Biology -Chapter 4 and 5 - incomplete

8/7/2019 Biology -Chapter 4 and 5 - incomplete

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History of DNA: section 4.1

Gregor Mendel

Mendel's First Law

The Law of Segregation: During gamete formation, two alleles of a gene pair segregate from each other. A

heterozygous plant that is Tt forms the gametes: T & t in equal numbers. The gametes do not blend.

Mendel's Second Law

The Law of Independent Assortment: Segregation for different pairs of alleles occur independently/ A plant thatis heterozygous for two pairs of alleles. In example, a heterozygous TtRr can form four types of gametes: TR, Tr,

tR & tr

Friedrich Miescher

Isolated non protein substance from nucleus of cells

Named this substance: Nuclein

Frederick Griffith

Experimented with mice and two different strains of pneumonia

Discovered the process of transformation

Joachim Hammerling

Experimented using green alga: Acetabularia

Hypothesized that hereditary information is stored in the nucleus

Oswald Avery, Maclyn McCarty, Colin MacLeod

Demonstrated that DNA was the transforming principle of pneumococcus bacteria

Erwin Chargoff

Discovered that DNA contains:

Equal amounts of Adenine and ThymineEqual amounts of Guanine and Cytosine

Alfred Hershey, Martha Chase

Experimenting with radioisotopes of phosphorus and sulphur and suggested that DNA was the hereditary

material

Rosalind Franklin

Produced and X-ray diffraction pattern of DNA

Suggested DNA was double helix in structure

James Watson, Francis CrickDiscovered the structure of DNA using information from Chargoff, Franklin, and Maurice Wilkins

Matthew Meselson, Franklin Stahl

Discovered that DNA replicated semi conservatively

Archibald Garrod

Hypothesized that genes code for the production of enzymes / proteins

Noticed that an error in hereditary material resulted in an error in a enzyme


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George Beadle, Edward Tatum

Hypothesized that one gene = one enxyme

Noticed that a lack of a particular enzyme corresponded to a mutation in a single gene.

Vernom Ingram

Discovered that sickle cell anemia is caused by the coding of one wrong amino acid.

Discovered that a gene specifies the kind of location of each amino acid in a polypeptide chain.

Thomas Morgan

Morgan was able to demonstrate that genes are carried on chromosomes and are the mechanical basis of

heredity.


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Structure of DNA: section 4.2

Chemical analysis by scientists revealed the general chemical composition of nucleic acids (DNA and

RNA): they are composed of nucleotides.

A nucleotide consists ofa phosphate group, a five-carbon sugar (deoxyribose in DNA and ribose in

RNA), and a nitrogenous base bonded together.

Each nucleotide in a DNA molecule has one of four nitrogenous bases:

Adenine, Guanine, Thymine, Cytosine, and Uracil in RNA.

Adenine and Guanine are purine bases. their structure consists oftwo rings of atoms.

Thymine and Cytosine are pyrimidine bases. Their structure consists a single ring of atoms.Uracil is another pyrimidine base found in RNA. Uracil replaces Thymine in RNA.


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DeoxyRibose Sugar Vs Ribose Sugar

DNA vs. RNA

Deoxyribonucleic acid Ribonucleic acid

- Contains Deoxyribose sugar - Contains Ribose sugar - Double Stranded - Single Stranded

- Adenine Thymine

- Guanine Cytosine

- Adenine Uracil

- Guanine Cytosine

- Resides in the Nucleus - Resides in both Nucleus andCytoplasm

Practise on DNA Structure: Chapter 4, section 4.2, Page 216, Questions #1 10.


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DNA Replication and Repair: section 4.3

http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

This website has an Awesome animation with reviewquestions regarding DNA replication

INTRODUCTION

DNA replication is the process whereby an entire double-stranded DNA is copied to produce a second,identical DNA double helix.

The objectives of this exercise are:

1. To understand the functions of the proteins responsible for DNA replication, including helicase, SSBprotein, primase, the sliding clamp, DNA polymerase, Rnase H and DNA ligase.

2. to understand why the leading strand is synthesized continuously and the lagging strand issynthesized discontinuously.

THE REPLICATION FACTORY

DNA replication is an intricate process requiring the concerted action of many different proteins. Thereplication proteins are clustered together in particular locations in the cell and may therefore be regardedas a small Replication Factory that manufactures DNA copies. The DNA to be copied is fed through thefactory, much as a reel of film is fed through a movie projector. The incoming DNA double helix is split intotwo single strands and each original single strand becomes half of a new DNA double helix. Because each

resulting DNA double helix retains one strand of the original DNA, DNA replication is said to be semi-conservative.

DNA REPLICATION PROTEINS

DNA replication requires a variety of proteins. Each protein performs a specific function in the production ofthe new DNA strands. Helicase, made of six proteins arranged in a ring shape, unwinds the DNA double

helix into two individual strands. Single-strand binding proteins, or SSBs, are tetramers that coat the single-stranded DNA. This prevents the DNA strands from reannealing to form double-stranded DNA. Primase isan RNA polymerase that synthesizes the short RNA primers needed to start the strand replication process.

