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Cell Theory

All Living things made of cells; cells are smallest unit of life; cells come from other cells

All cells have:

Plasma Membrane

Symplast

Living part of cell

Apoplast

Outside of cell (environment)

Prokaryotic Cells (DNA)

dsDNA, long strand, circular, few proteins, "naked DNA"

Nucleoid

Region of the prokaryotic DNA

Prokaryotic Ribosomes

70S

CW protein Euk. vs Prok

Prok: peptidoglycan
Euk: Glycogen

Prokaryotic Cells DON'T HAVE

Membrane bound organelles, Complex Internal membranes (ER, Golgi), true cytoskeletons

Eukaryotic cells have

PM; Cytosol; Dual membrane organelles; haploid or diploid; complex internal membranes; cytoskeleton

Euk DNA

dsDNA; in chromatin structure most of the time; 50% DNA 50% Protein

Prokaryotic Simple -

ONLY HAPLOID

Euk Ribosomes

Large (80S)

Dual Membrane Organelles

Nucleus, chloroplast, mitochondria

Single Membrane Organelles

Lysosomes, peroxisomes, endosomes, vesicles

Unicellular Euk

Yeast paramecium, amoeba; reproduce by fission because of chromosomes and mitosis some genetic modification

Multicellular Euk

Complex organisms; reproduce sexually/asexually, sex: HIGH level of genetic modification

Storage carbs

Plants: Starch Animals: Glycogen

Peripheral vs Integral proteins

Peripheral can be washed off, attached to Phospho heads or other proteins. Integral can't be removed w/o destroying membrane embedded.

Glycoproteins

Sugars covalently attached to protein (on external side of PM)

Functions of Proteins

Enzyme, receptors, transport, cell recognition

Chromatin

DNA+Protein

Nucleolus

site of ribosome synthesis; rRNA made first, then assembled into ribosome

Nuclear Pore Complex

Regulates entry/exit of nucleus

Nuclear Lamina

Gives shape to nucleus

What is the outer membrane of the Nucleus continuos with?

The RER

Mito Outer Membrane is___, ___ allow anything up to a certain size

Permeable; porins

Mito Inner membrane acts as ___ has ___ to increase surface area also contains enzymes for ____

PM; cristae; ETC

Mito Matrix is filled with __ home of ____, also has _____ (___ version)

liquid; krebs cycle; DNA/Ribosomes, tRNA, rRNA; prokaryotic.

Chloro Reactions

Light in Grana (Contains Chlorophyll) Dark in Stroma

Chloro Stroma has __

Enzymes for photosynthesis, DNA ribosomes, Prok. Versions

Chloro membranes are similar to ___

Mito membrane

Endosymbiant Theory

Mito/Cplast may have evolved from small bacteria that were engulfed by larger bacteria during evolution of life

Evidence for Endosymbiant Theory

Both have Prok. features; 70S ribosomes, bacterial gene structure, few proteins on DNA,

Mito are distant relatives

of purple nonsulphur bacteria

Chloro are distant relatives

of cyanobacteria

Vacoule is bound by a

tonoplast

List of microbodies

Perioxisome,gloxysome, lysosome, ribosome,

Function perioxisome

breaks down peroxide

Gloxysome

breaks down fatty acids

lysosome

breaks down proteins, lipids, and nucleic acids

Ribosome

only organelle that DOESN'T have a membrane, composed of 2 subunits composed equally of rRNA and protein

Ribosomes have __ nucleotides

modified

Endomembrane system flow

Nucleus, RER, vesicles, Golgi, PM or lysosomes

Nucleus (Flow)

mRNA exits through nuclear pore to RER

RER (Flow)

Protein synthesized on ribosomes on sufrace. Enters lumen of ER where its modified

Golgi (Flow)

protein from ER is modified then transferred to PM/Organelles.

