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3' or 5' DNA capping protein

3' or 5' DNA capping protein


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Does anyone know of a protein/molecule that can be attached to one end of the DNAs temporarily ? eg. i would like to only to allow one strand of DNA be ligated to another DNA molecule to either it's 3' or 5' but not both. thanks


KA1.3 DNA & the Production of Proteins

POWERPOINTS -Please click on the following links for Mr’s Smith’s PowerPoint presentations for Key Area 1.3 DNA & the Production of proteins. There is 2 subunits in this area.

LEARNING OUTCOMES: This gives you the opportunity to self-assess by traffic lighting your success Green, Amber or Red. Remember if you find gap’s in your knowledge you must work hard to fill the gaps.

WORDBANK – Use the wordbank to match to the definitions. When you get more confident can you do it without the wordbank? Perhaps you will find it useful to make the key terminology into flashcards. Remember Biology is vocabulary intensive. It is ESSENTIAL that you learn your definitions.

NOTES – We will not copy notes in class. These are your notes. It’s your responsibility to, read and learn these. This will leave us time to apply your learning in class. If you are able, please print these at home or in the library to form your notes (that way you can highlight and annotate wherever necessary). REMEMBER ANYTHING YOU DON’T UNDERSTAND, JOT DOWN TO ASK ME ASAP.

HOMEWORK: DNA & Protein synthesis Homework 1: This is a research task: TOPIC – “History of DNA Discovery and the scientists behind the discoveries“: Use the internet to produce a piece of research you may choose the format (Essay, Poster, News Article, Powerpoint, Model). below you will find an useful video for your project.

OR

You may prefer to focus your research on a specific scientist involved in DNA discovery, please find below FACTSHEETS with information and hints on how to complete the activity


Abstract

Over the past few years, several new 3′–5′ exonucleases have been identified. In vitro studies of these enzymes have uncovered much about their potential functions in vivo, and certain organisms with a defect in 3′–5′ exonucleases have an increased susceptibility to cancer, especially under conditions of stress. Here, we look at not only the newly discovered enzymes, but also at the roles of other 3′–5′ exonucleases in the quality control of DNA synthesis, where they act as proofreading exonucleases for DNA polymerases during DNA replication, repair and recombination.


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3' or 5' DNA capping protein - Biology

Chapter 12: Gene Function, Gene Regulation, and Biotechnology

You have open access (no log-in or password needed) to instructional materials on the Text web site. Select "Resources" from the upper left of the page and select the text chapter you want.

Moodle

You may also ask questions and see answers to your classmates' questions in Moodle in the "Talk to Ed" forum.

Objectives:

The content of today's lecture will help you answer the questions on these assignments:

Second Moodle Assignment, due in your TA's Moodle Forum by 8 AM Tuesday March 30.

After studying this material you should be able to:

Draw a diagram, create a concept map, or write a paragraph that explains the relationships among these terms:

chromosome allele gene expression
trait DNA RNA polymerase
messenger RNA transfer RNA ribosomal RNA
codons anticodons ribosomes
transcription translation RNA processing
amino acids polypeptides protein
protein folding primary structure secondary structure
tertiary structure quaternary structure introns and exons

Use models of DNA, RNA, and amino acids to illustrate the connection between the sequence of DNA nucleotides for a specific allele, such as the allele for sickle cell disease or the allele for cystic fibrosis, and the production of a specific version of a protein.

lllustrate transcription and translation, and the roles of RNA polymerase, messenger RNA, transfer RNA, ribosomal RNA, and ribosomes in carrying out these two processes.

Explain, in general terms, how the order and kinds of amino acids that make up a protein determine its final conformation and, ultimately, its function.

Web Resources:

Chose "Copying the Code" toward the bottom of the screen

then select "puting it together" from the top of the next screen.

Then choose the "Replication animation"

Chose "Copying the Code" toward the bottom of the screen

then select "puting it together" from the top of the next screen.

Then choose the "Transcription animation"

Chose "Reading the Code" toward the bottom of the screen

then select "puting it together" from the top of the next screen.

Then choose the "Translation animation"

DNA From The Beginning
Everything you would ever want to know about DNA with understandable animations and tutorials.

