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BIO 20A FINAL EXAM
FINAL EXAM
106
Biology
Undergraduate 2
06/03/2012

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Term
What are the steps in replication?
Definition

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 

Term
What does DNA ligase do?
Definition
It connectsthe gaps in the Okasaki fragments
Term
What are point mutations?
Definition
A chang in the nucleotide
Term
What are the types of chromosomal mutations?
Definition

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

2. Add a piece of DNA- duplications 

3.Rearrange DNA- insertions, inversions, translocations 

Term
What causes mutations?
Definition

-Breaks in DNA that are improperly repaired

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

Term
What happens mistakes occur in mitosis and meiosis?
Definition
Usually lethal, but rare rearrangments persist
Term
What are silent mutations?
Definition
Redundant condons, in noncoding, nonregulatory regions
Term
What is the effect of a change in an amino acid?
Definition
Can be bad, rarely good, often neutral
Term
What is the effect of the change in stop codon?
Definition
Get a truncated protein
Term
What is the effect of a change in the regulatory region of DNA?
Definition
Get too little or too much protein
Term
How do cells repair mutation?
Definition

There is proofreading by DNA polymerase that is highly efficient 

 

or 

 

methylation-directed mismatch repair 

 

Excision repair- cut out and replaced 

Term
What effect does mutation have on living systems?
Definition
It drives evolution of organisms and biological processes
Term
What is DNA hybridization?
Definition

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

Dependent on

-Tempurature 

-Length

-Base pair compositon 

Term
What is the Polymerase chain reaction (PCR)?
Definition

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 

Term
How would you use PCR to isolate a human gene?
Definition

-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

Term
What is the central dogma of molecular bio?
Definition

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 

Term
What is transcription?
Definition
The copying of DNA to RNA- both in the language of nucleotides. DNA Is transcribed
Term
What is translation?
Definition
The converting of nucleotide sequence of RNA into the amino acid sequence of protein. RNA is traslated
Term
Steps of transcription
Definition

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

 

Term
What is the promoter?
Definition
The region of a gene where RNA polymerase binds
Term
What is an intron?
Definition

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

 

 

Term
What are exons?
Definition
They are expressed sequences of a gene
Term
What is the final step in making mRNA?
Definition
To add a 5' methyl-G  cap and a poly-A tail which mark the RNA as functional
Term
What is needed to make a protein?
Definition

mRNA

ribosomes

aminoacytl tRNAs

Translation factors (helper proteins)

GTP

Term
How can genes be controlled?
Definition
Transcriptionally (Gene copied into RNA), translationally (mRNA made into protein) , and post-translationally (Is the protein active?)
Term
Who came up with the semi-conservative replication idea using "heavy" and "light" N isotopes? What does it show?
Definition

Messelson and Stalh 

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

Term
How do proteins get folded correctly?
Definition
Folding occurs spontaneously, driven by the amino acid sequence.
Term
What are prions?
Definition

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 

Term
How does splicing occur?
Definition

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 

Term
What are tRNAs?
Definition

L-shaped with about 80 nucleotides

One end has the anticodon 

The other end has an amino acid attached covalently 

 

Term
What are ribosomes composed of?
Definition

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

40% protein, many small polypeptides 

Term
How does the regulation of transcription in Eucaryotes work ?
Definition

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 

Term
What is the size of the genome of E coli?
Definition

4.6 x106 bps ,  4,300 genes 

 

1 gene for 1000 bases 

Term
What is the size of the genome of Neurospora?
Definition

38 x 10 6 bps, 10,000 genes 

 

one gene for 4,000 bases 

Term
What is the size of the genome of Arabidopsis?
Definition

119 x 106 bps

26,000 genes 

Term
What is the size of the genome of Drosophila?
Definition

180 x 10bps 

13,600 genes 

 

one gene for each 13,000 bases

Term
What is the size of the Human genome?
Definition

3000 x 106 bps 

25,000 genes 

 

One gene for each 100,000 bases 

Term
How long is the molecule of DNA in a eukaryotic cell?
Definition
About 6ft
Term
What is the gene structure in eukaryotes?
Definition
There are no operons, genes with related functions typically scattered throughout the genome.
Term
What is the relative size of genes of eukaryotic cells to prokaryotic cells?
Definition

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 

Term
What is alternative splicing?
Definition

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

 

Term
How is DNA packaged?
Definition

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

 

Term
What are nucleosomes?
Definition

Core of 8 proteins names histones 

DNA is wrapped around histones 2 times (200bps) 

 

Beads on a string structure

Term
What is Chromatin remodeling?
Definition

The nucleosome structure has to be modified when genes are transcribed 

(partially unwound from nucleosomes) 

Partly unfold then refold 

Protein complexes do the remodeling 

Term
What is histone modification?
Definition

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) 

Term
What is DNA methylation?
Definition

It regulates what genes will be inherited by inactivating them 

 

Term
What is demethylation?
Definition
Turns on genes
Term
What is cloning and how do you do it?
Definition

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
Term
What is a plasmid?
Definition

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) 
Term
The human body is made of?
Definition

Oxygen 65%

Carbon 18.5%

Hydrogen 9.5%

Nitrogen 3.3%

Calcium 1.5%

Phosphorus 1%

Term
What are the functional groups ?
Definition

Amino -NH2 


 

Hydroxyl -OH


 

Carboxyl - [image]


 

Phospahte- [image]

[image]

Term
What are the three basic groups of life ?
Definition

Bacteria

Archea

Eukaria 

Term
What did Louis Pasteur conclude from his experiment ?
Definition
Nothing will spontaneously generate unless something from the outside falls in 
Term
What were the starting materials in Stanley Miller's experiment? What were the end materials?
Definition

