Biology lecture

Question 1

Light microscope (LM)

Answer 1

Visible light is passed through the specimen and then through glass lenses. The lenses refract (bend) the light in such a way that the image of the specimen is magnified as it is projected into the eye or into a camera

Question 2

3 imp. Parameters in microscopy

Answer 2

Magnification- ratio of an objects image size to its real size .

Resolution- a measure of the clarity of the image ; it is the minimum distance two points can be separated and still be distinguished as separate points.

Contrast- the difference in brightness between the light and dark areas of an image this includes staining or labeling cell components to stand out visually.

Question 3

Electron microscope (EM)

Answer 3

Focused a beam of electrons through the specimen or onto its surface .

Resolution - inversely related to the wavelenght of the light (or electrons) a microscope uses for imaging ,and electrons beams have much shorter wavelengths than visible light.

Disadvantage - methods used to prepare the specimen kill the cells.

Question 4

Scanning electron microscope (SEM)

Answer 4

Useful for detailed study of the topography of a specimen .

The electron beam scans the surface of the sample ,usually coated with a thin film of gold. The beam excites electrons on the surface ,and these secondary electrons are detected by a device that translates the pattern of electrons into an electronic signal sent to a video screen.
The result is an image of the specimens surface that appears 3 dimensional .

Question 5

Transmission electron microscope (TEM)

Answer 5

Used to study the internal structure of cells .

TEM aims an electron beam through a very thin section of the specimen ,much as light microscope aims light through a sample on a slide.
Specimen has been stained with atoms of heavy metals ,which attach to certain cellular structures ,thus enhancing the electrons density of some parts of the cell more than others.Electrons passing through the specimen are scattered more in the denser regions ,so fewer are transmitted .

Question 6

Microscopes are the most important tools of CYTOLOGY & BIOCHEMISTRY

Answer 6

Cytology- the study of cell structure.

Biochemistry- the study of the chemical processes (metabolism) of cells.

Question 7

Cell fractionation

Answer 7

Technique for studying cell structure and function .

Enables researchers to prepare specific cell components in bulk and identify their functions ,a task not usually possible with intact cells.

Question 8

Prokaryotic cell Ex: of domains and what it is and DNA found ..

Answer 8

Ex: Bacteria and Archaea

DNA concentrated in a region that is not membrane enclosed called the nucleoid

Question 9

Eukaryotic cell Ex: of domains and what it is and DNA found ..

Answer 9

Ex: Protosts,fungi, animals and plants

DNA is an organelle called the nucleus which is bounded by a double membrane .

Interior of cell is called cytoplasm refers only to the region between the nucleus and plasma membrane .
Within the cytoplasm of a eukaryotic cell suspended in cytosol ,are a variety of organelles of specialized cells form and function.

Nucleus houses most of the cells DNA
. Nucleus-Contains most of the genes .

Ribosomes -use information from the DNA to make proteins

Nucleus envelope- encloses the nucleus separating its contents from the cytoplasm.
Nuclear envelope double membrane. Two membranes each a lipid bilayer with associated proteins .

Intricate protein structure Pore Complex - lines each pore and plays an imp. role in the cell by regulating the entry and exit of proteins and RNA .

Nuclear side of envelope is lined by Nuclear Lamina -a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope.

Within the nucleus ,the DNA is organized into discrete units called Chromosomes ,structures that carry the genetic information.

The complex of DNA and proteins making up chromosomes is called Chromatin.

A prominent structure within the non-dividing nucleus is the NUCLEOLUS which appears through the electron microscope as a mass of densely stained granules and fibers adjoining part of the chromatin

Question 10

what Ribosomes are?

Two cytoplasmic locales that ribosomes build :

Answer 10

Are complexes made of ribosomal RNA and protein ,are the cellular components that carry out protein synthesis

Two cytoplasmic locales : FREE RIBOSOMES suspended in cytosol while
FREE RIBOSOMES -> most proteins function within the cytosol; ex’s are enzymes that catalyze the first steps of sugar breakdown .
BOUND RIBOSOMES are attached to the outside of the endoplasmic reticulum or nuclear envelope .
BOUND RIBOSOMES ->Make proteins that are destined for insertion into membranes, for packing within certain organelles such as lysosomes,or for export from the cell (secretion).

Question 11

Endomembrane system

Answer 11

Includes the nuclear envelope,the endoplasmic reticulum ,golfi apparatus ,lysosomes and various kinds of vesicles and vacuoles and the plasma membrane .

