytic or food vacuoles where digestive enzymes break down macromolecules

Peroxisomes

-small organelles found in all eukaryotic cells
-consist of single membrane that encloses a fluid filled lumen
-hundreds are in typical eukaryotic cell
-premature peroxisomes form from ER, addition of proteins and lipids makes mature peroxisomes, which then can divide to make more peroxisomes
-catalyze certain chemical reactions, typically those that break down molecules by removing H or adding O
-in humans, large amounts are found in liver
-contain enzyme called catalase that breaks down hydrogen peroxide into water and oxygen gas

Glyoxysomes

-specialized organelles in plant seeds that are similar to peroxisomes
-contain enzymes that are needed to convert fats to sugars

Membrane transport

-some plasma membrane proteins function to transport essential nutrients or ions into the cell, and others are involved in the export of substances
-plasma membrane in selectively permeable (allows only certain substances in and out)

Cell signaling

-plasma membranes of all cells contain receptors that recognize signaling molecules (either environmental agents or molecules secreted by other cells)
-once signaling molecules bind to receptors, a series of steps occur and cell responds to signal

Cell adhesion

-in animal cells
-protein-protein interactions among plasma membranes of cells promote cell to cell adhesion
-allows cells in multicellular organisms to interact and recognize each other

2 Semiautonomous organelles in eukaryotes

1) mitochondria
2) chloroplasts
-can grow and divide to reproduce themselves
-arent completely autonomous because they depend on other parts of the cell for their internal components

Mitochondrion

-has an outer membrane and an inner membrane separated by intermembrane space
-inner membrane is highly folded to form projections called cristae which greatly increases the surface area of the inner membrane where ATP is made
-compartment enclosed by inner membrane is called mitochondrial matrix
-primary role is to make ATP
-converts chemical energy stored in covalent bonds of organic molecules into a form that can readily be used by cells
-breakdown of molecules to simpler molecules releases energy that is used to make ATP
-also involved in synthesis, modification, and breakdown of several types of cellular molecules

Chloroplasts

-organelles that can capture light energy and use some of that energy to synthesize organic molecules such as glucose (called photosynthesis)
-found in nearly all species of plants and algae
-contains outer and inner membrane with intermembrane space between
-third membrane called the thylakoid membrane forms flattened, fluid filled tubules that enclose a single compartment
-tubules stack on top of each other to form granum
-stroma is compartment between inner membrane and thylakoid membrane
-thylakoid lumen is enclosed by thylakoid membrane
-plastid

Plastids

-plant organelles
-derived from unspecialized proplastids
-various types are distinguished by synthetic abilities and pigments
-chloroplast have green pigment and give plants their color
-chromoplasts function in synthesizing and storing the yellow, red, and orange pigments of carotenoids (give fruits, flowers, and leaves in autumn their color)
-leucoplasts lack pigment molecules and synthesize and store starch

Mitochondrial genome

-chromosomes found in the mitochondria
-composed of a single, circular chromosome

Chloroplast genome

-chromosomes found in chloroplasts
-composed of a single, circular chromosome
-larger than mitochondrial genomes

Nuclear genome

-chromosomes found in the nucleus of the cell

Binary fission

-how mitochondria and chloroplasts are produced
-splitting in two
-genome is duplicated and the organelle divides into two separate organelles

Symbiotic relationship

-when two species live in direct contact with each other

Endosymbiosis

-a symbiotic relationship in which the smaller species (the symbiont) lives inside the larger species

Endosymbiosis theory

-proposes that mitochondria and chloroplasts originated from bacteria that took up residence within a primordial eukaryotic cell and gradually changed to mitochondria and chloroplasts
-chloroplasts derived from cyanobacteria that have the ability to carry out photosynthesis
-mitochondria derived from a-proteobacteria which enabled cells to synthesize more ATP

Sorting signals

-aka traffic signals
-short stretches of amino acid sequences that direct proteins to their correct cellular location

Cotranslational sorting

-occurs when proteins are destined for the ER, Golgi, lysosome, vacuole, plasma membrane, or secretion
-synthesis of protein begins in cytosol and stops temporarily until ribosome is bound to the ER membrane. after this, translation resumes and polypeptide is synthesized into ER lumen or membrane
-first step of sorting begins while translation is occuring

Post-translational sorting

-sorting that happens after translation is finished
-occurs when proteins are destined for nucleus, mitochondria, chloroplasts, and peroxisomes

ER signal sequence

-sorting signal that directs polypeptides to the rough ER membrane
-as the ribosome is making the polypeptide in cytosol, the ER signal sequence emerges and is recognized by a signal recognition particle

Signal recognition particle (SRP)

-2 functions:
1) recognizes the ER signal sequence and pauses translation
2) binds to a receptor in the ER membrane which docks the ribosome over a channel protein (SRP is then released and translation resumes through the channel)

Coat proteins

-facilitates vesicle formation
-coat is shed after a vesicle is released from one compartment

V-snares

-proteins that are incorporated into the vesicle membrane
-type of v-snare depends on type of cargo the vesicle carries

T-snares

-recognize v-snares in vesicle membranes and the vesicle fuses with the membrane containing the t-snares
-recognition between v-snares and t-snares ensures that a vesicle carrying specific cargo moves to correct target membrane in the cell

Chaperones

-keep proteins that are destined for the mitochondrial matrix in an unfolded state when they are made in the cytosol
-receptor proteins in the mitochondrial membrane recognizes matrix-targeting sequence
-because it is in its unfolded state, mitochondrial protein can be threaded through channel in mitochondrial membrane (protein is released from chaperone as this occurs and protein adopts active structure once threaded into the matrix)

Systems biology

-view of living organisms in terms of their underlying network structure

4 Parts that make up eukaryotic cell system

1) nucleus
2) cytosol
3) endomembrane system
4) semiautonomous organelles

Nucleus

-houses the genome
-genome plays key role in producing the proteome through gene expression
-gene regulation is important in creating specific cell types

Cytosol

-important coordination center for cell function and organization
-coordination of responses to environment
-coordination of metabolism
-synthesis of proteome

Endomembrane system

-includes nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane

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