DNA polymerase is a hand-shaped enzyme that strings nucleotides together to form a DNA strand. Thesliding clamp is an accessory protein that helps hold the DNA polymerase onto the DNA strand duringreplication. RNAse H removes the RNA primers that previously began the DNA strand synthesis. DNA

ligase links short stretches of DNA together to create one long continuous DNA strand.
http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html


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REPLICATION IN ACTION

1. The process begins when the helicase enzyme unwinds the double helix to expose two single DNAstrands and create two replication forks. DNA replication takes place simultaneously at each fork.

The mechanism of replication is identical at each fork. Remember that the proteins involved inreplication are clustered together and anchored in the cell. Thus, the replication proteins do nottravel down the length of the DNA. Instead, the DNA helix is fed through a stationary replication

factory like film is fed through a projector.

2. Single-strand binding proteins, or SSBs, coat the single DNA strands to prevent them fromsnapping back together. SSBs are easily displaced by DNA polymerase.

3. The primase enzyme uses the original DNA sequence as a template to synthesize a short RNAprimer. Primers are necessary because DNA polymerase can only extend a nucleotide chain, not

start one.4. DNA polymerase begins to synthesize a new DNA strand by extending an RNA primer in the 5' to 3'

direction. Each parental DNA strand is copied by one DNA polymerase. Remember, both templatestrands move through the replication factory in the same direction, and DNA polymerase can onlysynthesize DNA from the 5 end to the 3 end. Due to these two factors, one of the DNA strands

must be made discontinuously in short pieces which are later joined together.5. As replication proceeds, RNAse H recognizes RNA primers bound to the DNA template and

removes the primers by hydrolyzing the RNA.6. DNA polymerase can then fill in the gap left by RNase H.

7. The DNA replication process is completed when the ligase enzyme joins the short DNA piecestogether into one continuous strand.

Practise on DNA replication: Chapter 4, section 4.3, Page 223, Questions #1 10.

Practise on Chapter 4: Page 228. Page 229 231, Questions #1 24.


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Protein Synthesis: Section 5.2

Proteins are synthesized outside of the nucleus, in the cytoplasm, in ribosomes.

DNA does not ext the nucleus for safety and efficiency reasons.

Transcription: The process in which DNA is used as a template for the production of complimentarymessenger RNA molecules.

Translation: The process by which ribosomes assemble amino acids in a specific sequence to synthesizea specific polypeptide coded by mRNA.

Types of RNA Characteristics and Key functions

Messenger RNA (mRNA) - Varies in length depending on which gene is

being copied.

- Acts as an intermediary between DNA and

ribosomes.

- Translated into proteins by ribosomes.

Transfer RNA (tRNA) - Functions as the delivery system of amino acids

to ribosomes.

- Very short, only 70-90 base pairs long.

Ribosomal RNA (rRNA) - Binds with Proteins to form ribosomes.- Varies in length.

Amino acids are determined by Codons. There are 64 possible combinations of Codons that code for 20amino acids.

Codon: Sequence of three bases in a nucleotide that codes for amino acids.

Start Codon (AUG): Signals the ribosomes to start translation at this point.

Stop Codons (UAA, UAG, UGA) : Specific Codons that signal the end of translation to the ribosomes.

Practise on Protein synthesis: Chapter 5, section 5.2, page 241, Questions # 1 14.


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Transcription: Section 5.3

http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html

This website has an Awesome animation regarding

DNA transcriptionOccurs in the Nucleus, on DNA in chromosomes.

Initiation

The enzyme RNA Polymerase binds to the promoter region of the gene that is to be transcribed. At this

point, the DNA is unwound and the double helix is disrupted.

RNA Polymerase moves past the promoter region until it reaches the start sequence of the gene that is

to be transcribed.

Elongation

A complementary RNA strand is synthesized in the 5' to 3' direction, using the DNA.

Termination

Once the terminator sequence is reached by the RNA Polymerase, transcription ceases. The mRNA,RNA Polymerase and DNA are separated. The DNA reforms it's double helix.

Post transcriptional modifications

A 7'methyl guanosine is added to the 5' end of mRNA.A string of 200300 Adenine ribonucleotides are added to 3' end of mRNA.

This is known as capping and tailing.

Introns (non coding regions) are cut out of primary transcripts by enzymes known as spliceosomes. The

remaining Exons (coding regions) are joined together. This only occurs in Eukaryotes.

Now the mRNA transcript is ready to exit the nucleus.
http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.htmlhttp://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.htmlhttp://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html


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Practise on DNA Transcription: Chapter 5, section 5.3, Page 24, Questions # 1 12.