Protein Synthesis: An Overview

DNA to RNA to Protein (Figure 12.1, in Hoefnagels, page 236).
Information stored in DNA is copied to RNA (transcription), which is used to assemble proteins (translation).

Transcription: DNA to RNA

Transcription occurs in the nucleus.

Transcription is the process by which RNA is assembled from a DNA template by the enzyme RNA Polymerase.

Transcription DNA --> RNA From DNA Interactive - a MUST SEE.

Chose "Copying the Code" toward the bottom of the screen

then select "puting it together" from the top of the next screen.

Then choose the "Transcription animation"

The TAs pointed out a conceptual error in the narration of this movie. The text of the web page is correct, but the narration is wrong. Write to me in the "Talk to Ed" forum in Moodle and tell me what you think the problem is.

Transcription is the synthesis of a molecule of RNA that is complementary in nucleotide sequence to one side (the transcribed or template side) of a section of the DNA double helix (that would be an allele for a specific trait). The information is copied, but in a complementary form:

C in the RNA is complementary with G in the DNA

G in the RNA is complementary with C in the DNA

A in the RNA is complementary with T in the DNA

U not T in the RNA is complementary with A in the DNA

DNA vs. RNA (Figure 12.2, in Hoefnagels, page 237). RNA is a single-stranded molecule, its nucleotides have the sugar ribose instead of deoxyribose and the nucleotide base uracil instead of thymine.

Transcription Factors (Figure 12.11, in Hoefnagels, page 246) are protein molecules that determine which genes are expressed in which tissues at which stages of development. The promotor, a control sequence near the start of the gene, attracts a binding protein and then other transcription factors. It tells the enzyme RNA polymerase where to bind and begin making RNA.

Enzymes unwind the DNA strand, and RNA polymerase builds the RNA chain using the transcribed strand of the DNA double helix as a template.

The Three Stages of Transcription(Figure 12.3, in Hoefnagels, page 238). Many identical copies of RNA are simultaneously transcribed, with one RNA polymerase starting after another. RNA is relatively short-lived, so a cell must constantly transcribe certain genes to maintain supplies of essential proteins.

RNA Processing

RNA undergoes processing in the nucleus after transcription.

Messenger RNA Processing(See Figure 12.4 in your Hoefnagels text.)

A "cap" is added to the 5' end of the molecule, and a "poly-A tail" is added to the 3' end. (Think of this as a "hall pass," permitting the molecule to leave the nucleus.)

Noncoding sequences called introns are removed. Introns (intervening or noncoding sections of DNA) produce sections of RNA that are removed by enzymes, leaving only the sections of RNA produced by exons in the DNA to be put back together.

Animation of a complex series of enzyme steps that cut out introns and splice together exons from sumanasinc.com.
Select "mRNA Splicing".
Just watch the animation to get the "gist" of the concept of RNA processing.

The messenger RNA is now "mature" and can exit the nucleus. RNA molecules move into the cytoplasm via nuclear membane pores.

Three Types of RNA are Produced by Transcription of Specific Genes

Messenger RNA (mRNA) is a complimentary copy of one strand (the template, or transcribed strand) of a section of a DNA molecule making up an allele. It acts as a messenger to carry information stored in the DNA in the nucleus to the cytoplasm where the ribosomes on the Endoplasmic Reticulum can translate it to synthesize protein molecules. Each three mRNA bases in a row forms a Codon (from accessexcellence.org) that specifies a particular amino acid.

Transfer RNA (tRNA) (see Hoefnagels text fig. 12.6, pg. 241) is small and has a very specific secondary and tertiary structure such that it can bind an amino acid at one end and mRNA at the other. It carries each amino acid to the ribosome. tRNA contains a sequence of 3 nucleotide bases at one end of the molecule called an anticodon. This Anticodon (from accessexcellence.org) is complementary to a particular codon of an mRNA molecule.

Ribosomal RNA (rRNA) is one of the structural components of a Ribosome (see Hoefnagels text fig. 12.7, pg. 241). Ribosomes structurally support and catalyze protein synthesis. In eukaryotes, a ribosome has two subunits (large and small), containing 82 proteins and four rRNA molecules all together.

The Genetic Code

(Hoefnagels Text table 12.2, pg. 240)

The Genetic Code (from accessexcellence.org), for the translation of codons to amino acids

Three consecutive bases in a mRNA molecule form a Codon (from accessexcellence.org) that is a code for one amino acid.