Question 12

Endoplasmic reticulum (ER) 
Endoplasmic means “within the cell “
Reticulum means “ little net” 

what it is

Answer 12

An extensive network of membranes that it accounts for more than half the total membrane in many eukaryotic cells .

The ER. separates the internal compartment of the ER ,called the ER lumen (cavity) or cisternal space from the cytosol.

Question 13

Smooth ER -outer surface lacks ribosomes

Rough ER- studded with ribosomes on the outer surface of the membrane and thus appears rough through the electron microscope.

Functions :

Answer 13

Smooth ER : functions in diverse metabolic processes,which vary with cell type.
These processes include synthesis of lipids, metabolism of carbohydrates ,detoxification of drugs and poisons ,and storage of calcium ions.

Enzymes of smooth ER are imp in the synthesis of lipids,including oils,steroids ,and new membrane phospholipids .

Other enzymes of the smooth ER help detoxify drugs and poisons ,especially in liver cells .Detoxification usually involves adding hydroxyl groups to drug molecules ,making them more soluble and easier to flush from the body.

Also stores calcium ions .
In muscle cells ,for ex the smooth er membrane pumps calcium ions from the cytosol into the ER lumen.

Rough ER functions : aids in synthesis of secretory and other proteins from bound ribosomes ; adds carbohydrates to proteins to make glycoproteins ; produces new membrane.

Most secretory proteins are GLYCOPROTEINS: proteins with carbohydrates covalently bonded to them .The carbohydrates are attached to the proteins in the ER lumen by enzymes built into the ER membrane.

Question 14

Golgi apparatus :shipping and receiving center

Answer 14

We can think of the golgi as warehouse for receiving ,sorting ,shipping ,and even some manufacturing .

Products of the ER such as proteins are modified and stored then sent to other destinations.

Consists of flattened membraneous sacs- cisternae- looking like a stack of pita bread .

The two sides of a golgi are cis and trans act as the receiving and shipping departments of golgi apparatus.
Cis= same side ,located near the ER
Transport vesicles move material from the ER to the golgi apparatus .

Trans= opposite side ,gives rise to vesicles that pinch off and travel to other sites.

Products of the endoplasmic reticulum are usually modified during their transit from the cis to the trans region of the golgi apparatus .

Golgi function: modification of proteins ,carbohydrates on proteins and phospholipids ; synthesis of many polysaccharides ; sorting of golgi Products ,which are then released in vesicles.

Question 15

Lysosome :digestive compartment

Answer 15

What is a lysosome: a membraneous sac of hydrolytic enzymes that many eukaryotic cells use to digest (hydrolyze) macromolecules

Lysosome Function : breakdown of ingested substances ,cell macromolecules ,and damaged organelles for recycling .

Phagocytosis - amoebas and many other unicellular eukaryotes eat by engulfing smaller organisms or food particles.

Autophagy - lysosomes also use their hydrolytic enzymes to recycle the cells own organic mayerial.

Question 16

Vacuoles def. & variety of functions in diff kinds of cells

Answer 16

Vacuoles are large vesicles derived from the endoplasmic reticulum and golgi apparatus .
Function- digestion ,storage ,waste disposal ,water balance ,plant cell growth and protection.

Food vacuoles - formed by phagocytosis

Contractile vacuoles - pump excess water out of the cell ,thereby maintaining a suitable concentration of ions and molecules inside the cell .

plants - small vacuoles can hold reserves of imp organic compounds such as the proteins stockpiled in the storage cells in seeds.

Central vacuole - mature plant cells contain central vacuole which develops by the coalescence of smaller vacuoles . Plays a major role of growth of plants cells which enlarge as the vacuole absorbs water enabling the cell to become larger with a minimal investment in new cytoplasm.

Question 17

Mitochondria and chloroplasts change energy from one form to another .

Answer 17

Mitochondria -sites of cellular respiration, the metabolic process that uses oxygen to drive the generation of ATP by extracting energy from sugars ,fats, and other fuels.

Chloroplast found in plants and algae , are the sites of photosynthesis. This process in chloroplasts converts solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from carbon dioxide and water.

Question 18

Peroxisome

Answer 18

Peroxisome - contains enzymes that transfer hydrogen atoms from certain molecules to oxygen ,producing hydrogen peroxide (H2O2) as a by product ; h2O2 is converted to water by another enzyme.

