1. Strand separation, strands that avoid excress coiling. Helicase unwinds, topoisomerase regualtes the winding

2. RNA is used a primers. Primase

3.DNA polymerase incorporated nucleotides--adding to the 3' end

4.Proofreading by DNA polymerase 

5. Leading strand is made continuously 3'-5'

6. Lagging strand made in pieces called Okasaki fragments (DNA polymerase added to the 3' end

RNA sequences cut out and replaced by DNA, done by a different DNA polymerase 

Gap connected by DNA ligase 

1. Lose piece of DNA- a deletion of 1-many nucleotides

2. Add a piece of DNA- duplications 

3.Rearrange DNA- insertions, inversions, translocations 

-Breaks in DNA that are improperly repaired

-Double strand break, ends loses nucleotides- put back together 

There is proofreading by DNA polymerase that is highly efficient 

or 

methylation-directed mismatch repair 

Excision repair- cut out and replaced 

Processes that repair, read, regulate, DNA inthecells often depend on DNA hybridization 

Dependent on

-Tempurature 

-Length

-Base pair compositon 

1. Allows us the generate large amounts of DNA from almost undetectable amounts of DNA 

2. Allows us to find one particular region - one gene, in a mix of a million unrelated DNA fragments 

-look up the sequence of genes 

-make primers, that match the beginning and end of  the gene

-make a mixture of DNA, two primers, dATP,dTTP, dGTP, dCTP, DNA polymerase, special Taq

DNA--> RNA--> Protein 

DNA- storage of info 

RNA- copies info that is needed at a certain time, directs synthesis of protein 

Protein- acutal functional machinery, enzymes and structural proteins 

TATAAT often found 10 bases away from start

-Proteins called transcription factors bind to the DNA ( fall off once polymerase starts making RNA)

-The RNA polymerase binds and seperates the DNA strands

-The polymerase moved downstream

A region where the protein-coding is interrupted with nucleotides that do not code for amino acids

mRNA

ribosomes

aminoacytl tRNAs

Translation factors (helper proteins)

GTP

Messelson and Stalh 

-It shows that new DNA is half old DNA and half new DNA

mad-cow disease

-The proteins aren't folded correctly, if a correctly folded protein is mixed with an incorrectly folded one, the incorrect one can catalyze incorrect folding 

Introns are recognized by specific DNA sequence at the boundaries

-GTAAGT at one end and the CAG at the other

-The spliceosome is a complex of proteins and RNAs that recognizes these sequences and cuts out the intron 

L-shaped with about 80 nucleotides

One end has the anticodon 

The other end has an amino acid attached covalently 

60% RNA, called rRNA (4 different strands of RNA)

40% protein, many small polypeptides 

The enhancer sequences are found up to 20,000 bps from transcript start site

There are multiple transcription factors and DNA binding sites 

Proteins activated and inactivated by hormones , signaling mlcs like cAMP, proteins , phosphorylation 

4.6 x10⁶ bps ,  4,300 genes 

1 gene for 1000 bases 

38 x 10 ⁶ bps, 10,000 genes 

one gene for 4,000 bases 

119 x 10⁶ bps

26,000 genes 

180 x 10⁶ bps 

13,600 genes 

one gene for each 13,000 bases

3000 x 10⁶ bps 

25,000 genes 

One gene for each 100,000 bases 

The genes are much bigger

Coding region isn't bigger

Proteins are about the same size

5' region is bigger 

3' is a bit bigger 

Introns can be very large 

Genes have many introns (10 or mot is not unusual) 

There are many exons, not all are included in mRNAs

One gene can give rise to many variations in protein

It is packaged with proteins- chromatin (DNA + proteins) 

Core of 8 proteins names histones 

DNA is wrapped around histones 2 times (200bps) 

Beads on a string structure

The nucleosome structure has to be modified when genes are transcribed 

(partially unwound from nucleosomes) 

Partly unfold then refold 

Protein complexes do the remodeling 

A key regulatory feature

Histones have "tails" at N-terminus that can be activated by specific enzymes 

This blocks the + charge, makes it less tighly bound (activates transcription) 

It regulates what genes will be inherited by inactivating them 

Cloning is to make genetically identical copies 

1. PCR to get a small amount of the gene 
2. Cut the end with restriction endonucleases (enzyme made by bacteria, cut only DNA at pallindromes, makes sticky ends)
3. Cut plasmid DNA with the same endonuclease 
4. Mix human gene and plasmid (sticky ends will bind, ligate with ligase) 
5. Transform the bacteria (put in cell) 
6. Grow bacteria on a medium with penicillin

It is a DNA circle 

1. Origin of replication, in bacteria will be replicated very accurately by the bacterial enzymes 
2. Gene for antiobiotic resistance (penicillin) 

Oxygen 65%

Carbon 18.5%

Hydrogen 9.5%

Nitrogen 3.3%

Calcium 1.5%

Phosphorus 1%

Amino -NH₂ 

Hydroxyl -OH

Carboxyl - [image]

Phospahte- [image]

[image]

Bacteria

Archea

Eukaria 

Start: Hydrogen, ammonia, methane 

End: Sugars, 11 amino acids, 6 bases, fatty acids

Monomers: simple sugars 

Polymers : polysacharrides (complex sugars) 

Function: energy + structure 

Monomers: Amino acids

Polymers: Polypeptide chains (proteins)

Function: Structure, enzymes 

1. Primary structure- L & N terminals
2. Secondary structure- α helix (H bonds) β sheet 
3. Tertiary 3d whole structure 
4. Quarterey- if more than one polypeptide structure 

Nucleoid 

Cytoplasm

Cytosol

Ribosomes 

Nucleus ( nucleolus) 

plasma membrane

Golgi apratus 

RER, SER

Cytoskeleton

centrioles 

mitochondria 

• Cells are the fundamental units of life
• All organisms are composed of cells 
• All cells come from pre-existing cells 

• Found in the cytoplasm and inside the mitochondria and chloroplasts 
• Proteins are synthesized under the direction of nucleic acids 

RER- has ribosomes on it 

-segregated proteins and transports them 

-proteins can be chemically modified 

SER- no ribosomes 

-site of hydrolysis of glycogen 

-site of synthesis of lipids and sterols 

• Receives proteins from the ER to further modify them 
• Concentrates, packages, and sorts proteins before they are sent out 
• Some polysaccgarides for plant wall are synthesized here 

• Contain digestive enzymes 
• Site where macromolecules are hydrolyzed into their monomers 

• Converts the potential chemical energy of those fuel mlcs into a form the cell can use- ATP (cellular respiration) 

• Supports the cell and maintains shape
• Provideds cellular movement 

Microfilaments are made of actin

Myosin+ Micro- drive muscle action 

• Form rigid internal skeleton 
• Made of tubulin 
• Serve as a track for motor proteins (kinesin, dynein) 

They are speacialized mlcs that use energy to change their shape and move

Kinesin (- to +) 

Dynein (+ to -) 

N to C terminus 

3' end 

Purines: A adenine, G guanine 

Pyrimidines : C cytosine, T thymine, U uracil 

Look at all the human genes 

1. Use PCR

2. Spot of DNA at a marked spot on the glass 

3. Prepare mRNA for tumor and normal cells (use color coding by dye)  

4. Soak the slide in RNAs, they bind to the gene from which they are derived 

5. Determine how much is on each slide