Molec Bio Exam 3

Exon Shuffling

When exons are combined to create new genes

Vertical Gene Translation

From mother to daughter cell

Types of Horizontal Gene Translation

Transformation: Uptake from Environment
Transduction: Mediated by viruses
Conjugation: Bacterial “Sex”

Transposons

“Jumping Genes”, move around genome creating new genes at insertion
Requires “Transposase” enzyme to occur
Every organism has Transposons

Retrotransposons

Common in Eukaryotes

RNA intermediate phase

Converted to DNA via Reverse Transcriptase

Still requires Transposase

Virus Protein Covering

“Capsid”

Retroviruses/Proviruses

Must integrate into genome as dsDNA (antipararell)

Added to protein known as “Integrase”

LINEs/SINEs

Make up “Junk DNA”, often originating from pseudogenes, transposons, duplications

SNPs

Single Nucleotide Polymorphisms
Main way humans vary from one another
Used for DNA

Phospholipid Membrane Side Names

Outer leaflet
Inner leaflet

Most Common Plant/Animal Phospholipid

phosphatidylcholine
Choline = Phosphate = Glycerol = 2 Fatty Acid Tails
Double bonds saturate it

Phospholipid Movement Types

Flexion: Flexing of tails
Rotation: Spinning of Phospholipid
Flip-Flop: leaflet-to-leaflet movement, rare

Membrane Fluidity

Decreased by Tail Length, Sterol prescence, Saturated Fats

Flippases

Move phospholipids from outer to inner leaflet

Floppases

Move phospholipids from inner to outer leaflet

Scrambles Lipid Directions

Scramblases
Can be independent or dependent on Ca+

Smooth ER Phospholipid Depositing

Deposited into Cell Membrane’s Cytosolic (inside) Side before transport

Phospholipid Transport

Either independent or Done in vescicles

Membrane Protein Types

Transporters/Channels: Move materials through membrane

Anchors: Link cytoskeletal Proteins with extracellular matrix

Receptors: Involved in Cell Communications

Enzymes: Carry out reactions

Integral Membrane Protein Types

Transmembrane: Crosses bilayer
Monolayer (Leaflet) Associated: Associated with one side
Lipid Linked: Bonded to lipid in membrane

Pores

Made by Porins, Alpha Helices or Beta Sheets

Detergents

Amphipathic Molecules, best way to distrupt membranes

Cell Cortex

Part of Cytoskeleton

Has Spectrin Coils which meet at Actin Proteins
Attached via Attachment Proteins

Posttranslational Modifications

Proteins are often glycosylated with glycans, “high mannose sugars” to mature them

Glycoprotein/Glycolipid Complex

Glycocalyx, surface of cell
Cell Recognition, Protects Cell
Lubricates Cell

Recognize Carbohydrates on other cells

“Lectins”, transmembrane glycoproteins

Energy-Costing Cell Transport Means

Active Transport
Bulk Transport

Electrochemical Gradient

Cells are negatively charged

Have more salt/chloride in extracellular enviorn.

Have more potassium in intracellular enviorn.

Passive Transport Channels

Mechanically Gated
Ligand Gated (extra or intracellular ligands)

Voltage Gated

How water enters/leaves cell

Aquaporins

Active Transport Pumps

Coupled Reaction: Swap 2 substances, one thermodynamically favored

ATP Pump: ATP fights against gradient
Light Driven: Uses Light

Coupled Pumps:

Symport: 2 diff molecules in same direction

Antiport: 2 diff molecules in opposite direction

Globin

Allows for transport of oxygen molecule

Epithelial Cell Support Structure

Basal Lamina, an Extracellular Support Mat

Osmolarity

Amount of dissolved solutes in solvent

Where muscle cells store calcium

Action Potentials

Carried by voltage-gated channels

1: Cytosol starts off negatively charged

2: Change in charge balance opens gate, allowing potassium out

3: Extremity of voltage sensor is bent to block gate, closing it

4: Gate eventually reverts back to original state
This process repeats within a tube structure

Synaptic Vesicle

Acetyl-Choline Receptors

5 Transmembrane subunits, 2 bind to Acetylcholine
When both are bound, sodium-potassium transfer occurs

Hearing Gated Channels

“Fingertips” of stereocilia are linked by spring proteins, opened by stretching
This allows potassium inside vesicle
Depolarization causes vescicle output releasing neurotransmitters

Signal Sequence

A “Signal” sequence of RNA at the ends or center of proteins that signals the location of transport

Cytoskeleton of Nucleus

Nuclear Lamina, formed by Intermediate Filaments
Broken down by Kinases during Mitosis, reformed by Phosphotases

Nuclear Import Receptors

1: Bind to Nuclear Localization Signals, guide them to pores
2: Once inside cell seperate, then bond to Ran-GTP
3: Carries Ran-GTP out of cell, then dissociates

Nuclear Transport Energy

1: Ran-GDP in cytosol enters cell
2: Ran-GEF seperates GDP from Ran
3: Ran binds to GTP, leaves cell
4: Ran-GAP hydrolyzes Ran-GTP

