final:)) 9/29/10

BIOCHEMISTRY - BSMT2D :))

CEDELES, CHARITY
HAGHANI RAD, NASRIN
PEREZ, REISS
RAHIMI, KIMIA


DNA Replication.1

http://www.youtube.com/user/garlandscience#p/c/86FB28667714C01D/3/-mtLXpgjHL0

This video is from:
Essential Cell Biology, 3rd Edition
Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts, & Walter
ISBN: 978-0-8153-4129-1

In a replication fork, two DNA polymerases collaborate to copy the leading-strand template and the lagging-strand template DNA. This video shows the process by which DNA replication occurs. Achieving bilateral symmetry doesn't requireseparate sets of genes for each side.
I see lots of beauty and art in nature as well. Amazing example of irreducible complexity. This the most efficient, significant process inthe world. So finely tuned and designed, so much more than humans could ever produce on this scale.
Absolutely amazing, we were completely perplexed over the "backwards" description of the copying. So I was amazed to find this animation. Even then it’s taken me a couple of seconds to figure out what is happening because it is so fast.
DNA REPLICATION
http://www.youtube.com/watch?v=z685FFqmrpo&feature=related
-SIMPLE VERSION
In DNA replication T always pairs with A
A pairs with U during transcription in protein synthesis where complementary RNA bases are paired with the DNA on the sense strand.
"A double strand of DNA unwinds" make it seems like a spontaneous process, which isn't. At the body temperature, large activation energy is required to unwind DNA; and denatured strands anneal back.

DNA TRANSCRIPTION:
http://www.youtube.com/watch?v=WsofH466lqk
Molecules in the cell bump and jiggle and drift all the time. When they bump in such a way as to cause a reaction, a reaction occurs. This is a bit like kids in a mosh pit. They move fairly randomly around the crowd. When one friend finds another, he lifts him up to crowdsurf. If one finds his girlfriend, they hold hands. Substitute chemical affinity for friendship, and think of lifting the friend up as a reaction.
-Great clip! Clearly explains transcription!
-During transcription, the DNA needs to be single stranded to create an mRNA strand..
-Showing the template strand (non-coding) which is used by RNA polymerase to form a mRNA strand

DNA TRANCRITION:

http://www.youtube.com/watch?v=ztPkv7wc3yU&feature=related

BLUE blob going through the helix: That's called RNA polymerase, it's the enzyme that copies RNA using one of the DNA strands as a template

It's a great video... some mistakes here and there, but it's good overall.:))

TRANSLATION:
http://www.youtube.com/watch?v=5bLEDd-PSTQ

PROCESS OF TRANSLATION AND PROTEIN SYNTHESIS
-The codons found within the mRNA.
-The small subunit of the ribosome attached to the mRNA.
-A tRNA molecule.
-The tRNA anti-codon is complementary to the mRNA codon.
-The amino acid known as methionine.
-The first tRNA molecule attaches to the first site of translation.
-The second tRNA molecule attaches to the second site of translation.
-The amino acid from the first tRNA is transferred to the amino acid on the second tRNA.
-The first tRNA exits, the ribosome moves, a new tRNA enters, and the process is repeated.
-The process is repeated many times, and a peptide, or strand of amino acids, is formed.
-The release factor enters.
-Translation, or protein synthesis, ends.
-The completed peptide is released.

mRNA ININIATION ELONGATION TERMINATION

END: Protein synthesis is now complete. The peptide chain is ready to act as a protein or be combined with other chains to form larger, polypeptide proteins.

TRANSLATION.1
http://www.youtube.com/watch?v=-zb6r1MMTkc&feature=related

Pretty amazing that stuff like this occurs naturally. Starting to see why intelligent design people think the way they do.