Start: Hydrogen, ammonia, methane 

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

Term
What are the monomers, polymers and function of carbohydrates?
Definition

Monomers: simple sugars 

Polymers : polysacharrides (complex sugars) 

Function: energy + structure 

Term
What are the monomers, polymers and function of proteins?
Definition

Monomers: Amino acids

Polymers: Polypeptide chains (proteins)

Function: Structure, enzymes 

Term
Nucleic Acids?
Definition

Monomers: Nucleotides

Polymers: DNA, RNA 

Function: Information, protein synthesis 

Term
Lipids?
Definition

Monomers: Fatty acids, sterols

Polymers: Complex lipids 

Function: Energy, membrane 

Term
Ribose
Definition
[image]
Term
What is a condensation rxn?
Definition
Dehydration - H2O removed 
Term
What is a condensation rxn?
Definition
Break at H2O
Term
Protein Structure
Definition
[image]
Term
Polypeptide Bond
Definition
[image]
Term
Amino Acid structure
Definition
  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 
Term
Basic Nucleic Acid structure
Definition
[image]
Term
What are prokaryotic cells made up of ?
Definition

Nucleoid 

Cytoplasm

Cytosol

Ribosomes 

Term
What are Eukaryotic cells made of?
Definition

Nucleus ( nucleolus) 

plasma membrane

Golgi apratus 

RER, SER

Cytoskeleton

centrioles 

mitochondria 

Term
What is the cell theory?
Definition
  • Cells are the fundamental units of life
  • All organisms are composed of cells 
  • All cells come from pre-existing cells 
Term
Ribosomes
Definition
  • Found in the cytoplasm and inside the mitochondria and chloroplasts 
  • Proteins are synthesized under the direction of nucleic acids 
Term
Endoplasmic reticulum
Definition

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 

Term
Golgi Aparatus
Definition
  • 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 
Term
Lysosomes
Definition
  • Contain digestive enzymes 
  • Site where macromolecules are hydrolyzed into their monomers 
Term
Mitochondria
Definition
  • Converts the potential chemical energy of those fuel mlcs into a form the cell can use- ATP (cellular respiration) 
Term
Cytoskeleton
Definition
  • Supports the cell and maintains shape
  • Provideds cellular movement 
Term
What are microfilaments made of? What drives muscle action?
Definition

Microfilaments are made of actin

Myosin+ Micro- drive muscle action 

Term
Microtubules. What do they form? What are they made of ?
Definition
  • Form rigid internal skeleton 
  • Made of tubulin 
  • Serve as a track for motor proteins (kinesin, dynein) 
Term
What are motor proteins?
Definition

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

 

Kinesin (- to +) 

Dynein (+ to -) 

Term
Which way is DNA read in transcription and replication?
Definition
3'-5'
Term
In transcription, RNA is transcribed ___' to ___'
Definition
5' to 3' 
Term
The genetic code is....
Definition
unambiguous but redundant 
Term
Where does the removal of introns take place in eukaroytic cells?
Definition
In the nucleus 
Term
The joining of exons is catalyzed by...
Definition
spilceosomes 
Term
What does a promoter specify during transcription?
Definition
Where RNA polymerase initiates transcription and what strand will be used as a template 
Term
Where do capping and polyadenylation of mRNA occur and what is the purpose?
Definition
In the nucleus and they are important for translation and stability of mRNAs
Term
What is a major difference between RNA polymerase and DNA polymerase?
Definition
RNA polymerase doesn't require a primer like DNA polyermase does 
Term
Which way do tRNAs move along the ribosome?
Definition
A--> P --> E
Term
What do ribosomes do during translation?
Definition
Catalyze the formation of peptide bonds 
Term
A protein is synthesized from its ____ to ___ terminus as the ribosome moves toward the ___ end of the mRNA.
Definition

N to C terminus 

3' end 

Term
A bacterium contains a single gene encoding the tRNA that recognizes the codon UAC. DUe to a single base substitution, the gene now encodes a tRNA that recognizes the codon UAA. The mutation does not alter the ability of the tRNA to interact with the appropriate aminoacyl tRNA synthetase. What happens?
Definition
Some proteins will be longer than normal, some will be shorter than normall; some will be unaffected 
Term
A one base insertion just after the start codon will
Definition
most likely have a dramatic effect on the sequence of a protein 
Term
What is the function of the peroxysome?
Definition
To break down long chain fatty acids 
Term
Who came up with the one-gene one-enzyme theory ?
Definition
Beadle and Tatum 
Term
When lactose is absent what happens with the lac operon ?
Definition
The lac repressor binds to the lac operator, inhibiting transcription 
Term
ATP molecule
Definition
[image]
Term
NADH molecule
Definition
[image]
Term
What are the purines? Pyrimidines?
Definition

Purines: A adenine, G guanine 

 

Pyrimidines : C cytosine, T thymine, U uracil 

Term
Where are ribosomes made?
Definition
In the nucleolus 
Term
What are phospholipids composed of?
Definition
2 fatty acid + glycerol + phosphate 
Term
What group would most likely be found on an base?
Definition
amino 
Term
Where is this phosphate in a phospholipid?
Definition
Attached to a the glycerol 
Term
What do micorarrays allow us to do?
Definition

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 

Term
What is a silent mutation?
Definition
Redundant codon or in non coding, non-regulatory regions
Term
What happens when there is a change the regulatory region?
Definition
Get little or too much protein
Term
What are the ways that cells can repair mutations?
Definition
DNA polymerase
Methylation-directed mismatch repair
Excision repair
Term
Where is the TATAAT box found during transcription?
Definition
Often found 10 bases away from the start
Term
What separates DNA during transcription?
Definition
After transcription factors bind to DNA, RNA polymerase binds and separated DNA strands
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