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FIU / English / ENG 4023 / Basic principles of a cell.

Basic principles of a cell.

Basic principles of a cell.

Description

School: Florida International University
Department: English
Course: Cell Biology
Professor: Amy saldana-caboverde
Term: Spring 2017
Tags: Microscopes, Macromolecules, prokaryotes, eukayrotes, cloning, Enzymes, Thermodynamics, metabolism, and Cell Biology
Cost: 50
Name: First Cell Bio Exam Study Guide
Description: These notes cover everything we've learned from chapter 1, 2, 3, and 18
Uploaded: 01/30/2017
11 Pages 29 Views 6 Unlocks
Reviews


Exam 1 Study Guide 


Basic principles of a cell.



Chapter 1,2,3, and 18 

Chapter 1 

Cell Theory:

∙ Cell theory proposes that:

1. All organisms are composed of one or more cells

2. The cell is the basic unit of life

3. Cells can only arise from preexisting cells

Basic Principles of Cell:

∙ The most basic principle of the cell is life and death

∙ The basic properties of the cell are that:

1. Cells are highly complex and organized 

a. Complexity means that there is a great number of parts to the  whole

b. Organized means that although the cell has many parts, it still  maintains order to effectively regulate the cell


Differences between prokaryotes and eukaryotes.



2. Cells possess a genetic program can to use it 

a. Cells have DNA which contain genes that store information about the organism and the function of the cell

b. RNA converts DNA information to protein

3. Cells can produce more of themselves through reproduction a. Cells can divide through mitosis which makes copies of  themselves or through meiosis to make cells with a different  genetic combination

4. Cells acquire and use energy 

a. They get them from the sun

b. Animals get energy from plants in the form of glucose

5. Cells carry out many chemical reactions 

a. These reactions require enzymes

b. The total chemical reactions in a cell is it’s metabolism


What is an ocular lens?



6. Cells engage in mechanical activities Don't forget about the age old question of What is the principle task in management?

7. Cells can respond to stimuli 

a. They detect stimuli through receptors

8. Cells are capable of self-regulation Don't forget about the age old question of What are the three functions of the nervous system?
Don't forget about the age old question of What is the scientific method of economics?
Don't forget about the age old question of What type of things does geology study?

a. Cells can control themselves with regulatory mechanisms 9. Cells evolve 

a. All living organisms came from a single, common ancestral cell  called the last universal common ancestor (LCA)

Differences between Prokaryotes and Eukaryotes

Prokaryotes

Eukaryotes

∙ Structurally simpler

∙ Genetic material is in nucleoid which lacks membrane

∙ Have a single, circular  

chromosome

∙ Its DNA has no histone  

proteins

∙ Cytoplasm almost lacks  

membrane structures

∙ Directed intracytoplasmic  communication is less  

important

∙ Mostly uses simple diffusion ∙ Cytoskeleton much simpler ∙ No mitotic spindle

∙ No true fertilization, but do  conjugate (give pieces of DNA  to other cells)

∙ Have simple locomotor  

mechanisms

∙ Movement accomplished by  flagellum which rotates

∙ Live in biofilms, which are like  communities

∙ Metabolically sophisticated ∙ Include Bacteria and Archaea ∙ Divide through Binary Fission

∙ Structurally complex

∙ Genetic material present in  nucleus which has nuclear  

envelope

∙ Contains more DNA  

∙ Have a number of separate,  linear chromosomes

∙ DNA is tightly packed with  histone proteins (forms  

chromatin)

∙ Cytoplasm contains a great  diversity of structures which  

serve to compartmentalize the cytoplasm with specialized  

activities

∙ Has interconnecting channels  and vesicles that transport  

material

∙ Cytoskeleton much more  

complex and participates in  

movement and support

∙ Has mitotic spindle

∙ Have complex locomotor  

mechanisms

∙ Posses more simple flagella ∙ Includes Protists, Fungi, Plants, and Animals

∙ Different cells conduct  

specialized activities

∙ Can differentiate their cells  into specific cell types

We also discuss several other topics like What is the prior restraint on heart of the first amendment?

Similarities of Prokaryotes and Eukaryotes

∙ Share identical genetic language, metabolic pathways, and structural  features

∙ Both have nuclear region with genetic material

∙ Both posses ribosomes which assemble proteins

∙ Both reproduce

Model Organisms: Representative organisms used to study basic processesDon't forget about the age old question of Two or more bases that don’t mix, but are stably dispersed.