T ranslation: Section 5.4

http://www.youtube.com/watch?v=4PKjF7OumYo

This Video Is a great visual of Translation and

Transcription.Occurs in the Cytoplasm on free ribosomes and Rough Endoplasmic Reticulum where they are destined

to pass through a membrane or leave the cell completely. Proteins need modifications to allow

transport.

Ribosomes structure:

Small subunit: 40s

Large subunit: 60sand contains 3sites:

E-Site: The exit site for tRNA that have donated their amino acid.P-Site: Where the growing polypeptide is made.

A-site: Acceptor site where the frst tRNA binds.
http://www.youtube.com/watch?v=4PKjF7OumYohttp://www.youtube.com/watch?v=4PKjF7OumYo


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Charged tRNA contains an anticodon with an attached amino acid.Uncharged tRNA lacks the amino acid.

Initiation

Small subunit bins mRNA transcriptionLarge subunit binds and sandwiches mRNA

Met- tRNA enters the P-Site

Elongation

Next tRNA enters the A-site, recognizing the next codon in the RNA sequence.

Peptide bond forms between amino acids, temporarily moving polypeptide to A-site.

Ribosomes move forward three nucleotides to read the next codon. Uncharged Met tRNA is now in

the E-site.

Upon reading the next codon in the sequence, the uncharged Met-tRNA exits the ribosomes.

This process continues until a stop codon is read.

Termination

When the stop codon is reached, a termination enzyme binds and hydrolizes the polypeptide from the

last tRNA.


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Everything disassembles and the ribosomes bond to a new mRNA molecule to continue transcription.

Control Mechanisms: Section 5.5

The production of a protein can happen at all stages.

Type of Control Description

Transcriptional It regulates which genes are transcribed (DNA or mRNA) or controls the rate at which transcription

occurs.

Posttranscriptional The mRNA molecules undergo changes in the

nucleus before translation occurs. Introns areremoved and exons are spliced together.

Translational It controls how often and how rapidly mRNAtranscripts will be translated into proteins. This

control affects the length of time it takes for

mRNA to be activated and the speed at whichcytoplasmic enzymes destroy mRNA.

Posttranslational Before many proteins become functional, they

must pass through the cell membrane. A number

of control mechanisms affect the rate at which aprotein becomes active and the time that it

remains functional, including the addition of

various chemical groups.

Background: Bacteria lack introns, and produce proteins one after another. That means that one

promoter when activated will cause several genes to be transcribed.

Operons: Several genes in Prokaryotes controlled by the same promoter.

Examples:

Lac Operon: Inducible gene product.


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Trp Operon: Repressible gen product.

Operons as such are not known in eukaryotic cells (other than some possible candidates in yeast). Some

of the control mechanisms known for eukaryotic genes bear a resemblance to the operon controlsystem, but strings of contiguous genes, all under the control of a single promoter/operator region,

are not found in eukaryotic cells.


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Mutations: Section 5.6

Mutations are chang


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Prokaryotes vs. Eukaryotes: Section 5.7

1. Prokaryotic organisms do not possess a nuclear membrane. There fore, once transcription by

RNA polymerase has begun, translation can begin, even though the full gene has yet to betranscribed. This is known as coupled transcription-translation.

2. The genes of prokaryotic organimsm do not contain any noncoding regions (introns). Some

archaebacteria possess introns.

3. In prokaryotes, the ribosome recognizes the start of a mRNA transcript by a unique sequence ofpurine rich bases known as teh Shine-Dalgarno sequence. In eukaryotes, ribosomes recognize

the 5 cap that has been placed on mRNA.

4. Ribosomes in Eukaryotes are largere than those in prokaryotes.5. In prokaryotes, the methionine at the start of translation is tagged with a formyl group.

6. Eukaryotic organisms do not possess operons.

7. The prokaryotic genome is a circular chromsome.The eukaryotic genome is organized intochromosomes.

Mitochondria in eukaryotic cells resemble prokaryotic cells:

1.Mitochondria have circular genomes that are not contained within a nucleus.

2.The sequence of mitochondrial DNA is similar to the genomes of bacteria cells.

3.Mitochondria divide by the process of fisson within a eukaryotic cell, similar to bacteria.

4.Mitochondria possess their own system of DNA synthesis, transcription, and translation,indicating that mitochondria may once have been free living cells.

Key DifferencesProkaryotes Eukaryotes

Genome Small and circular

All regions are coding,

except for promoters andoperators

Presence of Operons

Large and arranged inchromosomes

Consists of coding andnon coding regions

Absence of operons

Transcription Coupled with translation

lack of introns means no

excision

Occurs in the nucleus

Introns excised by spliceosomes

and exons joined together.

Translation Commences with formyl-methionine

ribosomes recognize

Commences withmethionine

ribosomes recognize 5


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Shine-Dalgarno sequence

on mRNA as binding site

ribosomes are smaller

than eukaryotes.

cap on mRNA as binding

site

Occurs in cytoplasm

ribosomes are larger than

prokaryotes


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Biology -Chapter 4 and 5 - incomplete

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