The code is redundant, with some amino acids having more than one codon. For example, the codons GCU, GCC, GCA, and GCG all code for alanine (Ala).

A change in the first or second bases of a codon are more likely to affect the "meaning" of a codon than a change in the third base.

The codon AUG starts translation, and the codons UGA, UAA, and UAG stop translation.

Translation: RNA to Protein

Translation occurs in the cytoplasm at the ribosomes on the E.R.

Translation is the process by which the information carried in messenger RNA is used to direct the synthesis of a polypeptide. See Fig. 12.8, pg. 242 in Hoefnagels text.

Translation mRNA --> Protein From DNA Interactive - a MUST SEE.

Chose "Reading the Code" toward the bottom of the screen

then select "puting it together" from the top of the next screen.

Then choose the "Translation animation"

The Three Stages of Translation

Initiation: the first mRNA codon AUG forms a complex with an initiator tRNA (carrying the amino acid methionine) and the small ribosomal subunit. See Fig. 12.8, pg. 242 in Hoefnagels text. The large ribosomal subunit then joins this complex to begin the next stage.

Elongation: the stepwise addition of amino acids to a growing polypeptide chain. The amino acids are carried to the ribosome by the tRNAs. The ribosome moves along the mRNA one codon at a time, transferring new amino acids to the growing polypeptide chain via peptide bonds. See Fig. 12.8, pg. 242 in Hoefnagels text.

Termination: elongation stops at an mRNA stop codon (UGA, UAA, UAG), and the new polypeptide is released. The ribosome breaks into its large and small subunits, releasing the new protein and the mRNA. See Fig. 12.8, pg. 242 in Hoefnagels text.

Several ribosomes (polyribosomes) can translate the same mRNA molecule simultaneously. See fig. 12.9, pg. 244 in Hoefnagels text.
Chaparone proteins help guide the folding of the new protein (polypeptide).

Examples of Transcription and Translation

In this illustration the transcribed strand of the DNA is the upper line of letters (TAC CAC, etc).

Note that the mRNA sequence looks very much like the non-transcribed side of the DNA except, of course, that there are U's in the RNA and T's in the DNA.

RNA transcript of the beta-globin gene and corresponding amino acid sequence, from from Dr. Robert J. Huskey.

Here you can see the entire transcript (new mRNA molecule) just as it is produced by the RNA polymerase from the transcribed strand of DNA.

The introns, magenta colored sections, are cut out by enzymes in the nucleus.

The exons, the black sections, are spliced back together by other enzymes and sent out to the ribosomes for translation.

The abreviations of the amino acids are lined up with the codons in the exons so you can see the primary structure of the protein beta-globin.

Post-translation

Newly synthesized proteins are often modified after translation (post-translation) before they can carry out their function.

Proteins fold into a specific 3-D structure (conformation) as they emerge from the ribosome.

Chaparone Proteins oversee the process of proper folding. Fig. 12.9, pg. 244 in Hoefnagels text.

Animation of proteins being modified by the ER and Golgi bodies prior to secretion from a cell. from sumanasinc.com. Select "Protein Secretion".
Remember your answer to the Take-Home Assignment question dealing with human milk protein secretion?

Proteins may join other polypeptide units to form a larger, functional protein, as we saw with Hemoglobin from Medline Plus. (Hemoglobin is made up of two alpha globin chains and two beta globin chains plus 4 heme groups that carry oxygen.)

Errors in protein folding can cause illness, such as sickle cell disease or cystic fibrosis.

For more information on protein structure, see our last lecture.

Summary

Genes (DNA) are transcribed into RNA by the enzyme RNA polymerase. This process is controlled by proteins called transcription factors.

Prior to leaving the nucleus, the RNA is processed. To mRNA, a cap and tail are added and noncoding sequences (introns) are removed.

In the cytoplasm, mRNA molecules are translated by ribosomes (rRNA + ribosomal proteins) which match the 3-base codons of the mRNA to the 3-base anticodons of the appropriate tRNA molecules. The first AUG codon initiates translation, the message is read three consecutive bases at a time, and translation ceases when a stop codon is reached.

Newly synthesized proteins are often modified after translation, so that they can do their job properly.