Stem Cells:

Hematopoeitic Cell (HSC) 

∙ Is an adult stem cell

∙ Can replace the tissue they were found in (autologous treatment) ∙ Do not face immunological rejection as they are taken from the same  patient being treated

Embryonic Stem Cells (ESC) 

∙ Can differentiate into any cell

∙ Are capable of forming tumors

∙ Face immune rejection

Induced Pluripotent Stem cells (iPS) 

∙ Fully differentiated cells that were turned back into a pluripotent stem  cells

∙ No embryo needed

∙ Increases cancer risk

∙ Immune rejection risk

∙ Can cause genetic abnormalities

Direct Cell Reprogramming:

∙ Concerts a differentiated cell into another differentiated cell without going through the stem cell step

Cells Size:

∙ Limited by area/volume ratio

∙ Limited by cytoplasmic volume as it would take longer to synthesize the  messages it needs

∙ Limited by diffusion as it would take longer to get to the material if the  cell was too big

Chapter 18 

Light Microscope:

∙ Light source, situated at the bottom of the microscope illuminates the  specimen

∙ Condenser lens focuses the light from the light source to the specimen

∙ Objective lens gathers light from specimen and forms an enlarged image ∙ Ocular lens forms an enlarged real image

∙ Total magnification = magnification of ocular lens times the magnification  of the objective lens

∙ Resolution is the amount of detail you can see in an image o The ability to see two close points as separate

o Limited by diffraction because if 2 points overlap, the place from  which each point came from cannot be distinguished

o The shorter the wavelength of light, the better the resolution ∙ Visibility is the ability of an object to be seen

o Specimen and background must have different refractive indexes o Dyes can makes cell visible

Bright-Field Microscope: 

∙ Illuminates the species with a bright background so the specimen can be  contrasted with light and seen

o Suited for specimens of high contrast (with dye)

o Most cells must be sectioned by killing cell with fixative ∙ Think: the field of the cell is bright in this microscope

Phase-Contrast Microscopy: 

∙ Makes highly transparent specimens visible

∙ Converts differences in refractive indexes of each part of cell into  differences in light intensity

∙ Better for unstained living cells

∙ Think: The phases of the cells are contrasted

∙ Differential interference contrast gives a 3D image look to it

Transmission Electron Microscopy (TEM): 

∙ Form images using electrons transmitted through a specimen ∙ Used to study internal structure of cell

∙ Has short wavelength so better resolution

o Wavelength depends on the speed electrons travel

Scanning Electron Microscopy (SEM): 

∙ Image is formed by electrons reflected back from specimen o Image formation is indirect

∙ Used to examine surfaces of objects

∙ Specimens must be dehydrated and coated with a layer of metal for the  electron to target

Fluorescence Microscopy 

∙ Allows you to see cellular events occurring at molecular level o Can do this with fluorophore

o Light (short wavelength) excites fluorophore which emits light of a  visible wavelength

∙ Fluorophores absorb photons of a certain wavelength and release a  portion of energy in longer wavelengths

∙ Fluorescent proteins can be synthetically attached to molecules or they  can be natural as they are in jellyfish

o fluorescent proteins in jellyfish (GFP) make it glow

o can incorporate GFP into other organisms in the coding region of  interest to track the protein in the cell after it is synthesized ∙ Variants of GFP have been generated by mutagenesis to produce different colors

∙ Can be used to simultaneously track 2 proteins

∙ Some synthetic fluorophores can target specific molecules but others  need assistance to target specific substrates

Immunofluorescence: 

∙ Uses antibodies to detect proteins in cells

∙ Antibodies have a high degree of specificity and immunofluorescence  takes advantage of this

o Can be used to distinguish proteins

∙ To obtain a specific antibody, an antigen is injected into an animal  repeatedly and then their blood is drawn getting what’s called an  antiserum

o Antiserum with many antibodies that bind to the same antigen is a  polyclonal

o Monoclonal only contains one antibody

∙ Direct immunofluorescence complexes antibodies with fluorescent  molecules which are then incubated in cells and observed with a  fluorescent microscope

∙ Indirect immunofluorescence used two antibodies: an unlabeled primary  antibody that binds to an antigen and a labelled antibody that reveals the  location of the primary antibody

Western Blot: 

∙ Antibodies are used to identify a particular protein

Polyacrylamide Gel Electrophoresis (PAGE):

∙ Based on migration of proteins in electric field

∙ The heavier the protein, the less they move

∙ Movement also depends on shape and size

SDS-PAGE: 

∙ PAGE carried out in sodium dodecyl sulfate (SDS) which is charged ∙ These proteins are denatured