Glycosylation

Adding sugars to protein

SER

Site of lipid synthesis, drug detox, Calcium storage, connected with RER

Vesicle movement is

very specific, done via motor proteins and microtubule highway

Golgi's 2 sides

Forming/Cis side, faces ER.
Maturing/Trans side faces PM

3 Main components of cytoskeleton

Microtubules, microfilaments, intermediate filaments

Microtubules

Composed of tubulin (hollow) intracellular transport, spindle fibers

Microfilaments

composed of Actin, Located below PM, gives shape involved with different kinds of movement

Intermediate filaments

Can join between cells, nuclear lamina, scaffold of the cell, many different kinds of proteins are IF

Cell Wall - function

Protection from viruses, prevents lysing, gives shape to cell.

Cell Wall - structure

Fiber: Cellulose,
Hydrated Matrix: Hemicelloulose (carb), Extensin (Protein)
Adhesive: Pectins (carb)

CW formation

Primary CW formed first, Secondary CW formed second (2-3 layers)

CW is very ___ and ___ is tightly controlled

organized, structure

Middle Lamella

Composed of Calcium pectate, sticks cells together

Plasmodesmata

Entire outer pore complex of plant cell

Plasmodesmata function

Cell communication via SMALL chemical signals or electrical signals

Destotubulue

Connection between the ER's of both plant cells

Amount of Plasmodesmata depends on...

amount of cell communication

Extracellular Matrix is in what organism

Animals only

ECM Structure

Fiber: Collagen, elastin
Hydrated Matrix: Proteoglycan
Adhesive Molecule: Fibronectin, laminates

Gap Junctions (Connexons)

Connects Adjacent animal cells

Gap Junction Function

Communication via electrical signals (membrane potential) or small chemical signals

Main components of organic life

CHOPNS

4 Macromolecules

Carbs, Lipids, Nucleic Acids, Protein

5 bonds in organic molecules

Covalent, Disulphide, Ionic, Hydrogen, Hydrophobic interactions

Aldo vs Keto sugar

Aldo has carbonyl at the end of the chain 6 sided ring; Keto carbonyl in the middle 5 sided ring

If OH is below ring

Alpha form sugar

if OH is above ring

Beta form sugar

Bond between sugars

Glycosidic

Branches of sugars more common in ____ than ___

Glycogen; Starch

Types of polysach.

Storage Structure

Structure Polysach

Can't be broken down (beta bond) Cellulose

Storage Polysach.

Can be broken down (alpha bond)

Lipid Function

Structural, Store energy, signal molecules

Fatty Acids

Long chain HC w/ carboxyl group usually 12-20C

Phospholipid structure

Glycerol 2FA tails 1 P group - charged

FA-Phospholipids spontaneously form structures in order of complexity:

Micelles, film, bilayer

Steroids

Lipids, 4 ring structure

Steroid function

Structural (cholest) Signal (estrogen)

Terpene subunit

isoprene, 5C

NA Functions

Informational, Structural, enzymes

NA informational

DNA/RNA

NA Structural

Part of Ribosomes, 7S RNA part of SRP, snRNPs

NA enzymes

Ribozymes

Ribozymes

short RNAs that act as enzymes

NA structure

5C sugar, Nitrogenous base, Phosphate

If C2 sugar has OH

Ribose (RNA)

If C2 sugar has H

Deoxyribose (DNA)

Thymine vs. Uracil

Thymine has methyl while uracil has hydrogen

First NA has

5' Phosphate

Last NA has

3' Hydroxyl

Bonds between Nitrogenous bases

H-Bonds (3 for G-C, 2 A-T)

Bonds between backbones

Phosphodiester

Types of RNA

mRNA, rRNA, tRNA, snRNA, Ribozymes, Nucleotides, Nucleotide Derivs.

snRNA

small nuclear RNA, snRNPs

Nucleotide Derivs.

