MCDB 1A: Cell Biology

epitope

the antigen's binding site -- used in process of finding a protein in a cell

How do we find a protein in the cell?

an antibody is used to bind to a specific antigen's epitope. A secondary antibody tagged w/a fluorescent cmpd is added and binds to primary antibody. The image can be seen w/a fluorescent microscope.

Cell theory: what is it and who discovered it

all life comes from preexisting life -- discovered by Louis Pasteur .

Why are cells so small?

Large SA:V ratio allows for quicker rate of diffusion for monitoring what goes in and out of a cell. We want to bring in nutrients and release waste

Unicellular

a single cell, like bacteria. Bc they're single cells, they can develop into biofilm or communities like coral

Multicellular

many cells, like humans. Carry out different functions

What are the 3 major domains of life?

Bacteria, Archaea, Eukarya
BA= prokaryotes E=eukaryotes (fungi, protists, plants, animals)

What is the cell wall in prokaryotes made of?

peptidoglycan

How many membranes do prokaryotes have?

some have 2 membranes: the outer and inner

What is the inner membrane in a prokaryotic cell called?

periplasmic space

Where is DNA stored for a prokaryotic cell?

the nucleoid contained in the cytoplasm

What is the flagella?

a tail that allows the cell to swim. Can make bacteria spin: clockwise is a forward motion while counterclockwise is TUMBLING

What is the pili?

It's used for sex amongst bacteria; allows adhesion to other bacteria or surfaces.
It builds bridges between inferiors and exchange cytoplasmic material

What is another word for bacterial sex?

conjugation

bacterial sex

1. the pili connects them together
2. plasmids that enclose circular DNA are transferred through the pili during replication

Who discovered penicillin and how?

Alexander Fleming; grew penicillin mold and saw that bacteria couldn't grow near it. Discovered it killed bacterial cells and prokaryotes b/c they tend to have a cell wall

pencillin

it links peptides to sugars

What is the nucleolus?

a part of the nucleus with ribosomal genes. It's where ribosomes are made and assembled

What is the double membrane of the nucleus called and what supports it?

The nuclear envelope; it is supported by the lamina ['laminates"=support] and is contiguous of the ER. Holds different proteins and keeps nucleus from being compressed

What is the function of nuclear pores?

to regulate what comes in and out of a cell

What does a mutation in lamin-A cause?

early aging due to a collapsed nucleus

Describe the nuclear pore complex

it forms channels to allow passage of macromolecules and is important for trafficking. '
it is inside the nuclear envelope
- mRNAs binded to proteins go out while nuclear proteins go in. They must have a NLS attached in order to be recognized by the pores

cytosol

Where are proteins sythesized?

What protein recognizes a NLS?

an importin protein

NLS are ______ for import of protein into nucleus and __________ to direct a normally cytoplasmic protein into the nucleus

necessary; sufficient

What is C-myc?

a transcription factor; binds to DNA & turns on transcription of genes associated with replication.
- if turned back on unnecessarily it leads to cancer due to overexposure

What size are mitochondria?

about the size of a bacterial cell

What are the 3 functions of mitochondria?

1. produce energy, ATP
2. regulate calcium levels
3. regulate signals that mediate cell death

how do mitochondria grow and divide?

binary fission; pinching off in the middle

describe the structure of mitochondria

- it has an inner and outer membrane
- the outer is smooth and semipermeable
- the inner has a lot of folds (cristae)
- it has a matrix inside & mitochondrial localization sequence

what is the matrix?

- the matrix is the inner part of the mitochondria. It holds rna, trna, ATP synthases, and the electron transport chain.

a mutation in NADH leads to this

blindness

how is the pH gradient created and what is its purpose

it is part of the electron transport chain; hydrogen is pumped out to create a gradient across the inner membrane and then hydrogen flows in to create ATP.
- it is more acidic bc of the hydrogen drive
- it is a source of energy

what are plastids?

plants; they have a double membrane
- serve for photosynthesis and storage

what is the third membrane of the cytoplasm? Function?

the thylakoid; has proteins to bind chlorophyll & light pigments for photosynthesis

what is the middle of the cytoplasm called? What is its function?

the stroma; holds DNA & ribosomes

what are the 2 reactions of chloroplasts?