"E site" next to the "P site" and "A site": EXIT - POLIPEPTIDE - AND ARRIVE

Start and stop codons used to separate genes: start and stop codons are more a matter of translation (mRNA to protein) than a matter of gene separation. Genes in DNA are not necessarily contiguous sequences; that gets rather complicated. But within the gene there would be tri-nucleotides complementary to start and stop codons. As you know, the start and stop codon simply indicate where the protein product is to start and stop

BIOCHEMISTRY - BSMT2D :))

CEDELES, CHARITY
HAGHANI RAD, NASRIN
PEREZ, REISS
RAHIMI, KIMIA


DNA Replication.1

http://www.youtube.com/user/garlandscience#p/c/86FB28667714C01D/3/-mtLXpgjHL0

In a replication fork, two DNA polymerases collaborate to copy the leading-strand template and the lagging-strand template DNA. This video shows the process by which DNA replication occurs.

This video is from:
Essential Cell Biology, 3rd Edition
Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts, & Walter
ISBN: 978-0-8153-4129-1

Achieving bilateral symmetry doesn't require separate sets of genes for each side.

I see lots of beauty and art in nature as well.Amazing example of irreducible complexity. This the most efficient, significant process in the world. So finely tuned and designed, so much more than humans could ever produce on this scale.

Absolutely amazing. I was completely perplexed over the "backwards" description of the copying. So I was amazed to find this animation. Even then It's taken me a couple of seconds to figure out what is happening because it is so fast.

DNA REPLICATION

http://www.youtube.com/watch?v=z685FFqmrpo&feature=related

in DNA replication T always pairs with A

A pairs with U during transcription in protein synthesis where complementary RNA bases are paired with the DNA on the sense strand.

simple version

"A double strand of DNA unwinds" make it seems like a spontaneous process, which isn't. At the body temperature, a large activation energy is required to unwind DNA; and denatured strands anneal back

DNA TRANSCRIPTION:

http://www.youtube.com/watch?v=WsofH466lqk

Molecules in the cell bump and jiggle and drift all the time. When they bump in such a way as to cause a reaction, a reaction occurs. This is a bit like kids in a mosh pit. They move fairly randomly around the crowd. When one friend finds another, he lifts him up to crowdsurf. If one finds his girlfriend, they hold hands. Substitute chemical affinity for friendship, and think of lifting the friend up as a reaction.

great clip! clearly explains transcription!

during transcription, the DNA needs to be single stranded to create a mRNA strand

showing the template strand(non-coding) which is used by RNA polymerase to form a mRNA strand

DNA TRANCRITION:

http://www.youtube.com/watch?v=ztPkv7wc3yU&feature=related

BLUE blob going through the helix:That's called RNA polymerase, it's the enzyme that copies RNA using one of the DNA strands as a template

It's a great video... some mistakes here and there, but it's good overall.:))

TRANSLATION:
http://www.youtube.com/watch?v=5bLEDd-PSTQ

A.)mRNA

-The codons found within the mRNA.
-The small subunit of the ribosome attached to the mRNA.
-A tRNA molecule.
-The tRNA anti-codon is complementary to the mRNA codon.
-The amino acid known as methionine.
-The first tRNA molecule attaches to the first site of translation.
-The second tRNA molecule attaches to the second site of translation.
-The amino acid from the first tRNA is transferred to the amino acid on the second tRNA.
-The first tRNA exits, the ribosome moves, a new tRNA enters, and the process is repeated.
-The process is repeated many times, and a peptide, or strand of amino acids, is formed.
-The release factor enters.
-Translation, or protein synthesis, ends.
-The completed peptide is released.

B.) ININIATION
C.) ELONGATION
D.) TERMINATION

END: Protein synthesis is now complete. The peptide chain is ready to act as a protein or be combined with other chains to form larger, polypeptide proteins.

TRANSLATION.1
http://www.youtube.com/watch?v=-zb6r1MMTkc&feature=related

Pretty amazing that stuff like this occurs naturally. Starting to see why intelligent design people think the way they do.

"E site" next to the "P site" and "A site": EXIT - POLIPEPTIDE - AND ARRIVE

start and stop codons used to separate genes: start and stop codons are more a matter of translation (mRNA to protein) than a matter of gene separation. Genes in DNA are not necessarily contiguous sequences; that gets rather complicated. But within the gene there would be trinucleotides complementary to start and stop codons. As you know, the start and stop codon simply indicate where the protein product is to start and stop

assignment:)) 9/17/10

REISS PEREZ

A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are universal in living things, as they are found in all cells and viruses. Nucleic acids were first discovered by Friedrich Miescher in 1871.