∙ SDS linearizes protein and imparts an equivalent negative charge ∙ Migration is ONLY based on mass

Recombinant DNA:

∙ Molecules with various DNA sequences from more than one source

Restriction Endonucleases:

∙ Restriction enzymes

∙ Can cleave backbone of DNA

∙ Used in bacteria to protect against viruses

∙ Every enzyme recognizes different DNA sequence

∙ Allows DNA to be dissected into specific set of fragments DNA Cloning:

∙ To clone DNA, a piece of DNA is placed in a host cell, using a vehicle, then  the cell is left to replicate to daughter cells, thus increasing the amount of desired DNA

∙ In eukaryotes, DNA can be packaged in a virus and injected (transduction) o Can also introduce naked DNA into cells (transfection)

Transgenic Animals:

∙ Can act as animal models for disease

∙ Genetically modified animals that carry foreign genes

Knockout Mice:

∙ Mice that lack a functional gene

∙ Can be used to study human diseases

Chapter 2 

∙ Covalent bonds are a pair of electrons shared between two atoms o Are stable

∙ Atoms want full outer shell

∙ Nonpolar molecules have no partial charge

o Their atoms have similar electronegativity

o Unually nonreactive

∙ Polar molecules have atoms with different electronegativity resulting in  partial charges

∙ Cation=ion with positive charge

∙ Anion=ion with negatice charge

∙ Free radicals=atoms with a single unpaired electron

o Very unstable

∙ Superoxide radicals are oxygens that snatches an extra electron  becoming a radical

o Destructive to cell

∙ Superoxide Dismutase (SOD) is an enzyme that destroys these radicals ∙ Rats with increased levels of SOD live longer

∙ Although some studies suggest free radicals cause aging, others show  that it actually increases life span

∙ Noncovalent bonds are attractive forces between two atoms with opposite charges

o Do NOT share electrons

o Are weak

∙ Ionic bonds are attractions between charged atoms

∙ Hydrogen bonds are attractive forces between a partially charged  hydrogen in a polar molecule and an electronegative atom o Easily broken

o Their strength, however, is additive

∙ Hydrophilic=water loving

o Polar molecules

∙ Hydrophobic=water fearing

o Nonpolar molecules

∙ Hydrophobic interactions are the interactions between nonpolar molecules that want to escape their polar environment

Life Supporting Properties of Water:

1. Highly symmetric

2. Covalent bonds in water are highly polarized

3. All 3 molecules in water can form hydrogen bonds

Water is important because:

1. It interacts with many chemical groups

2. Maintains structure and function of macromolecules

∙ Acid donates hydrogen atom

∙ Base accepts hydrogen atom

∙ Amphoteric molecule can act as either base or acid

∙ pH is the acidity of a solution measured by the concentration of hydrogen  ions

∙ Biological processes are sensitive to pH so require buffers which resist  changes in pH

∙ Biochemicals are compounds produced by living organisms ∙ Functional groups are groups of atoms that act as a unit and give similar  properties to organic molecules

Carbohydrates: 

∙ Sugars

∙ Stores energy

∙ Glycosidic bonds are covalent bonds that join sugars together ∙ Polysaccharides are polymers of sugar

Lipids: 

∙ Hydrophobic nonpolar molecules tha can dissolve in organic solvents ∙ Fatty acids are long unbranched hydrocarbon chains with a carboxyl o Hydrocarbon is hydrophobic

o Carboxyl is negatively charged and hydrophilic

o Saturated fats are compact

o Unsaturated fats have a double that creates a kink which makes  them not so compact

∙ Fat is a glycerol molecule linked to 3 fatty acids

o Reserves energy for long term use

∙ Steroids are built around 4 ring hydrocarbons

∙ Phospholipid is a glycerol molecule attached to two fatty acids and a  phosphate

o Fatty acid is hydrophobic

o Phosphate is hydrophilic

Proteins: 

R-Groups of Proteins:

1. Polar charged

a. Aspartic acid, glutamic acid, lysine, arginine, histidine b. Can form ionic bonds

2. Polar, uncharged

a. Serine, threonine, glutamine, asparagine, tyrosine

b. Have partial charges

c. Can form hydrogen bonds

3. Nonpolar

a. Alanine, valine, leucine, isoleucine, methionine, phenylalanine,  tryptophan

b. Hydrophobic

4. The other amino acids

a. Glycine, cysteine, proline

Structures of proteins:

Primary:

∙ Specific amino acid sequence

∙ Provides information on protein’s 3D structure

Secondary:

