So long, farewell….

BrandnB: Okay guys, farewell till next time meaning a month or two till our next post… Ok you caught us… We will be back soon to share our understanding in the subject of Biochemistry. BrandnB here yet again expressing my thanks for the new followers, viewers, especially the viewers from other countries and also my fellow bloggers you know yourselves once again thanks till next time.

Hazel-Ann: Well guys this brings us to the end of blogging for this semester (don’t worry we’ll be back :P)! I must say the journey has just begun and so far it has been quite prosperous and I am honoured to have worked alongside all of the other members of Twisteddnas: Breaking the Bond! I have learned from this blogging activity that great team work is an important asset to a holistic individual. Constant blogging has also helped me in remembering what was taught by my amazing lecturer, Mr. Jason Matthew. Through this activity I was able to express my thoughts about Biochemistry thus far. I have also seen a great improvement in my creativity skills and have become more of an innovative thinker because of this blogging. I have learnt skills I have never been exposed to before like how to do a wordle, a video review, a reflection, even how to blog and much more! I am grateful for the experience and surely look forward to moving on to year two of Biochemistry and to embrace what it has to offer. I hope that Twisteddnas: Breaking the Bond has been helpful to you in many ways. So goodbye for now and I wish all of my colleagues good luck in final exams!

Kevin: Hello friends. This is Kevin here. It’s been a long and hard semester and we have finally completed our creative and helpful blog. This is definitely not a goodbye note but it’s simply a conclusion of all our work during this semester. I had absolute fun with this blog because it was a new, creative form of learning, not for just me but also for all our viewers and the other member of Twisted DNAs. I’d also like to thank our lecturer Mr. Jason Matthew for his guidance and effective teaching abilities. Additionally, I know I speak for everyone when I say that we all enjoyed making this blog and we hope you guys enjoy it as well. See you guys!!

Aaliyah: Hey guys! Well this semester has finally come to an end and that means blogging is over. *sad face* It definitely was an enjoyable experience, hard at times, but fun and helpful anyway. Continue to be the amazing Biochemians you are and work hard towards your goal! Thank you all for viewing our blog and I hope that it helped in some way J Farewell for now, wishing my peers (and myself lol) all the best in finals!

Kim: Hey guys its Kim. It has been great over the past few months blogging about biochemistry. I have learnt a lot while teaching the world biochemistry. Hopefully this is not the last time you guys hear from us. Certainly I have enjoyed blogging and so much so I have decided to take it up as a hobby of mine. Thanks guys for reading our blog and wish us luck for finals, they are in a couple weeks!

 

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Youtube Review 2 – Glycolysis!

The video of review is a You Tube video entitled, “Glycolysis: The Reactions,” published by the NDSU VCell Production’s Animation. This five minute video covered the basic aspects of glycolysis such as what it does, where it occurs, the products of the reaction and the division into two phases. The video became more detailed as they included the ten reactions of glycolysis. For each reaction, they even named the enzyme catalyst, the products of the reactions and stated which reactions were irreversible. Additionally, chemical structures were provided in each reaction for better understanding of the changes that occur.
However, despite its great detail, the video failed to describe the importance of the some of the enzymes for example PFK-1 being of great significance with respect to regulation and Triose Phosphate Isomerase being a kinectically perfect enzyme. The video also lacked all the fates that the pyruvate molecule can undergo and the products of these fates. The only fate that was mentioned in the video was under aerobic conditions but no details were provided on this process. However, for a five minute video, it is quite detailed and helpful to persons trying to acquire a quick understanding of glycolysis. It is a video that I would highly recommend because of its organization and effectiveness in five minutes of teaching.
Kevin and Aaliyah signing out!

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MULTIPLE CHOICE QUESTIONS

For the following question ON ENZYMES:

Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:

A) 1, 2 and 3 are correct

B) 1 and 3 are correct

C) 2 and 4 are correct

D) Only 4 is correct

E) All are correct

 

A)    Which one is not a characteristic of competitive inhibition?