Question 19

Similarities btw mitochondria and chloroplasts

Answer 19

Endosymbiont theory -which states that an early ancestor of eukaryotic cells engulfed an oxygen using non photosynthetic prokaryotic cell.
Eventually, the engulfed cell formed a relationship with the host cell in which it was enclosed becoming an endosymbiont (a cell living within another cell) .

Question 20

Mitochondria: Chemical Energy Conversion

Answer 20

Each of the two membranes enclosing the mitochondrion is a phospholipid bilayer with a unique collection of embedded proteins .

The outer membrane is smooth ,but the inner membrane is convoluted ,with infoldings called CRISTAE.

The inner membrane divides the mitochondrion into two internal compartments.
The first is the inter-membrane space, the narrow region btw the inner and outer membranes. The second compartment ,the MITOCHONDRIAL MATRIX ,is enclosed by the inner membrane. The matrix contains many different enzymes as well as the mitochondrial DNA and ribosomes.

Question 21

Chloroplasts: Capture of Light Energy

Answer 21

Contain the green pigment chlorophyll .

Inside the chloroplast is another membraneous system in the form of flattened ,interconnected sacs called THYLAKOIDS .
Some regions ,thylakoids are stacked like poke chips ;each stack is called GRANUM,plural GRANA.

Fluid outside the thylakoids is the STROMA ,which contains the chloroplast DNA and ribosomes as well as many enzymes.Membrane of the chloroplast divide the chloroplast space into 3 compartments :
The inter-membrane space ,the stroma, and the thylakoid space.

Chloroplast is a specialized member of a family of closely related plant organelles called PLASTIDS.
1.Type of Plastid
AMYLOPLAST ,colorless organelle that stores starch (amylose) particularly in roots and tubers.

2.Type of Plastid
CHROMOPLAST, which has pigments that give fruits and flowers their orange and yellow hues.

Question 22

Peroxisomes: Oxidation

Answer 22

Is a specialized metabolic compartment bounded by a single membrane.

Peroxisomes contain enzymes that remove hydrogen atoms from certain molecules, molecules and transfer them to oxygen (O2) producing hydrogen peroxide (H2O2)

Peroxisomes grow larger by incorporating proteins made in the cytosol and ER, as well as lipids made in the ER and within the peroxisome itself.

Question 23

The cytoskeleton is a network of fibers that organizes structures and activities in the cell . And its role .

Answer 23

Cytoskeleton- a network of fibers extending throughout the cytoplasm.

The cytoskeleton plays a major role in organizing the structures and activities of the cell.

Roles of cytoskeleton: Support & Motility
Give mechanical support to the cell and maintain its shape.

Cytoskeleton provides anchorage for many organelles and even cytosolic enzyme molecules.

Cell motility includes both changes in cell location and more limited movements of cell parts .
CELL MOTILITY- requires the interaction of the cytoskeleton with motor proteins.
Cytoskeleton and motor proteins work together with plasma membrane molecules to allow whole cells to move along fibers outside the cell.
Inside the cell, vesicles and other organalles often use motor protein “feet” to “walk” to their destinations along a track provided by the cytoskeleton.

The cytoskeleton also manipulates the plasma membrane, bending it inward to form food vacuoles or other phagocytic vesicles.

Question 24

Three types of fibers that make up the cytoskeleton .

Answer 24

Microtubules ,the thickest .
Structure: hollow tubes
Diameter: 25nm with 15nm lumen
Protein subunits : tubulin, a dimer consisting of a-tubulin and B-tubulin.
Main functions: Mantainenance of cell shape; cell motility ; chromosome movements in cell division; organalle movements.

Microfilaments (Actin filaments) ,the thinnest
Structure: 7nm
Protein subunits: Actin
Main functions: Maintenance of cell shape ; changes in cell shape ; muscle contraction ; cytoplasmic streaming (plant cells) ; cell motility ;cell division (animal cells)

Intermediate filaments ,are fibers with diameters in a middle range .
Structure: Fibrous proteins coiled into cables
Diameter: 8-12nm
Protein subunits: One of several different proteins (such as keratins)
Main functions: Maintenance of cell shape; anchorage of nucleus and certain other organelles ; formation of nuclear lamina.

Question 25

Microtubules

Answer 25

Hollow rods constructed from a globular protein called tubulin.

