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What makes/breaks the hydrogen bonds between DNA and RNA during transcription?

What makes/breaks the hydrogen bonds between DNA and RNA during transcription?


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So I know that RNA polymerase catalyzes the phosphodiester bonds that hold the sugar backbones of a growing mRNA molecule together during transcription. However, I'm less sure about the hydrogen bonds between the nitrogenous bases of the forming RNA and the template DNA strands.

I do assume that hydrogen bonds are forming, but they must be short-lived. Their existence are confirmed here:

ribonucleotides containing 3 phosphate groups hydrogen bond through the process of complementary base pairing with the exposed deoxyribonucleotides on the unwound strand that is to be transcribed

and represented in this gif:

Is RNA polymerase responsible for creating the hydrogen bonds between DNA and RNA? Is it, then -- I assume -- also responsible for breaking these bonds? Are the breaking bonds driven by chemical reactions or more due to the physical movement of the polymerase along the DNA template?

This site mentions the transient H-bonds formed by holoenzyme at promoter sites, but I haven't been ale to fnd a reputable source discussing the transient H-bonds between nucleic acid strands.

I'd appreciate if someone can provide a clearer molecular description of what's going on here. Pictures/animations are a plus!


I wouldn't really say RNA polymerase is "creating" the hydrogen bonds so much as it's thermodynamics that creates them. When we talk about an enzyme "creating" a bond, what we're generally referring to is an enzyme facilitating a reaction by lowering its activation energy so that it can proceed.

However, in the hydrogen bonding between base pairs, there's not really much activation energy to overcome. Before the formation, the nucleotide is just floating around in the cell (solvated by water), and forming a base pair is more energetically stable than not being paired. When a ribonucleotide happens to diffuse into contact with the unpaired DNA strand, the hydrogen bond will spontaneously form because it's energetically favorable. The thing about hydrogen bonds, though, is they're fairly weak, so there's an equilibrium between formation and breaking. When a mismatched nucleotide diffuses into that space, the hydrogen bonding isn't as strong, and it might be in an improper orientation, so it'll diffuse out again. When the correct nucleotide enters, the hydrogen bonds will form spontaneously, hold it there longer, and orientate it properly. This properly places the phosphates for backbone formation, which allows RNA polymerase to proceed with making the backbone.

As for the breaking of the hydrogen bonds, it's the energy released from the phosphodiester bond formation that causes the bonds to break at the other end of the RNA-DNA hybrid. To simplify things a lot, it's kind of like a zipper, where forward translocation of RNA polymerase along the DNA strand is driven by phosphodiester bond formation, which breaks the hydrogen bonds of the RNA-DNA hybrid somewhat mechanically, as the nascent RNA strand leaves through a different channel than the DNA does.

References:

Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Route

Transcription elongation: Heterogeneous tracking of RNA polymerase and its biological implications


Although the answer provided by @StephenB is essentially correct, I'd like to supplement this with more visual illustrations - including a link to an animation which the poster requested - as well as reiterating the important points he makes about enzymes. This is a question about enzymology and structural biology and is essentially chemical in nature.

Enzymes and Chemistry

To answer the specific question posed:

No. Enzymes are not responsible for creating any sort of bond.

The creation of bonds - including the hydrogen bonds of base-pairs - is governed by the thermodynamics. Enzymes are catalysts and only affect the speed of reactions that are thermodynamically favourable. In brief:

1. Reactions only occur which result in a decrease in Gibbs free energy.
We are always comparing two alternative situations. In the case of nucleic acid hybridization, for example, we may at different stages of transcription have to consider ssDNA v. dsDNA, ssDNA and ssRNA v. RNA-DNA heteroduplex, DNA-DNA homoduplex v. RNA-DNA heteroduplex. The problem with transcription is not why rNTPs bind to DNA, but why different hydrogen-bonded structures, of necessity, occur at different stages in the cycle.