1. light --> takes energy from the sun to make O2, ATP, NADPH
2. dark --> use ATP and NADPH to make CO2 which is then sugar

endosymbiosis

the belief that mitochondria & chloroplast originated when large eukaryotes ate small prokaryotes

Peroxisomes

squared granular or crystalline arrays of enzymes that catalase to destroy toxic peroxides

Chromoplasts

pigment storage
- attract insects for pollinating

Plant vacuole (3 functions)

1. store toxic waste materials, food & nutrients
2. provide TURGOR aka stiffness for structure
3. can contain hydrolytic enzymes

leucoplasts- what and found where?

store starch, lipids or proteins
found in roots/nonphotosynthetic tissue

amyloplasts

store starch in potatoes

diabetes: 2 types

- high blood sugar, weakness, lethargy, and weight loss
- Type 1: juvenile--lack of insulin. The own immune system attacks beta cells of pancreas
- Type II: lack of insulin responsiveness

insulin: what and discovered by who

- peptide hormone secreted into blood by beta cells in pancreas
- binds to cell surface of muscle & fat cells : signals to import and store glucose
- discovered by Banting and Best

Endomembrane system

- network of closed membrane tubules, closed vesicles, and closed sacs
- divides cytoplasm in 2 (inside and outside membrane sacs)

3 Functions of Endomembrane System (STC)

Sequestration: of molecules/particles into cysternal space of vesicles
Transport: of sequestered molecules/particles from place to place w/in cytoplasm or to nucleus
Chemical modification

What makes up the endomembrane system?

1. Rough ER
2. Smooth ER
3. Golgi Complex
4. Vesicles

Rough ER

- has ribosomes attached
- is where integral membrane proteins & proteins that are secreted are made
- they're then translocated across the membrane into cysternal space

Smooth ER

- lipid synthesis
- detoxification of hydrophobic toxins

Golgi complex (post office)

- modifies carbs/proteins and ships them to the cell surface

Vesicles

- lysosomes, peroxisomes, secretory ; move to cell surface

Secretory pathway

rough ER --> golgi --> vesicles

Integral Membrane proteins

- secreted proteins with signal sequence at N-terminus
- direct ribosome to rough ER
signal removed in lumen of ER

Golgi apparatus

- has a cis/trans region
- vesicles from ER fuse with the cis region
- pinch off and fuse with medial and trans region
- pinch off trans and fuse with plasma membrane
- proteins inside vesicle secreted outside cell
- proteins in vesicle membrane inserted in plasma membrane

lysosomes

pinched off the golgi
- cells recycling center
- has digestive enzymes break down old cellular materials
- digest ingested bacteria

Tay-Sachs Disease

- lysosomal storage disease
- mutation in gene for hexose-aminidase A prevents lysosomes from breaking down certain membrane glycolipids
- leads to blindness, dementia, death

Phagocytosis

- when macrofuge ingests bacteria
- the phagosome fuses with lysosome to kill bacteria

Randy Schekman (schek, shake)

- isolated yeast cells that had secretion defects
- called them sec genes
encode membrane proteins that are involved in membrane traffic

The eukaryotic cytoskeleton's 3 different skeletal fibers

1. Microfilaments
2. Intermediate Filaments
3. Microtubules

Microfilaments

- made up of actin monomer
- polarization on plus end
- depolarization on minus end
- assembled by noncovalent bonds at the end of filaments
- partakes in treadmilling

Intermediate filaments

- build similar cable like filaments
- very stable
NOT DYNAMIC

Cell shape of microfilaments

- Stress fibers: bundled actin, maintain skin cell shape attach to focal adhesion
-Microvili: project from cell surface
most found in intestine
- actin join integrin