NADH, FADH2, NADPH, cAMP; high energy compounds involved in e- transport, redox reactions

DNA replication enzymes

Helicase, topoisomerase, SSBP, Primase, DNA poly 3, DNA poly 1, Ligase

PCR Purpose

Make millions of copies of a specific DNA sequence

Needed for PCR

Template DNA,
dnTPS (Deoxyribose Nucleotides, dA/G/C/TTPS)
2 Primers one for each strand
Buffer (needs Mg)
Enzyme - taq DNA poly

3 Steps of PCR

Denaturing, Annealing, Extension

Formula for amount of DNA made from PCR

2^n n=number of cycles

Two ways to do DNA fingerprinting

RFLP; PCR

Variable Number Tandem Repeat (VNTR)

How many times a DNA sequence appears

Protein Functions

Enzymes, structures, receptors, transport proteins, hormones, electron transport

Polar AA have

Carboxyl, Hydroxyl, Amino, Sulfhydrul
Charged: Carboxyl=Acidic, Amino=Basic

Bonds in Proteins

Disulfide, Hydrogen, Ionic, Hydrophobic Interactions

Disulfide bonds in proteins

Bend structure

Hydrogen in proteins

very common and important in proteins usually H + Amino or carboxyl

Primary Structure and Bonds involved

String of AA; peptide

Secondary Structure and Bonds involved

Alpha helix beta pleated sheet; H bonds

Tertiary Structure and Bonds involved

3D structure; Disulfide, ionic, hydrophobic interactions, H bonds

Quaternary Structure and Bonds involved

1+ subunit Disulfide, ionic, hydrophobic interactions, H bonds

Domain of Protein

Part of protein that does a specific function

Homeotic Gene

Genes that determine which parts of body from what body parts

Structural Motifs

Found in many proteins, do the same function

7TM

7 Transmembrane domains
Usually a G protein linked receptor
Found in both animals and plants same function

Types of structural motifs

Helix-Turn-Helix, Helix-Loop-Helix, Zinc Finger, Leucine Zipper All bind to DNA, transcription factors

Heat's effect on denaturation

Disrupts H and ionic bonds

pH's effect on denaturation

Disrupts charge of groups, ionic H bonds

Reducing Agent; Denaturation

Sulfhydrul bonds

Organic Solvent; Denaturation

Destroys entire structure

Which bond is NOT affected by denaturation?

Peptide

Few proteins ___ spontaneously

renature

Catalysts

Increase rate of reaction
Not used up by reaction
only small amount needed
Don't alter equilibrium

Steady State vs. Equilibrium

Steady state is in living cells, equilibrium in solutions

Characteristics of Enzymes

Specific, Efficient, Regulated

Substrates go through ________

activated transition states

Induced Fit Model

Enzyme confirms to substrate

Covalent Intermediates

Temporary covalent bonds between enzyme/substrate
Temp. Donation of H+ or e-
Enzyme can temp. stress substrate

Factors that affect enzyme activity

pH, Temp

small pH effect on enzyme

changes binding of protons on substrate, changes charge on sub/enzymes
may not be able to bind at all or as well

Large pH effect on enzyme

disrupt tertiary structure of protein
if partially unfolded, enzyme less active
if completely unfolded enzyme totally inactive

Additional factors needed for enzymes

Coenzymes, prosthetic group, Metal Ions

Coenzymes

Small organic molecules
Bind reversibly and noncovalentely to enzyme
Can be released

Prosthetic group

organic compound (heme)
Tightly bound to enzyme (covalent)
NEEDED FOR ENZYME TO FUNCTION

Metal Ions

Bind to enzyme or Pros. Group
Required for proper 3D structure

Allosteric Enzymes have ____ subunit

More than one

Catalytic vs. Regulatory

Cata: site of reaction, Reg: controls activity of catalytic site

Effector

small organic molecule that controls activity of enzyme

Feedback inhibition

products inhibit enzyme

Covalent Modification

Add or remove chemical groups from enzyme

Kinase

adds P group to enzyme

Phosphatase

removes P group from enzyme

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