1)      The inhibitor binds to the enzyme-substrate complex

2)      It can be overcome by increasing the substrate concentration

3)      Km increases while Vmax decreases

4)      The inhibitor is similar in shape to the substrate

 

 

Multiple Choice 2 –Glycolysis

1)      For every glucose molecule entering glycolysis

a)      2ATP & 2NAD+ are used, 8ATP & 4NADH generated

b)      4ATP & 3NAD+ are used, 8ATP & 3NADH generated

c)      2ATP & 2NAD+ are used, 2ATP & 6NADH generated

d)     2ATP & 6NAD+ are used, 4ATP & 2NADH generated

 

 

YOUTUBE REVIEW 1

 Review of the video: LET’S TEST YOUR ATTENTIVENESS!!!

Hey guys this is Hazel-Ann and Kimberly here to bring you the YouTube review. So this video is sooo informative it’s just amazing…Mr. Jason Matthew basically explains everything you need to know about cells (at this introductory level of Biochemistry) in the most interesting, student friendly way possible. Apart from that, what I really love about this video is the presentation of the information. Mr. Jason ensures that he leaves you with visual representations of every topic he speaks about…so either way, it will be quite easier for the listener to recall what he has heard and observed. Below is a breakdown of information gathered from the entire video. We tried my best to present it in a creative, fun way to see how well both you and I have retained what we saw and heard in the video. The main points are listed below. I hope you enjoy it 🙂

-There are two main types of cell, prokaryotes and eukaryotes:
-Eukaryotes cells have a membrane bounded nucleus
-However prokaryote cells lack a nuclei.
-Prokaryotes have 70s ribosomes and eukaryotes have 80s ribosomes.
-Prokaryotes have circular DNA
-Eukaryotes have DNA in the form of linear chromosomes
-*NB*: ribosomes are measured in Svedsburg units, denoted by “s”, which is used to measure how fast molecules move within the cell.

Therefore we can officially say:

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Figure 1- The cell model showing its structures. (msrosenreads.com)

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The table below shows the composition and functions of various structures of plant and animal cells. However, the FUNCTION column is not in order!! You must carefully read the contents of each column and match each structure to its corresponding function from the FUNCTION column. If you get all correct……you are a BIOCHEMATIC!

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Also the differences between prokaryotes and eukaryotes were clearly stated in which the main distinction is whether the cell lacks a nucleus. The video was very informative and interactive which made me want to learn more. So I researched the cell and found out that mitochondria is inherited from the maternal line only! HOW COOL! Believe it or not we have our mother’s mitochondria. Mr. Matthews allows learning to be seen in a new light and actually makes you want to study. He explains everything thoroughly and allows you to answer questions to make sure you were not sleeping during the video or wake you up if you were. Lol just kidding.

Anyways guys that’s all about this youtube review! Hope you enjoy the video as much as we did!

bye2

 

PUBLISHED PAPER REVIEW 2.

Hello there!! This is Hazel-Ann and today I have a review of a published paper “Amino Acid Fingerprints Revealed in New Study” by Arizona State University. So it was a bright and sunny day and I decided to randomly browse the internet when BAM!!! I came upon the most interesting piece of science I have ever read! What I saw in this article augmented my knowledge in unexplainable ways. Yesss…I’m dead serious! So of course I couldn’t wait to share this new finding with you all.    