∙ Conformation of a portion of the protein

∙ Alpha helix = coiled, cylindrical confromation

∙ Beta sheets = folded conformation

∙ Sites of protein without conformation are where most of the activity  occurs

Tertiary:

∙ Conformation of the ENTIRE protein

∙ Stabilized by covalent bonds

∙ Fibrous protein=elongated shape

∙ Globular protein=compact shape

∙ May reveal similarities between the functions of proteins

Quaternary:

∙ Have more than one polypeptide

Additional Information on Proteins:

∙ Multiprotein complexes have more than one protein

o Not very stable

∙ Proteins are able to fold themselves

∙ Secondary structure formation and compaction occur at the same time ∙ Tertiary structure of protein can be determined by primary structure ∙ Molecular chaperones help the proteins fold

∙ Chaperonins let proteins fold within them so they don’t interact with the  environment

Nucleic Acid: 

∙ Constructed of nucleotides

∙ Stored genetic information

∙ Two types:

o Deoxyribonuclease(DNA)

o Ribonuclease(RNA)

∙ Pyrimidines

o Have single rings

o Cytosine in both DNA and RNA

o Uracil in RNA, Thymine in DNA

∙ Purine

o Has 2 rings

o Adenine and guanine in both DNA and RNA

o Keep in mind Purine is Pure As Gold

∙ Ribozymes have catalytic activity

Chapter 3 

First Law of Thermodynamics: 

Energy cannot be created or destroyed

Second Law of Thermodynamics: 

Events in the universe go from a higher state of energy to a lower state of  energy

∙ Free energy is the change in the energy available to do work o Tells you which direction the process will proceed

∙ If delta G is negative, the reaction will be spontaneous or, in other words,  thermodynamically favored

∙ If delta G is positive, the reaction is not favored and not spontaneous ∙ Reactions with a large positive delta G need an input of energy which can  be supplied if ATP is coupled with the reaction

∙ Many of the reactions for metabolism is at equilibrium, but there needs to  be some that are not to make them irreversible

o These irreversible reactions keep the pathway going a single  direction and regulators the cell

∙ Continual flow of materials into and out of cell allows cell’s metabolism to  be at a steady state where the concentration of products and reactants  remain relatively constant

Enzymes: 

∙ Mediators of metabolism

∙ Speeds up reaction

∙ Contain cofactors which are non-protein components that carry out the  activities enzymes can’t do

∙ Substrates bind to active site on enzyme

∙ Enzymes speed up reaction by binding tightly to the high energy  transition state of a substrate which stabilizes it and helps it overcome the energy barrier of the reaction

Properties of enzymes:

1. Only small amounts are needed

2. Can be recycled

3. Does not effect thermodynamics of reaction

4. Highly specific to a substrate

5. Can be regulated to meet the needs of a cell

Mechanisms of Enzyme Catalysis:

1. Substrates have to be in the proper orientation for the enzymes to bind 2. Enzymes have amino acids that can act as an acid or base which alters  the electrostatic properties of substrate, allowing it to bind 3. Atoms of enzyme can shift to accommodate substrate

Enzyme Kinetics:

∙ Maximal velocity is the velocity when the enzyme reaches its saturation  point or its full capacity in catalyzing reactions

∙ Michaelis constant is the substrate concentration at half the maximal  velocity

o Tells you about the affinity of an enzyme

o The higher the constant, the lesser the affinity

Enzyme Inhibitors: 

∙ Irreversible: bind to enzyme with a covalent bond

∙ Reversible: bind loosely to an enzyme

∙ Competitive inhibitors are reversible inhibitors that compete with the  substrate for the active site

∙ Noncompetitive inhibitors bind to a different site of the enzyme and don’t  compete with the substrate

Overview of Metabolism:

∙ Anabolic pathways: synthesis of molecules

∙ Catabolic pathways= break down of molecules

Oxidation and Reduction:

LEO says GER: Lose Electrons Oxidation (says) Gain Electrons Reduction

ATP Production: 

∙ Oxidative Phosphorylation:

o Indirect way of making ATP

o ATP is formed using the energy released during the transport of  electrons  

∙ Substrate-level Phosphorylation:

o Direct way of making ATP

o Phosphate group is transferred from 1,3 bisphosphoglycerate  directly to ADP by phosphoglycerate kinase to make ATP

Fermentation: 

∙ Regenerates NAD+ when oxygen levels are low or absent ∙ Humans can turn pyruvate to lactate when exercising to regenerate NAD+ ∙ Yeast turns pyruvate to ethanol to regenerate NAD+

∙ A cells’ reservoir of NADPH is its reducing power

o NADPH helps synthesize fats

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