5. Proteins

A protein is a molecule that performs reactions necessary to sustain the life of an organism. One cell can contain thousands of proteins.

5.1 RNA translation

Following transcription, translation is the next step of protein biosynthesis. In translation, mRNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or a polypeptide, that will later fold into a protein. Ribosomes read mRNA sequence in a ticker tape fashion three bases at a time, inserting the appropriate amino acid encoded by each three-base code word or codon into the appropriate position of the growing protein chain. This process is called mRNA translation. In particular, the mRNA sequence directly relates to the polypeptide sequence by binding to transfer RNA (tRNA) adapter molecules in binding pockets within the ribosome. Each amino acid is encoded by a sequence of three successive bases. Because there are four code letters (A, C, G, and U), and because sequences read in the 5′ → 3′ direction have a different biologic meaning than sequences read in the 3′ → 5′ direction, there are 4 3 =64, possible codons consisting of three bases. Some specialized codons serve as punctuation points during translation. The methionine codon (AUG), serves as the initiator codon signaling the first amino acid to be incorporated. All proteins thus begin with a methionine residue, but this is often removed later in the translational process. Three codons, UAG, UAA, and UGA, serve as translation terminators, signaling the end of translation. The completed polypeptide chain then folds into a functional three-dimensional protein molecule and is transferred to other organelles for further processing or released into cytosol for association of the newly completed chain with other subunits to form complex multimeric proteins.


39 Transcription: from DNA to RNA

Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with the important difference of the membrane-bound nucleus in eukaryotes. With the genes bound in the nucleus, transcription occurs in the nucleus of the cell and the mRNA transcript must be transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack membrane-bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell.

Transcription requires the DNA double helix to partially unwind in the region of mRNA synthesis. The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the process is called a promoter. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all of the time, some of the time, or hardly at all.

Figure 2: The initiation of transcription begins when DNA is unwound, forming a transcription bubble. Enzymes and other proteins involved in transcription bind at the promoter. Note the base-pairing between the RNA transcript and the template strand of DNA. From: Wikimedia public domain.

Transcription always proceeds from one of the two DNA strands, which is called the template strand. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the non-template strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. This means that the base-pairing rules between a DNA molecule and an RNA molecule are:

DNA RNA
A U
T A
C G
G C

An enzyme called RNA polymerase proceeds along the DNA template adding nucleotides by base pairing with the DNA template in a manner similar to DNA replication.

Figure 3: During elongation, RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5′ to 3′ direction, and unwinds then rewinds the DNA as it is read. Again, notice the base-pairing between the template strand of DNA and the newly forming RNA.

Once a gene is transcribed, the RNA polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA.

In a prokaryotic cell, by the time transcription ends, the transcript would already have been used to begin making copies of the encoded protein because the processes of transcription and translation can occur at the same time since both occur in the cytoplasm (Figure 4). In contrast, transcription and translation cannot occur simultaneously in eukaryotic cells since transcription occurs inside the nucleus and translation occurs outside in the cytoplasm.

Figure 4: Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.


  • Protein synthesis is the process in which cells make proteins. It occurs in two stages: transcription and translation.
  • Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It includes three steps: initiation, elongation, and termination. After the mRNA is processed, it carries the instructions to a ribosome in the cytoplasm.
  • Translation occurs at the ribosome, which consists of rRNA and proteins. In translation, the instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the ribosome. Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain.
  • After a polypeptide chain is synthesized, it may undergo additional processing to form the finished protein.
  1. Relate protein synthesis and its two major phases to the central dogma of molecular biology.
  2. Explain how mRNA is processed before it leaves the nucleus.
  3. What additional processes might a polypeptide chain undergo after it is synthesized?
  4. Where does transcription take place in eukaryotes?
  5. Where does translation take place?

Answers and Replies

When a textbook states that DNA can only be replicated in the 5' to 3' direction, it is referring to the synthesis of DNA. Each strand of DNA has a 5' end and a 3' end. In order to make that strand longer, you could imagine adding new DNA to the 3' end of the strand or to the 5' end of the strand. As it turns out, DNA polymerases can only add new nucleotides to the 3' end of the strand and not the 5' end of the strand, so DNA gets synthesized in the 5' --> 3' direction.