By now, the human genome project is no stranger to society. The human genome comprises three billion base pairs. Through the project, this code was decrypted effectively by 2003. This breakthrough in science has provided limitless insights and ideas pertaining to disease and the human health. If researchers can unlock the amino acid sequences from which protein is composed, scientists can have a better insight of diseases and the DNA. A group of researchers of Arizona State University led by Stuart Lindsay have embarked on an experiment to identify amino acids. Using state-of-the-art equipment, the team placed each amino acid between two electrodes and measured the current that went through each amino acid. Depending on this chain of current, which is characteristic of the amino acid, the scientists programmed a computer to identify each burst of electricity which indicated binding of an amino acid between the electrodes. Noise signals represented fingerprints and identified amino acids as well as modified variants. Currently, information on cancer, diabetes, Alzheimer’s and many other diseases are obtained from proteins. Protein sequencing will not only aid in patient treatment, but it will also be the means of advancement of molecularly examining the reaction of disease to therapeutics. Proteome is a huge amount of proteins.  Proteins are inevitably vital for growth, repair defense and catalysis. From the Human Genome Project, it was found that only 1.5% of genome codes for proteins. It is quite alarming that the human contains such a low gene number. But this can be accounted for by the modification of proteins generated from the DNA blueprint. It has been found that these proteins can alter their functions or become inoperable and this is detrimental to human health. This modification of proteins is caused by either alternative splicing (when exons are spliced and introns are cut off before translating into proteins) or post-translational modification (when markers like methylation and phosphorylation are added after production of proteins). Numerous cancers are linked with these modified protein faults. This makes for useful diagnostic indications. Once these proteins are identified, there will be a great revolution in Biomedicine. This led scientists to use the recognition tunneling method (used to determine the presence of particular nucleotide bases) for identifying the twenty amino acids in proteins instead of the four bases in DNA. This method has identified proteins that have been modified post transitionally from their unmodified precursor. As well as to distinguish between enantiomers and isobaric molecules (mirror image molecules). Lindsay states that many more researches and experiments are being executed for rapid progression of creating an amino acid fingerprints. This idea has solely been derived from the accomplishment of the human genome project. The hi-tech equipment are available for making this leap in Biochemistry and Biomedicine a successful one. Once the amino acid fingerprints are achieved, they can be applied to diagnostic medicine and can lead to a new era of research and findings for the cures of various diseases. The potentials of this project is limitless! So that’s it folks! Interesting, huh?? Can you imagine how easy it will be to diagnose diseases by knowing the amino acid sequence? What about using the fingerprints to find cures for various cancers? A new era of science dawns…

 

Reference:

 

Arizona State University. 2014. “Amino acid fingerprints revealed in new study.”                                                           ScienceDaily.www.sciencedaily.com/releases/2014/04/140406162416.htm (accessed April 8, 2014).

NUCLEOTIDES AND NUCLEIC ACIDS

Hey guys, Kimberly and Aaliyah here this week and we’re talking nucleotides and nucleic acids!

So we’ve learned before about the “central dogma” of molecular biology that basically encompasses the transcription from DNA to RNA and then the translation from RNA to protein.

Did you ever stop to think about what these things might be made of, however? Well today you’re gonna get the long-awaited answer for your question 😛

DNA and RNA are made up of nucleotides. These are the basic units or the building blocks of nucleic acids. Nucleotides are made up of three components- a sugar, a base and a phosphate group.

Components of Nucleotides:

Sugar: The first component we will talk about is the sugar part of a nucleotide. This is a 5-carbon sugar otherwise known as a pentose. Two kinds of these sugars are found in nucleotides. These are deoxyribose, which has a single hydrogen atom (H) attached to its carbon 2, and ribose, which has a hydroxyl group (-OH) attached to the carbon 2 instead. Deoxyribose is found in DNA while ribose is found in RNA. Deoxyribose gets its name simply because it is ribose that has lost an oxygen atom.

 

Base: The bases used in making up nucleotides are heterocyclic bases or nitrogenous bases (because they have a nitrogen incorporated into the ring, duh!). These bases can be separated into two types- the pyramidines and the purines. These have one ring, and are cytosine (C), thymine (T) and uracil (U), and two rings, and are adenine (A) and guanine (G) respectively. The pyramidines in DNA are cytosine and thymine and the pyramidines in RNA are cytosine and uracil, while the two purines, adanine and guanine are found in both DNA and RNA.

Phosphate: For nucleotide polymerization to occur and for these nucleic acids to be formed, a phosphate group must be present.

Altogether, these groups make up one nucleotide illustrated in the picture below.

When a pentose sugar is bonded to the base alone, the structure is called a nucleoside. When  phosphate group is added to the nucleoside, it becomes a nucletotide 🙂

DNAis made up of two polynucleotide chains, which are chains that are made by the joining together of nucleotide monomers that coil around each other. They not only coil around each other, but have bonds between the chains that hold the two polynucleotide chains together. This double helix is held together by hydrogen bonds that are formed between the bases of both chains. This occurs via complementary base pairing where adenine forms two hydrogen bonds with thymine and cytosine forms three hydrogen bonds with guanine.

