The Genome Project

How complete is it?

How was it found, what type of sequenc?

10% of the genome is__ ____ ___ ___

97% complete

It was found using a shotgun sequence.

Long Intersperse Nuclear Elements

200,000 to 2,ooo,000

Ex. Insulin

A paper found some interesting about the cell...

What resolution did it look at and what did it find...

clue stuff about poly A arent true!

@ 5 nucleotide resolution, it found that

In terms of transcripts, mRNA may not have a poly A tail,

47% of transcripts never had a poly A tail,

36.9% of transcripts had poly A tail removed, 19.4% have a poly A tail...

Only 30% of mRNA associated with ribosomes had a poly A tail

has a really short half life

something about polyamines

1.water solvates proteins

2.helps determine protein structure

.3breating role of water

4. polar configuration not symmetrical

What can you tell me about Electrostatic Interactions

(4)

1.weak in water

2.can be changed

3.ions can change the ability to interact

4.salts can change the function of proteins

Example: Potassium acetate and Potassium Cl, quantitatively they are the same, qualitatively they are different, so graph will be!

What is the percentage of water in a cell?

How many different types of water are there?

70% of water

1 type

1%

20 types

1%

250 types

Percentage of amino Acids and precursors?

how many types?

.4%

100 types

.4%

100 types

Percentage of fatty acids and precursors?

Types?

1%

50 types

.2

~300 types

Percentage of macromolecules?

(Proteins, nucleic acids, and polysaccharides)

types

26%

~3000 types

What are the functions of sugars and precursors?

Give their percentage as well...

1% 250 types

1. Intermediate Metabolism (energy)

2. Signaling

I M S (I am sugar)

Give some examples of sugars

(4)

Glucose

Mannose

Galactose

Trehalose

~.4%

1. Building Blocks of Nucleic acids

2. Energy Currency

3. Coenzymes

4. Carrier Molecules

5. Redox Balace

1%

1. Intermediate Metabolism

2. Structural membrane formation

3. Beta Oxidation: Synthesis of Acetyl CoA in mitochondria

4. Cholesterol- membrane fluidity

5. Hormones and signaling

Amino Acids and Precursors

Function

Percentage in Cell

.4% , 20 types

Most of times L enantiomer, but you can find d enantiomer

1. Hormones, signaling type molecules

2. Metabolic Intermediates

3. Osmotic effects

4. Buffering Capacity

What can you tell me about

polar, non polar, acidic and basic amino acids?

In terms of R side chains

acidic side chains are attracted to water

non polar side chains are found on interior of proteins

electrostatic interactions can occur, such as van der waals forces can occur

Peptide four amina acids long

20 * 20 * 20 * 20 = 160,000

Avg protein is 300 amino acids long

What can you tell me about peptide bonds?

Loss of water molecule

amine forms with carboxyl group

N-terminus is start of protein

C-terminus is end of protein

N-terminus has a regulatory role

C-terminus has more catalytic effects

linear

amino acid sequence

3D structure of the polypeptide chain

Disulfide bonds

van der waals forces

globular

alpha helix + alpha helix

multiple alpha helices together

stable structure because of the amount of hydrogen bonding

alpha helices is a common secondary motif in protein structure

functional homology: subset of proteins

proteins as chunks of domain

evolutionary sequence

protein that has distinct role over time

18,000

388 of 18,000 have a protein kinase domain

66 of 18,000 have DNA/RNA helicase domain

43 SH2 domains

70 immunoglobulin domains

88 DNA binding homeodomain (have bigger role based on sheer numbers)

28,000 genes

1000 immunoglobulin domain

500 protein kinase domains

Receptor Interacting Protein

has a kinase domain that doesn't phosphorylate. RIP has a role in cell death

assymetry leads to lipid rafts

plasma membrand of animal cells can transiently assemble into specialized domains

artificial phospholipid bilayer formed from an aqueous suspension

association of certain proteins with lipids

rafts are thicker than other parts of bilayer, and can better accomodaten certain proteins

storage of fats that later get retrieved as building blocks for membrane and food source

neutral lipids, triglicerides

hydrophobic only, don't have hydrophilic head groups

form rapidly when exposed to high concentrations of fatty acid

form from discrete regions of ER membrane

ones that have Chlorine in head group

Phosphatidycholine

Sphingomeyelin

ones that contain a terminal primary amino group

PS

PE

Phospholipid Signaling

function

and key intermediates

Phosphatidylinosital

can be cleaved by phospholipase C

to get IP3, what is left over is DAG

IP3 opens calcium channels and and activates PKC

sugar containing lipid molecules

found on non cytosylic monolayer of lipid bilayer

extremely assymetrical

made from sphingosene

What is the fucntion of glycolipids

1. Electrical conduction

2. cell to cell recognition

3. receptor function

4. protection against low ph

5. extracellular signaling

Peripheral Membrane Protein

protein that is retained in a membrane by virtue of one or more domains that span or are embedded in the lipid bilayer

1. Single alpha helix (carboxyl group of one amine acid interacting with N-H group of another amino acid 4 amino acids away.

2. multi pass (creating coiled coiled domain) rigid and stable

3. beta barrel

4. alpha helix on cytosolic side

5. attached to cytosolic side by fatty acid or prenel group

6. oligosaccharide linked to a fatty acid constituent

7. protein protein interaction with van der waals

8. extracellular side as well

by covalent attachement

amide

ester

thioester

how hydrophobic or hydrophilic and amino acid is

positive value- indicates that free energy is required to transfer to water and the value assigned to this index is the amt of energy required

proteolytic cleavage of one loop to create two fragments that stay together and function normally

expression of the same two fragments from seperate genes gives rise to similar protein that functions normally

1. Post translation cleave

2. creat multiple subunits and bring them together

1. tertiary folded membrane structure

2. transmembrane proteins inserted into lipid bilayer by PROTEIN TRANSLOCATORS.

3. They get surrounded by lipids in the bilayer.

4. Folds into final structure and makes protein protein contacts that replace lipid contacts.

5. finally form coiled coiled domain thru lateral diffusion.

1. biological catalyst

2. bind of active site of substrate

3. couple two ractions, creating ATP

1. control the synthesis of the enzyme, how much you make.

2. control the degradation rate (p57 stabilization)

3. control the concentration of the substrate

4. Allostery

5. Cooperativity

6. Post translational modifications

7. metabolon

The name of the prevailing model for membrane structure

______ _______ _______

model

singer fluid mosaic

the membrane state that is too rigid and leaks due to lack of flexibility is know as the _____ state.

what is the the state that is very fluid?

gel

sol

Describe one of the three discussed mechanisms for driving active transport.

(be specific)

1. coupled transporter cpl uphill transport of solute across structured membrane to the downhill transport of another

2. ATP driven pump- cpl uphill transport to hydrolysis of ATP

voltage gated

ligand gated

mechanically gated