FUNCTIONS OF DNA:

• Deoxyribonucleic acid (DNA) is the genetic code which ensures that daughter cells inherit the same characteristics as the parent cells
• DNA is the code from which all protein is synthesised
• All prokaryotes, eukaryote and some viruses have DNA
• All DNA code is composed from four nucleotide bases, Adenine, Cytosine, Guanine and Thymine.

DNA also contains all the genetic coding which is used to control functions, behaviour and development of an organism. DNA is also used as a long term storage device to store the genetic instructions. These instructions must be correct so the DNA can make an exact copy of itslef.

The function of DNA in a cell is to code the way proteins turn genes on or off.

FUNCTIONS OF RNA:

mRNA - messenger RNA - is a "copy" of the DNA base sequence of a gene after processing (capping, addition of 3' tail and splicing). It is used to transfer the genetic information from DNA, which is a storage molecule and quite inaccessible, to ribosomes, which perform translation to synthesise polypeptides.

tRNA - transfer RNA - is "charged" with an amino acid and used to recognize the code in the mRNA and "translate" it into the amino acid it is carrying. There are specific tRNA molecules for each amino acid.

rRNA - ribosomal RNA - makes up parts of the ribosome and has the catalytic transpeptidase action required to create polypeptide chains during translation.

snRNA - small nuclear RNA - regulates and provides the catalytic machinery for splicing or mRNA.

gRNA - guide RNA - directs editing of RNA to specific sites.

miRNA - micro RNA - inhibits translation by base pairing with complementary sequences of mRNA.

Signal Recognition Particle - RNA/protein molecule that binds to the "Signal Sequence" on polypeptides to be sent to the endoplasmic reticulum, causing translation to pause until polypeptide has been fed into translocon for entry into ER.

What components do DNA and RNA?

It is easier to say which componants are different as the two types of molecule are very similar. RNA uses ribose in the sugar-phosphate backbone rather than deoxyribose, as in DNA. And in RNA uracil (U) is used in place of (T) as a base. These are the two major differences. If you want a list of similarities then:

-both use a sugar phosphate backbone onto which bases are assembled

-Both use four bases to encode information (A,T,C,G - DNA) and(A,U,C,G- RNA)

-both use hydrogen bonding between bases to join sense and antisense strands (both sides of the ladder)

-all nucleotides (bases) used to make to both DNA and RNA have 3 phosphate groups attatched to them before they are added to the growing chain.

A chromosome is an organized building of DNA and protein that is found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greek χρῶμα (chroma, colour) and σῶμα (soma, body) due to their property of being very strongly stained by particular dyes.

A gene is a unit of heredity in a living organism. It is normally a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. All living things depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring.

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA.

Nucleosides are glycosylamines consisting of a nucleobase (often referred to as simply base) bound to a ribose or deoxyribose sugar via a beta-glycosidic linkage. Examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine and inosine.

genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA.

histones are strongly alkaline proteins found in eukaryotic cell nuclei, which package and order the DNA into structural units called nucleosomes.^[1][2] They are the chief protein components of chromatin, act as spools around which DNA winds, and play a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to one in human DNA). For example, each human cell has about 1.8 meters of DNA, but wound on the histones it has about 90 millimeters of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.^[3]

Nucleosomes are the basic unit of DNA packaging in eukaryotes (cells with a nucleus), consisting of a segment of DNA wound around a histone protein core.^[1] This structure is often compared to thread wrapped around a spool.^[2]

Chromatin is the combination of DNA and proteins that makes up chromosomes. It is found inside the nuclei of eukaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms.^{[1] [2]} The major components of chromatin are DNA and histone proteins, although other proteins have prominent roles too. The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to serve as a mechanism to control expression and DNA replication. Chromatin contains genetic material-instructions to direct cell functions.