It’s pretty simple once you see it in a picture isn’t it? Kinda looks like a twisted ladder, right? Lol Just think of the ladder rungs being the amine bases all paired up joined by hydrogen bonding, and the backbones being the sugar and phosphate parts! Easy like a Sunday morning.

Now where do bases attach to nucleic acids?

  • C1 position of ribose or deoxyribose
  • Pyrimidines attach via their N1 position of the ring to the pentose
  • Purines attach through the N9 position
  • Other bases(minor) have different attachments.
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ROLES OF NUCLEOTIDES

  • Building material of nucleic acids (RNA,DNA)
  • Provide energy in cellular metabolism (energy currency- ATP)
  • Allosteric effectors
  • Enzyme cofactors are structurally made up of nucleotides eg NAD

 

ROLES OF NUCLEIC ACIDS

  • DNA contains:

1)      genes – information needed for functional protein and RNA synthesis

2)      promotors- segments which are involved in gene expression regulators

  • rRNAs (ribosome RNA) – made up of ribosomes which are involved in synthesis of proteins.
  • mRNAs (messenger RNA) – acts as a messenger owl carrying genetic information from gene to ribosome.
  • tRNA (transfer RNA) – information taken from mRNA is then translated into an amino acid sequence.
  • In some cases, RNAs perform catalysis.

Huh guys, imagine life without nucleotides or nucleic acids, do you think we would have even existed!  So I guess you can’t imagine life cause there would be none!

 

ATP

  • Adenosine triphosphate (nucleotide)
  • Contains adenine, ribose and triphosphate group
  • Energy carrier
  • Provides energy for other cells which perform jobs such as biosynthetic reactions, ion transport and cell movement.
  • Energy of ATP is made when the transfer of 1 or 2 of its phosphate groups to another molecule occurs. ADP + Pi —–à ATP
  • Reverse reaction is the hydrolysis of ATP to ADP.

http://hyperphysics.phy-astr.gsu.edu/hbase/biology/atp.html

NAD

    

NUCLEOTIDE REGULATION

  • COVALENT MODFICATION– activates some enzymes and inactivates others because enzymes are inactive until they are covalently modified so they could work. Eg Phosphorylation
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NUCLEIC ACIDS

–          Polynucleotides

–          Oxygen at 5’ end of one nucleotide is connected to the oxygen of the 3’ end of another.

–         

 

NUCLEIC ACID STRUCTURE

–          The sugar phosphate is the backbone of the nucleotide

–          There are 2 separate strands:

1)      Parallel (3’à5’ direction)

2)      Antiparallel (5’à3’ direction)

 

–          Base pairing – hydrogen bonding holding the 2 strands together.

–         

–          http://www.visionlearning.com/en/library/Biology/2/DNA-II/160

This structure is important in:

–          DNA replication

–          RNA transcription

–          Backbones are the sugar –phosphate which are negatively charged so it is located outside

 

–          Planner bases are stacked above each other like pancakes however on the inside

 

HOW ARE NUCLEIC ACIDS FORMED?

–          Monomers of nucleotides are joined by phosphodiester linkage which is a formation between the hydroxyl (OH) group at the 3’ end of nucleotide and phosphate of a next nucleotide.

–          The 5’end then lacks a nucleotide at the 5’ position and the 3’ end lacks a nucleotide at the 3’ position.

 

HELICAL TURN

–          10 base pairs per turn

–          34 amino acids per turn

–          There are 3 helices called:

1)      A form

2)      B form

3)      Z form

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NUCLEIC ACIDS

–          Most common form for DNA is the B form. It is the standard DNA double helix.

–          Most common form for RNA is the A form. WHY?

–          Because of its deeper minor groove and shallow major groove. It is also favoured in low water conditions.