2. Reactions involve an equilibrium between the forward and reverse direction.
Unless a reaction product is removed, there is generally no conceptual difficulty about the reaction also occurring in the reverse direction. The extent to which this happens will depend on the position of the equilibrium. For transcription such reversal is important because stretches of RNA, initially hydrogen-bonded to DNA, need to be released from it, and stretches of DNA have to alternate between being double-stranded and single-stranded.

3. Enzymes speed up reactions (in both forward and reverse direction). They have no effect on whether or not a reaction is thermodynamically favourable.
As @StephenB mentioned, enzymes speed up reactions by affecting the activation energy - generally raising the ground state or lowering the activation energy by facilitating an alternative reaction sequence. In the case of the binding of the an rNTP we know from chemistry that the strength of a hydrogen bond depends on its directionality. Hence many random collisions will be unproductive. Without knowing anything about the real situation, we can speculate that weak bonds to residues on the rNTP binding-site of RNA polymerase may facilitate a reorientation to the optimal position for base pairing.

This material is covered more fully in textbooks of biochemistry, e.g. Berg et al. Ch. 8.

Transcription - The Movie

In a Cell Perspectives article in 2012, Cheung and Cramer described a movie of mRNA transcription by RNA polymerase II and other factors based on published structures of various intermediates. Although this was produced by interpolating between static 'snapshots' of structures, it is a comprehensive attempt using three-dimensional structures to address different stages of transcription - melting of the dsDNA, movement relative to the DNA duplex, and dissociation of the transient heteroduplex. This is illustrated in a figure from the paper:

I have constructed my own composite of screen shots of that section of the movie (from about 3.00 min) that deals with binding of rNTPs. In contrast to the figure above, it shows only a small section of RNA polymerase in order to focus on the dynamic changes that occur in two sections of this protein on binding the substrate (another feature of many enzymes).

The rNTP-binding step

The depiction of rNTP-binding in the movie is summarized as:

… an NTP substrate first binds to an open active center conformation, adopting a preinsertion state… . The NTP then moves slightly to occupy the insertion site as the trigger loop folds to close the active center… . Closure of the active site around the NTP generates contacts that are required for correct NTP selection and leads to catalytic nucleotide incorporation and RNA extension… .

This is based on the work of Vassylyev et al. who describe the molecular interactions in more detail. I quote an extract from their paper to illustrate that the supposition about interaction of the substrate with residues on the enzyme is borne out, but also that the complexity of the interactions is such that it is not possible to make a simple summary:

In the ttEC/AMPcPP complex, AMPcPP forms a Watson-Crick base pair with the acceptor template sandwiched between the 39 end of the RNA/DNA hybrid on one side and the protein residues from the TH and BH on the other. Met b91238 (TH) and Thr b91088 (BH), which stack directly on the substrate and template bases, respectively, seem essential for the positioning and selection of the substrate (Fig. 2); the corresponding RNAPII residues Leu 1081 and Thr 831 seem to have similar functions in the yeast EC13. In agreement with modelling and biochemical studies1,4,15, Asn b9737 forms hydrogen bonds with both O39 and O29 of the substrate ribose, thereby permitting discrimination against the non-cognate dNTPs lacking either or both of these atoms (Fig. 2b, c).

The interested reader will need to study the paper himself. I restrict myself to reminding him that the structures of enzymes are dynamic because there may be an equilibrium between different possible structures and the position of this equilibrium can be changed by the binding of other molecules to the enzyme. It's still chemistry - not magic!

Coda - Why no straight answer?

The reader accustomed to having reaction mechanisms of enzymes presented in dogmatic form may wonder why there are so many ifs and buts and molecular dynamics involved in working out how the rNTP gets to the correct conformation to bind to the DNA template. The answer is that although the structure of the binding site (actually there appear to be two alternatives) is known in detail, the successive positions of the rNTP are not, because there is no way of 'freezing' it at these different stages. Generally one captures intermediates in a reaction by making derivatives of them that will bind but not react, for example. So it is relatively easy to get structures for the rNTP bound and hydrogen-bonded, but not on its way in. A 2017 paper in the Journal of Biophysics indicates that mathematical methods are still being used as the basis of arguments about the detailed binding mechanism.