Each tubulin protein is a dimer,a molecule made up of two subunits . A tubulin dimer consists of two slightly different different polypeptides,a- tubulin and B -tubulin.

Microtubules shape and support the cell and serve as tracks along which organelles equipped with motor proteins can move ;also involved with separation of chromosomes during cell division.

In animal cells ,microtubules grow out from a CENTROSOME,a region that is often located near the nucleus and is considered a “microtubule organizing center” .
Within the centrosome is a pair of CENTRIOLES ,each composed of 9 sets of triplet microtubules arranged in a ring.

In eukaryotes ,a specialized arrangemwnt of microtubules is responsible for the beating of FLAGELLA and CILIA microtubule- containing extensions that project from some cells.

Question 26

Microfilaments (Actin filaments)

Answer 26

Are thin solid rods .
Called actin filaments bc they are built from molecules of ACTIN ,a globular protein. A microfilament is a twisted double chain of actin subunits .

The structural role of microfilaments in the cytoskeleton is to bear tension.(pulling forces)

Microfilaments are well known for their role in cell motility.Thousands of actin filaments and thicker filaments of a motor protein called MYOSIN interact to cause contraction of muscle cells.

In plant cells, actin myosin interaction contributes to cytoplasmic streaming, a circular flow of cytoplasm within cells. This movement ,which is especially common in large plant cells ,speeds the distribution of materials within the cell.

Question 27

Intermediate filaments

Answer 27

Named for their diameter which is larger than the diameter of microfilaments but smaller than that of microtubules .

Intermediate filaments are only found in the cells of some animals ,including vertebrates .

Each type is constructed from a particularly molecular subunit belonging to a family of proteins whose members include the keratins in hair and nails.

Intermediate filaments are more permanent fixtures of cells ,and intermediate filaments also persist .
Are specially sturdy and play an important role in reinforcing the shape of a cell and fixing the position of certain organelles .

Other intermediate filaments make up the nuclear lamina ,which lines the interior of the nuclear envelope .In general intermediate filaments seem to function together as the permanent framework of the entire cell.

CELL WALL- extracellular structure of plant cells .the wall protects the plant cell ,mantains its shape and prevents excessive uptake of water .
Microfibrils made of the polysaccharides cellulose are synthezised by an enzyme called cellulose synthase and secreated to the extracellular space,where they become embedded in a matrix of other polysaccharides and proteins.
Young plant first secretes a relatively thin and flexible wall called the PRIMARY CELL WALL.Btw primary walls of adjacent cells is the MIDDLE LAMELLA, a thin layer rich in sticky polysaccharides called pectins. (PECTIN is used as a thickening agent in jams and jellies.)
Other cells add a SECNDRY CELL WALL btw the plasma membrne and the prmry wall.Scndry wall often deposited in several laminated layers ,has a strong and double matrix tht affrds the cel protection and support.

Extracellular MATRIX (ECM) main ingredients are glycoproteins and other carbohydrate containing molecules secreted by the cells. (Recall glycoproteins are proteins with covalently bonded carbohydrates.
Most abundant glycoprotein of most animal cells is COLLAGEN,which forms strong fibers outside the cells. The collagen fibers are embedded in a network woven of secreted PROTEOGLYCANS ,which consist of a small core protein with many carbohydrate chains covalently attached. 
Some cells are attchd to the ECM BY ECM glycoproteins such as FIBRONECTIN .fibronectin and other ECM proteins bind to cell surface receptor proteins called INTEGRINS tht r built into the plasma membrane. Integrins span the membrane and bind on their cytolasmic side to associated proteins attached to microfilaments of the cytoskeleton. 
Integrin-integrate 

Cell junctions connect neighboring cells in plants and animals . Plants have plasdesmata that pass through adjoining cell walla.Animal cells have tight juncions ,desmosomes,and gap junctions.
TIGHT JUNCTIONS- plasma membranes of neighboring cells are very tightly pressed against each other ,bound together by specific proteins,prevents leakage of extracellular fluid across a layer of epithelial cells.
DESMOSOMES- fastening cells together into strong sheets ,attach muscle cells to each other in a muscle. 
GAP JUNCTIONS ( communicating junctions)- provide cytoplasmic channels from one cell to an adjacent cell ,consist of membrane proteins that surround a pore through which ions ,sugars amino acids ,and other small molecules may pass . Gap junctions necessary for communication btw many types of tissues ,such as heart muscle ,and in animal embryos.