–          Z form:

–          Has a narrow, deep minor groove

–          Has no major groove

–          Can form some DNA

–          However requires alternating syn and anti base configurations

–          It is a laboratory anomaly

–          Because of its high salt or charge neutralization and it is left handed while most helices are right handed.

B- DNA

–          Has a deeper major groove  and a

–          Shallow minor groove

 

RNA

–          rRNA – RNA + PROTEIN -à RIBOSOMES

–          mRNA

o   carries DNA code to cytosol for protein synthesis or ribosomes.

o   Are read in codons  or triplets from (5’ to 3’ direction)

–          tRNA

o    carries amino acids to mRNA and like a puzzle matches up by base-pairing of anti codon with mRNA codon.

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STABILITY OF NUCLEIC ACIDS

There are many factors which stabilize and destabilize the helix of nucleic acids. They are:

1)      HYDROGEN BONDING

o   Contributes to DNA double helix, RNA secondary structure

2)      STACKING INTERACTION OR HYDROPHOBIC INTERACTION BETWEEN BASE PAIRS

o   It is energetically favourable

o   Maximized stacking in double-stranded DNA

 

EFFECT OF ACID ON NUCLEIC ACIDS

–          Strong acid and high temperatures

o   They are hydrolysed to base,riboses  or deoxyriboses and phosphate.

–          At pH 3-4 apurinic nucleic acids are formed. This is due to the glycosylic bonds attaching the purine A and G bases to the ribose ring are broken.

–          However formic acid regenerates this.

 

 

EFFECT OF ALKALI ON NUCLEIC ACIDS

–          HIGH pH (>7-8)

o   Small effects on DNA structure

–          HIGH pH

o   Changes the tautomeric (keto and enol forms) state of bases.

–          Change in tautomeric states of bases results in DNA denaturation therefore it results in unstable base pairing.

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–          RNA  is unstable at higher pH because of its 2 OH groups.

 

CHEMICAL DENATURATION OF NUCLEIC ACIDS

Two chemical which denature nucleic acids are:

-Urea (H2NCONH2)

– Formamide (HCONH2)

HOW IT OCCURS?

-Disrupts hydrogen bonding of water solution

-Reduction of hydrophobic effect between bases

-Denaturation of strands in double helix

 

BUOYANT DENSITY OF DNA

–          1.7gcm-3 = 8M CsCl

–          It is used in DNA purification

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C3 SPECTROSCOPIC AND THERMAL PROPERTIES OF NUCLEIC ACIDS

1)      UV SPECTROSCOPY

o   Absorption of UV light due to bases

o   Maximum wavelength absorption by both DNA and RNA (Max=260nm)

o   Applications: detection, quantitation , assessment of purity (A260/ A280)

2)      HYPOCHROMICITY

o   Creation of hydrophobic environment by stacking of bases making them less accessible to UV absorption (dsDNA, ssDNA or RNA nucleotide)

o

3)      QUANTITATION OF NUCLEIC ACIDS

o   Extinction coefficient- 1mg/ml dsDNA has an A260 of 20 ssDNA and  25 RNA

o   The values for ssDNA and RNA are approximate

o   Values are the sum of absorbance of different bases (purines are more than pyrimidines)

o   Absorbance values depend on the amount of secondary structures due to hypochromicity or stacking of bases.

4)      PURITY OF DNA

o   A260/ A280

o   DsDNA – 1.8

o   Pure RNA -2.0

o   Protein – 0.5

5)      THERMAL DENATURATION/MELTING

o   Destruction of the double stranded hydrogen bonded regions of DNA and RNA

o   RNA – absorbance increases gradually and irregularly

o   DNA- increases cooperatively.

o   Tm- melting temperature. This the temperature at which a 40% increase in absorbance is achieved

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6)      RENATURATION

o   Rapid cooling- only allows formation of the local base pairs and absorbance is slightly lowered.

o   Slow cooling- the formation of the whole complementation of dsDNA and absorbance decreases gradually and cooperatively just like denaturation

OK guys i think that’s enough for nucleotides and nucleic acids. SEE YOU NEXT TIME! have a great weekend!

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