Transcription (biology)

Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). Averaged over multiple cell types in a given tissue, the quantity of mRNA is more than 10 times the quantity of ncRNA (though in particular single cell types ncRNAs may exceed mRNAs). [1] The general preponderance of mRNA in cells is valid even though less than 2% of the human genome can be transcribed into mRNA (Human genome#Coding vs. noncoding DNA), while at least 80% of mammalian genomic DNA can be actively transcribed (in one or more types of cells), with the majority of this 80% considered to be ncRNA. [2]

Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript.

Transcription proceeds in the following general steps:

  1. RNA polymerase, together with one or more general transcription factors, binds to promoter DNA.
  2. RNA polymerase generates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides.
  3. RNA polymerase adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand).
  4. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand.
  5. Hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand.
  6. If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing.
  7. The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore complex.

If the stretch of DNA is transcribed into an RNA molecule that encodes a protein, the RNA is termed messenger RNA (mRNA) the mRNA, in turn, serves as a template for the protein's synthesis through translation. Other stretches of DNA may be transcribed into small non-coding RNAs such as microRNA, transfer RNA (tRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), or enzymatic RNA molecules called ribozymes [3] as well as larger non-coding RNAs such as ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Overall, RNA helps synthesize, regulate, and process proteins it therefore plays a fundamental role in performing functions within a cell.

In virology, the term transcription may also be used when referring to mRNA synthesis from an RNA molecule (i.e., equivalent to RNA replication). For instance, the genome of a negative-sense single-stranded RNA (ssRNA -) virus may be a template for a positive-sense single-stranded RNA (ssRNA +) [ clarification needed ] . This is because the positive-sense strand contains the sequence information needed to translate the viral proteins needed for viral replication. This process is catalyzed by a viral RNA replicase. [4] [ clarification needed ]


02 Molecular biology

This page lists the understandings and skills expected for topic two.
Helpful for revision.
Detailed revison notes, activities and questions can be found on each of the sub-topic pages.

  • 2.1 Molecules to metabolism.2
  • 2.2 Water
  • 2.3 Carbohydrates and lipids
  • 2.4 Proteins
  • 2.5 Enzymes
  • 2.6 Structure of DNA and RNA
  • 2.7 DNA replication, transcription and translation
  • 2.8 Cell respiration
  • 2.9 Photosynthesis

2.1 Molecules to metabolism

  • Molecular biology is explaining biological processes in terms of the chemicals involved.
  • The is a diversity of Carbon based compounds in living things because carbon atoms can form four covalent bonds.
    e.g. carbohydrates, lipids, proteins & nucleic acids.
  • All the enzyme-catalysed reactions in a cell make up its metabolism. There are two types:
    • Anabolism: forming macromolecules from monomers by condensation.
    • Catabolism: breaking complex macromolecules into simpler molecules by hydrolysis.
    • Draw diagrams of:
      • &alphaD-glucose & &betaD-glucose,
      • D-ribose,
      • a fatty acid
      • an amino acid with generalised R-group.
      • monosaccharides
      • disaccharides,
      • lipids (triglycerides, phospholipids and steroids)
      • amino acids
      • polypeptides and peptide bonds.