BASES OF DNA AND RNA:

The DNA bases are adenine, guanine, thymine, and cytosine . In RNA, Thymine is replaced by Uracil. Adenine and guanine are known as purines and cytosine and thymine are known as pyrimidines.

Although scientists have made some minor changes to the Watson and Crick model, or have elaborated upon it, since its inception in 1953, the model's four major features remain the same yet today. These features are as follows:

• DNA is a double-stranded helix, with the two strands connected by hydrogen bonds. A bases are always paired with Ts, and Cs are always paired with Gs, which is consistent with and accounts for Chargaff's rule.
• Most DNA double helices are right-handed; that is, if you were to hold your right hand out, with your thumb pointed up and your fingers curled around your thumb, your thumb would represent the axis of the helix and your fingers would represent the sugar-phosphate backbone. Only one type of DNA, called Z-DNA, is left-handed.
• The DNA double helix is anti-parallel, which means that the 5' end of one strand is paired with the 3' end of its complementary strand (and vice versa). As shown in Figure 4, nucleotides are linked to each other by their phosphate groups, which bind the 3' end of one sugar to the 5' end of the next sugar.
• Not only are the DNA base pairs connected via hydrogen bonding, but the outer edges of the nitrogen-containing bases are exposed and available for potential hydrogen bonding as well. These hydrogen bonds provide easy access to the DNA for other molecules, including the proteins that play vital roles in the replication and expression of DNA (Figure 4).

Summary

Watson and Crick were not the discoverers of DNA, but rather the first scientists to formulate an accurate description of this molecule's complex, double-helical structure. Moreover, Watson and Crick's work was directly dependent on the research of numerous scientists before them, including Friedrich Miescher, Phoebus Levene, and Erwin Chargaff. Thanks to researchers such as these, we now know a great deal about genetic structure, and we continue to make great strides in understanding the human genome and the importance of DNA to life and health.

Putting the Evidence Together: Watson and Crick Propose the Double Helix

Chargaff's realization that A = T and C = G, combined with some crucially important X-ray crystallography work by English researchers Rosalind Franklin and Maurice Wilkins, contributed to Watson and Crick's derivation of the three-dimensional, double-helical model for the structure of DNA. Watson and Crick's discovery was also made possible by recent advances in model building, or the assembly of possible three-dimensional structures based upon known molecular distances and bond angles, a technique advanced by American biochemist Linus Pauling. In fact, Watson and Crick were worried that they would be "scooped" by Pauling, who proposed a different model for the three-dimensional structure of DNA just months before they did. In the end, however, Pauling's prediction was incorrect.

Using cardboard cutouts representing the individual chemical components of the four bases and other nucleotide subunits, Watson and Crick shifted molecules around on their desktops, as though putting together a puzzle. They were misled for a while by an erroneous understanding of how the different elements in thymine and guanine (specifically, the carbon, nitrogen, hydrogen, and oxygen rings) were configured. Only upon the suggestion of American scientist Jerry Donohue did Watson decide to make new cardboard cutouts of the two bases, to see if perhaps a different atomic configuration would make a difference. It did. Not only did the complementary bases now fit together perfectly (i.e., A with T and C with G), with each pair held together by hydrogen bonds, but the structure also reflected Chargaff's rule (Figure 3).

complementary base pairs in the DNA:

The mRNA transcribed from the antisense DNA strand is not identical to that DNA strand; it is complementary. -the mRNA has the 'partners' of the bases on the DNA template
(remembering that RNA uses U instead of T)
-it IS identical to the sense strand; therefore, it carries the code for the protein.
-if the DNA says ACC, the mRNA says UGG.

Complementary base pairs are: adenine and thymine (A - T )
guanine and cytosine (G - C)

Base pairs in DNA

DNA (Deoxyribonucleic acid), is a chemical found primarily in the nucleus of cells. DNA carries the instructions for making all the structures and materials the body needs to function.

DNA is organized as two complementary strands, head-to-toe, with bonds between them that can be "unzipped" like a zipper, separating the strands.