Mitochondria/Chloroplast Protein Transfer

1: Proteins made in Translocators, TIM (inner) and TOM (outer)
2: Proteins with signal sequence enter translocator into membrane

Protein Production in ER

1: Ribosome with “Signal Sequence” bonds to other ribosomes in cytosol

2: Polysome line translocates RNA into membrane

ER Translocation

1: Signal Recognition Particle binds Ribosome Signal Sequence to Translocator location
2: After protein is formed, “Signal Peptidase” cuts it off

Double+ Pass Membrane Proteins

1: Hydrophobic Start-Transfer Sequence enters first, stopping at translocator
2: Stop-Transfer Sequence enters, stops at same place

Endosomes

Large vesicles containing nutrients, broken down by lysosomes

Exocytosis

Done by vesicles budding from Golgi

Cell budding process

1: Adaptin is binded to by Chlarathin coating, creating round shape
2: Bud is cut off by dynamin to create vesicle

Vesicle Docking

1: Rab Protein molecular markers bind to vesicles
2: Tether Protein binds onto vesicle
3: V-snare (on vesicle) binds to C-Snare (on membrane), allowing fusion

Glycosylation

1: “Dolichol” membrane lipid holding Oligosaccharide binds to Asparagine in “Oligosaccharyl Transferase” protein

Cis Vs. Trans Golgi

Cis Golgi is entry point for proteins, ER materials
Trans Golgi is exit point for proteins

Golgi Hole name

“Cisterna”

Golgi function

Folds proteins, adds high-mannose sugars, glycans

Constitutive Secretion

vs. Regulated, where Phospholipid Secretion is regulated via hormones/transmitters

Pinocytosis

“Cell Drinking” of nutrients in vesicles

Phagocytosis Steps:

Prokaryotes only

1: Particle/Body is enveloped by new membrane to create “Phagosome”
2: Phagosome fuses with the Lysosome, which degrades it

Autophagy

How cells get rid of damaged organelles
1: Organelle covered in membrane, “Autophagosome”
2: Merges with lysosome, which breaks it down

Nuclear Envelope

Bilayer Structure around Nucleus
Inner Layer is “Nuclear Lamina”, made from Intermediate Filaments

Intermediate Filaments

Nonpolar Antipararell Alpha Helices
N terminus: Unstructured, NH2
C terminus: COOH

Can form massive Alpha Helices of 8 tetramers or 32 Monomers

Intermed. Filament Types

Nuclear: Nuclear Lamina in animals
Cytoplasmic:
Keratin Filaments in epithilial cell
Vimenten-related in muscle, glial (support) cells
Neurofilaments in Nerve Cells

Nail Beds are made of

Secreted Keratin Filaments

Provide Stability to Axon Nodes

Neurofilaments

Plectin

Lets Intermediate Filaments bind to Cytoskeletal Proteins

KASH and SUN proteins

Bind to each other within membrane
KASH domain proteins bind to external particles
SUN domain proteins bind to Chromatin or Nuclear Lamina

Microtubules

Built by alternating alpha-beta “Tubulin” protein chains in a “Dimer”
Polar, Plus End is Positive, Minus End is Negative
13 Protofilaments make one Tubule

Tubilin Dimer Formation

Called “Nucleation”
Made from 13 Microtubules, form around “y-Tubulin” around “Centrosome”

Centrosome

Microtubule Organization Center
Contains 2 “Centrioles”, next to Matrix
Positive Microtubule End is inside Cytoplasm

Microtubule Instability

Composed of GDP-Tubulin with GTP-Tubulin “Cap”
If cap is ever degraded, whole structure falls apart

Protein-Microtubule Interactions

Nucleating Proteins
Sever Proteins
Stabilizing Proteins
Branching Proteins (augmin

Axon Terminals

Ridden by:
Kenisins (→ positive end)

Dyneins (→ negative end)

Become more tightly bound with ATP

Become more loosely bound on hydrolysis

Connect to Cargo by Adaptor Proteins

Cilia Vs. Flagella

Cilia move lipids, particles
Flagella move whole cells

Flagella/Cilia Structure

Ask what’s important about it

Allows Microtubule sliding

Dyenin

Microfilaments

“Actin Filaments”
Help with cell structure, division, mobility

“+” end at front, “-” end at back

Highly flexible

Actin “Treadmilling”

ATP bound Actin filaments break are hydrolyzed (+ end) after addition, eventually breaking off (- end), but stay same length

Forms Actin Filaments

ARP Complex

Myosin I

“Boots” move cargo across actin fibrils towards “+” end

Eukaryote Cell Movement

Cell sends out frontmost protrusions, crawling along substrate like slug

Driven by “Lamellipodium” actin filament network
“Filopodium” used to sense area in front of cell

Myosin II

2 “golf club” heads, and coiled tails which associate with one another in large structures

Branches out in both directions on actin filaments when uncapped, allowing for muscle stretching

Actin Filament Formation

“ARP Complex” Encourages the growing of actin filaments
Need to memorize other info