      2.2 Water

      • Hydrogen bonds form between polar water molecules.
      • This force give water special properties, e.g. cohesiveness, adhesiveness, thermal
        and solvent properties.
      • Glucose, amino acids and salts are hydrophilic while cholesterol and fats are hydrophobic.
      • Compare the thermal properties of water with those of methane and explain how this affects its use as a coolant in sweat.
      • Compare the solubility of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in water and link this to the way they are transported.
      • Explain benefits of water properties to living organisms (Transparency and density not required.)
      • Evaluate how significant hydrogen bonding is in the properties of water

      2.3 Carbohydrates & Lipids

      • Condensation reactions link Monosaccharide monomers together to
        form disaccharides (Sucrose, lactose and maltose) and polysaccharides.(cellulose starch and glycogen)
      • Fatty acids can be saturated, monounsaturated or polyunsaturated.
        and cis or trans isomers if they are unsaturated. (molecule names not required)
      • Three fatty acids and one glycerol molecules can form a Triglycerides by condensation reactions.
      • How the structure of cellulose and starch (amylose & amylopectin) in plants and glycogen in humans relates to function.
      • For long-term energy storage in humans
        lipids are better than carbohydrates.
      • Potatoes have been genetically modified to reduce the level of amylose to
        produce a more effective adhesive.
      • Evaluate the conflicting evidence for health risks of trans fats and saturated fatty acids and evaluate the methods used
      • Abiliy to use molecular visualization software like jmol to compare cellulose, starch and glycogen.
      • Ability to work out a BMI using a nomogram or by calculation

      2.4 Proteins

      • Amino acids are linked together by condensation reactions to form a di-peptides and polypeptides.
      • Genes and mRNA strands code for 20 different amino acids which are built into polypeptides on ribosomes.
      • Amino acids can be linked together in any sequence (coded for by genes) giving a huge range of possible polypeptides.
      • A protein may be a single polypeptide or more than one polypeptide joined together.
      • The three-dimensional shape of a protein is determined by the sequence of amino acids.
      • Living organisms synthesize many different proteins with a wide range of functions (not structure)
        e.g. Rubisco, insulin, immunoglobulins, rhodopsin, collagen & spider silk.
      • Every individual has a unique proteome.
      • Proteomics and the production of proteins by cells cultured in fermenters
        offer many opportunities for the food, pharmaceutical and other industries
        (a utilisation)

      2.5 Enzymes

      • The role of the active site where specific substrates bind.
      • The effect of the motion of molecules and the collision of substrates with the active site.
      • The effect of Temperature, pH and substrate concentration on the rate of activity of enzymes. (including denaturing)
      • Enzymes (often immobilized) are extensively used in industry for the production of items including Lactose-free milk, fruit juice and washing powder.
      • Advantages of latose-free milk, and ways of producing it, including immobilization in alginate beads.
      • Knowledge of possible designs of experiments to test the effect of temperature, pH and substrate concentration on enzyme activity.
      • Practical 3: Investigation of a factor affecting enzyme activity.
      • The skill of sketching a graph of expected results in enzymes experiments and the ability to explain reasons for their shapes.

      2.6 Structure of DNA and RNA

      • DNA and RNA are polymers each made of nucleotides.
      • A DNA nucleotide is made from phosphate, deoxyribose (pentose sugar), and nucleotide bases (T, A,G,C)
      • RNA nucleotides are made from phosphate, ribose (pentose sugar) and nucleotide bases (U, A, G, C)
      • Base pairing is "complementary"
      • DNA is a double helix made of two strands of nucleotides linked by hydrogen bonding RNA is a single strand of nucleotides.
      • Students should be able to draw simple diagrams of DNA and RNA nucleotides - using simple shapes (not chemical symbols)
      • Students should learn to draw two antiparallel strands of DNA showing base pairing, A 'ladder' structure is enough, and details of purines / pyrimidines are not required