Movement of Eukaryotic Cytoskeleton

- DUE TO MICROFILAMENTS
proven bc of amoeba experiment
where Cytochalisin B blocks formation of microfilaments leading to movement

An example of intermediates

nuclear lamins
- support nucleus, attachment points for DNA
keratin filaments
- support skin, hair

Microtubules

- made of alpha beat tubulin dimers
- both ends have different properties

Two functions of microtubules

- Dynamic instablity: switching b/w growth and shortening ends
- Treadmilling

Function of microtubules in animals

centrioles surrounded by pericentriolar matrix
- centriole = set of 9 triplet microtubules

Dynein motor proteins

- help move the cilia and flagella
- negative directed
- make microtubules slide past each other

Type of microtubules vesicles use to move

- dynein and kinesin motors

How microtubules move

using the cilia or flagella!

Lipid rafts

-high in cholesterol --> less fluidity
- more rigid

3 types of molecule transportation

1. Passive diffusion
2. Carrier mediated diffusion
3. Active transport

Passive diffusion

- no ATP required
- from high concentration to low

Type of molecules that can't diffuse passively

- most water soluble
- any with a positive or negative charge
ex. sugars, AA, proteins

How do molecules that can't diffuse passively get across the membrane?

- channel proteins
ex. Ion channels

Carrier mediated diffusion

ex. glucose carrier protein
NO ENERGY REQUIRED

Active transport

- needs energy and ion gradient
- moves molecules against their concentration gradient

Uniporter

- active transport: moves one substance in one direction

Symporter

- active transport: two substances in same direction

Antiporter

- active transport: two substances moving in opposite directions

Types of gated ion channel

ligand binding and voltage

Endocytosis & exocytosis

moving complex molecules into cells
fusion of membrane vesicle to plasma membrane

3 types of endocytosis

1. Phagocytosis: large particles and small cells engulfed inside vesicles
2. Pinocytosis: cell drinking; taking up water into vesicles
3. Receptor mediated endocytosis: specialized form--takes in certain kinds of macromolecules into cells

Process of receptor mediated endocytosis

-clathrin coats cytoplasmic side of membrane
- creates a coated pit
- vesicle forms on cell surface
- gets brought into cytoplasm
- becomes uncoated and released

Cholesterol

- a steroid
- in animal membranes
- makes membrane less fluid

Endocytosis of LDL

- low density lipoprotein particles bind to LDL receptors at cell surface
- particles taken into clathrin coated vesicle
- vesicle uncoats, LDL binds off the receptor
- receptor forms new vesicle recycled to plasma membrane
- vesicle fuses with lysosome
- lysosome digests contents of vesicle releasing the cholesterol
- inserted into plasma membrane

Extracellular matrix

- GLUE
- connective tissue in animals
- acts as filter in kidneys
- instruct a cell what to be

basal lamina

- is between blood and urine
- separates kidney cells from blood vessel

collagen

most abundant protein in the body
- provides strength

cartilage

made of proteoglycans
found in joints

integrins

- on cell surface
- integral membrane proteins receptors for ECM
- dimer of 2 subunits

apoptosis

- programmed cell death
- due to lost attachment to matrix

plant cell walls

- made of cellulose
- rigidity and strength
- hold shape
- glue cells together
- limit entry of large molecules

cell junctions

1. cell-cell adhesion: holds tissues together
2. cell-cell communication: transport of molecules b/w cells

Animal cell junction: tight junction

link cells together
- prevent passage of materials between cells

animal cell junction: desmosomes

anchor to int. filaments
- give strength, hold cells together, coupled to keratin

gap junctions

cellular communication
- link cells
- form channels made up of CONNEXINS b/w proteins to allow passage of molecules

prokaryotic cell division

DNA replication, elongation, segregation, fission

Eukaryotic cell division

Mphase, G1, S phase, G2