In your example, you have the right idea. Both strands of DNA can be copied, and when they're being copied the DNA polymerases will be moving in opposite directions. When synthesizing the top strand, DNA polymerase can only synthesize it from left to right (5' to 3'), and when synthesizing the bottom strand, the polymerase will be moving from right to left. You could not have the case where the top strand is synthesized by a polymerase moving from the right to left because DNA polymerase cannot work in the 3' to 5' direction.

Why can't polymerase add nucleotides to the 5' end of the DNA? DNA synthesis is powered by the release of pyrophosphate (the final two phosphates on the nucleotide triphosphates) that occurs during DNA synthesis. These phosphates are attached to the 5' end of the nucleotides. These triphosphate groups are somewhat unstable and can sometimes break off on their own. If nucleotides were added to the 5' end of the DNA, accidental loss of the 5' triphosphate would be a big problem without the 5' triphosphate, DNA synthesis could not continue. However, if new nucleotides are added to the 3' end of the DNA, it doesn't matter if the 5' triphosphate of the DNA strand gets damaged. For 5' to 3' synthesis, loss of triphosphates from the nucleotides would cause problems, but there are so many nucleotides in the cell that the low rate of tirphosphate loss from the nucleotides does not affect the rate of DNA synthesis.

I hope that clears up your question. Let me know if anything is still unclear.

What you are asking, we are presuming, is why couldn't you have the growing DNA chain with -5'PPP at its end and then a mononucleoside 5'-triphosphate condense its 3'-OH onto that with elimination of pyrophosphate which would give a chain one nucleotide longer with 5'PPP at the end ready to do the same thing again.

Watson in his textbook gives much the same explanation as Ygggdrasil except instead of random loss of the terminal phosphate or pyrophosphate he invokes proofreading, which is the exonuclease eating back the new strand for error correction. This is hydrolysis which is energetically favoured, while if it had to leave PPP at the end of the eaten-back strand, it would have to be an pyrophosphate transfer energetically driven by say ATP at every step. It sounds awkward and hard to imagine it being preferred.

If instead the question is couldn't you have mononucleoside-3'-triphosphates that condense on a 5'OH end of growing DNA and so extend it in the 3'->5' direction I don't know anyone can give a reason. In fact I'd say you could but you don't, in life on earth.

The thing to remember is 5'(mono, di and triphosphates are queens, kings and aces in biochemistry on earth. Think ATP - 5'ATP. This is reflected even in the terminology I think. You could consider a DNA strand to be a polymer either of nucleoside 5' or of 3' phosphates. But considering 5' king, you divide mentally the chain up into 5'-PN-3'OH monomeric units, and so define a 5'->3' direction, the only way I find the terminology not confusing.

The empire of 5'- is not a fact about chemistry. The energetics of phosphate or pyrophosphate transfer from 3'- or 5'- NTP or from dNTP should be about the same. It's a fact of biology. Enzymes recognise and catalyse reactions with the 5'-P- compounds. The reason must go back to the origin and early history of life. I guess a 5' with its extra O-C-O- can explore a much larger volume and variety of interacting complementary structures so a catalyst has a greater chance of evolving.

I have never heard any considerations on this - it's not the sort of thing you are very encouraged to ask in biology. If that reflects on anyone it's not the person asking the question IMHO.


Cell Signaling and Recognition

Cell signaling is how cells communicate with each other, with cells typically communicating using chemical signals such as neurotransmitters. A sending cell releases the proper chemical where it is transported to a target cell with the proper receptor for the chemical. The chemical then binds to the receptor and triggers a change in the cell. There are four basic types of cell signaling: paracrine signaling, autocrine signaling, endocrine signaling, and signaling by direct contact.

A variable R group can also be bound to the head of a phospholipid, similarly to amino acids. This R group is typically a simple organic molecule such as choline, which can associate with some proteins and allow cells to recruit certain proteins to the cell membrane. This is important for cell communication.

Sphingolipids are another type of lipid found in the cell membrane separate from phospholipids. They play essential roles in cell signaling, with certain types of sphingolipids being involved in cell signaling and recognition. The core of a sphingolipid is an amino alcohol called sphingosine.


Watch the video: A full explanation about the Telomerase and the end replication problem (May 2022).