      2.7 DNA Replication

      • DNA replication
      • Complementary base pairing leads to the semi-conservative replication of DNA.
      • The enzyme helicase unwinds the double helix and breaks hydrogen bonds which hold the two DNA strands together.
      • DNA polymerase (generalised name) links DNA nucleotides together to form a new strand DNA,using the pre-existing strand as a template.
      • Transcription is the synthesis of mRNA by RNA polymerase using the DNA base sequence as a template
      • Translation is the synthesis of polypeptides on ribosomes.
      • The amino acid sequence of polypeptides is determined by mRNA according to the genetic code.
      • Three bases of mRNA is called a codon and corresponds to one amino acid in the polypeptide.
      • Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA.
      • Awareness that in polymerase chain reaction (PCR) an enzymes called Taq DNA polymerase produces multiple copies of DNA.
      • Ability to explain how Meselson and Stahl&rsquos results support for the theory of semi-conservative replication of DNA.
      • knowledge that human insulin can be produced in bacteria because of the "universality" of the genetic code. This allows genes to be transferred between species.
      • Ability to use a table of the genetic code to deduce which codon(s) corresponds to which amino acid and to deduce the sequence of amino acids coded by a short mRNA or the DNA base sequence for a given mRNA strand

      2.8 Respiration

      • Cell respiration definition,"the controlled release of energy from organic compounds to produce ATP"
      • ATP produced is a source of energy ready for immediate use in the cell.
      • Anaerobic cell respiration gives a small yield of ATP from glucose compared to aerobic respiration whose yield is large.
      • Aerobic cell respiration also requires oxygen.
      • Substrates (e.g. glucose) and final waste products (e.g. water, CO2, lactate, ethanol) should be known.
      • Anaerobic cell respiration in yeasts is used to produce ethanol and carbon dioxide in baking.
      • In the human body anaerobic respiration is used to maximize the power of muscle contractions & produces lactate.
      • Know how to use simple respirometers to measure the rate of respiration.
      • to know that an alkali is used to absorb CO2 produced in respirometers, so that reductions in gas volume are due to oxygen use.
      • to keep the temperature constant, so that gas volumes don't change through expansion / contraction of gas.

      2.9 Photosynthesis

      • Photosynthesis uses light energy to produce carbon compounds in cells.
      • Visible light ranges from violet (400nm) the shortest wavelength to red (700nm) the longest.
        (Students are not expected to recall the wavelengths of other colours.)
      • Absorption spectrum shows - red and blue light absorbed most and green light least (it is reflected).
      • Photolysis of water produces oxygen
        (and also ATP & NADPH)
      • Energy ( from photolysis) is needed to produce carbohydrates and other carbon compounds from carbon dioxide.
      • Limiting factors of photosynthesis can be Temperature, light intensity and carbon dioxide concentration.
      • Understand that photosynthesis have caused changes to the Earth&rsquos atmosphere, oceans and rock deposition.
      • Learn how to draw
        • an absorption spectrum for chlorophyll and
        • an action spectrum for photosynthesis.

        Molecules to metabolism 2.1

        The structure of living organisms can be partly explained by the molecules which they are made from. Live is based on carbon because the way in which carbon atoms form covalent bonds is central to the structure of the molecules which make up organisms.

        Water 2.2

        In this section you will learn everything about the water, about its composition, polarity, hydrogen bonds and what makes water so unique in terms of its physical properties.

        Carbohydrates & Lipids 2.3

        This is a topic about three types of carbohydrates, monosaccharides, disaccharides and polysaccharides as well as lipids such as triglycerides which make up many oils in the human body. It includes the analysis of molecule shapes and their functions.

        Proteins 2.4

        This topic is all about proteins which are the most diverse of molecules. They are built from just twenty amino acids and show a huge variety of forms, from spider's silk to insulin hormones.

        Enzymes 2.5

        Enzymes control almost everything which happens inside the cells of all living organisms. In this topic we consider how enzymes make reactions faster as well as the effects of different environmental factors on the rate of enzyme controlled reactions.

        Structure of DNA and RNA 2.6

        In this topic a knowledge of the structure of nucleotides of DNA and RNA is required, as is a simple understanding of the structure of the double stranded, double helix, DNA.

        DNA Replication, transcription, translation 2.7

        This topic looks at these methods, DNA replication making an exact copy of the genetic material as well as Transcription and translation in the expression of a gene to make a protein.

        Respiration 2.8

        This topic covers the basics of aerobic and anaerobic respiration. It is important to know what the role of ATP is in cells and also to have experience of using a respirometer to measure the rate of respiration.

        Photosynthesis 2.9

        Photosynthesis is introduced in this topic. The main new idea is that the process is not a single step reaction but a sequence of reactions which occur in different parts of the chloroplast.


        Examiners report

        This was generally well answered with most candidates able to give enough of the important features of enzyme action to score well. One mistake seen in a number of responses was to state that the active site is on the substrate rather than on the enzyme.

        Knowledgeable candidates had no difficulty in scoring full marks by giving an accurate description of the role of enzymes in DNA replication. It was not necessary to focus on the leading and lagging strands as the action of the various enzymes is largely the same, though of course primers are repeatedly added to the lagging strand and then replaced. Some candidates were obviously concerned that they were being asked about prokaryote DNA replication. This is of course the type of DNA replication that is specified by the programme and has been for many years. It is worth making sure that candidates know that they have learned about this rather than eukaryote replication.

        This part was very well answered with many candidates scoring full marks. There were a few errors in notation with different letters of the alphabet used for alleles of the same gene or X and Y chromosomes indicating confusion between autosomal and sex-linked genes.


        Biochem second objective assessment review

        Quaternary Structure - Protein has more than 1 polypeptide chain.

        Chemical reaction - -absorb and release energy -activation energy -energy is released (heat &amp light) when bonds are broken.

        Exothermic reaction - Exo=to release Thermo=heat -chemical reaction that releases more energy than it absorbs (as heat &amp light)

        Example of exothermic reaction - Cellular respiration: breaks down glucose to make cellular energy

        Endothermic reaction - Endo=absorb Thermos=heat -absorbs more energy than it releases

        Example of endothermic reaction - Photosynthesis- takes in light to break down to create glucose

        Catalyst - Substance that will decrease the activation energy needed to start a chemical reaction

        Enzymes - -catalysts used by cells -increase the rate of chemical reaction -specific to substrates

        Enzyme structure - -they are proteins -twist, fold, bend to final shape -shape attracts specific molecules

        Substrate - Molecules that bind to the enzyme

        Active site - -location on enzyme where substrate binds

        Function of DNA polymerase in process of PCR. - -increase expression -2 genes -SIRT1 &amp SIRT

        Function of a molecule - Structural component of the lipid bilayer

        How would lipid production in a cell change in order to maintain fluidity of its cell membrane as it adapts to lower temperatures? - Produce lipids with shorter fatty acid chains

        Function of cholesterol - Maintains membrane fluidity

        Lipid (fat) soluble vitamins - A, D, E, K

        What stimulates beta-oxidation of fatty acids? - An increase in NAD+ concentration in the mitochondrial matrix

        What occurs in an otherwise healthy person whose diet has very few carbs and high levels of fats? - Acetone is produced in the blood

        Amino acids - -Non-polar (hydrophobic) -Polar charged -Polar uncharged

        Which type of mammalian DNA damage repair requires the presence of the chromosome that is homologous to the damaged chromosome? - Recombination

        Xeroxerma Pigmentosum (XP) - A recessive genetic disease that occurs when one or more of the genes that perform nucleotide excision repair are nonfunctional

        Why do XP patients have a much higher incidence of skin cancer than the general population? - The mutation of all other genes is higher due to failure to repair.

        Assuming 100% reaction efficiency, how many DNA copies are created after the completion of 4 complete PCR cycles? - 16

        What is the function of DNA polymerase in the process of PCR? - It recognizes the primers and uses the available dNTPs to replicate the template DNA sequence.

        What difference in the regions of the SIRT1 &amp SIRT2 genes in people addicted to cocaine increases their expression? - The nucleosomes become more widely spaced.

        What occurs during the process of alternative splicing of RNA? - Alternate combinations of Exons within the same gene are linked together.

        Polypeptides - -functional proteins

        Nonsense mutation - -premature stop codon incorporated into the sequence -leads to a shorter protein

        Carbohydrates - -linear -CH2O formula -energy=glucose -structure=cellulose

        Lipids - -energy storage -signaling -high amount of C

        DNA - -twisted ladder -double helix -in nucleus -deoxyribose -bases= Anine, Thymine, Cytosine, Guarine -in all molecules -have nucleotides

        RNA - -plays &quotmessenger&quot -in &amp outside nucleus -ribose -Adenine, Uracil, Guarine, Cytosine -mRNA=messenger (takes message to ribosome) -rRNA=ribosomal RNA -tRNA=transfers amino acids

        Transcription - -comes first! Transcribes DNA into message. (RNA polymerase will connect complementary bases. mRNA can go out of nucleus to attach to ribosome of rRNA)

        How do rising blood CO2 levels promote the deoxygenated confirmation of hemoglobin? - CO reacts with H2O in the blood &amp decreases pH, which promotes the dome confirmation of the heme group.

        How does hemoglobin keep blood pH neutral during exercise? - Deoxygenated hemoglobin binds to excess H+

        What is occurring in surrounding tissues as the amount of hemoglobin saturated with oxygen increases? - The concentration of hydrogen ions decreases.

        Translation - -2nd step -builds protein (tRNA leaves behind its amino acid, built chain of amino acids)

        Factors that favor the oxygenated form of hemoglobin: - -increased pH -decreased CO

        Which metal ion is bound to the porphyrin ring in hemoglobin? - Iron

        Which feature of hemoglobin makes it an effective O2 transport molecule? - It's affinity for O2 is regulated by pH.

        What is a temporary modification to protein structure by kinases that alters enzyme function? - Phosphorylation

        Which type of inhibition occurs when a particular drug binds to the allosteric site of an enzyme and subsequently changes the enzyme's structure? - Noncompetitive

        Proteases - -a class of enzymes -hydrolyze protein strands into smaller units -increase pH= significant decrease in protease activity

        How do the rates of enzyme catalyzed reactions compare to those of corresponding uncatalyzed reactions? - They are 10^6 to 10^12 times faster.

        Which change will likely increase the activity of an enzyme currently at optimal conditions? - Significantly increasing substrate concentrations

        What occurs immediately after the appropriate molecule enters the active site of the enzyme? - The enzyme binds to the molecule to form an enzyme molecule complex.

        Are enzymes specific? - Yes

        What process is disrupted after a patient invests excessive antacid that neutralizes the pH of the stomach? - Protein catabolism

        In Alzheimer's patients, which biochemical event is responsible for their behavior? - Protein aggregation

        In which situation would altering a protein structure lead to a disease state? - A mutation aconitase blocks essential step in aerobic metabolism

        Which force is most influential in determining the tertiary structure of a protein? - Hydrophobic effect

        Quaternary structure - Large, functional protein structure composed or smaller proteins with multiple subunits.

        Primary - Level of protein structure established through the dehydration synthesis of peptide bonds

        Mismatch repair - -happens in mistakes with DNA replication -DNA polymerase proofreads to see if make a right choice, but makes a mistake. -remove big section of damage and replace all of it

        Homologous recombination - -use 2nd copy of the DNA to copy back the correct info

        Non-homologous end-joining - -happens before DNA replication -trim the ends-stuck back together

        PCR - -DNA replication in a test tube -Denature, Anneal, Elongation, Repeat

        Denature - -step 1 of PCR -increase heat to separate the DNA

        Anneal - -step 2 of PCR -use DNA primers that match the gene to find only the gene we want (ex: to find BRCA gene)

        Elongation - -step 3 of PCR -use DNA polymerase to make copies of our genes

        Which ingredients/molecules are required to set up a PCR? - -DNA polymerase (elongation) -DNA nucleotides (dNTPs) -primers (annealing) -template DNA (patient DNA)

        DNA polymerase always makes strands : - 5'-3'

        What breaks ionic bonds? - -pH changes -salt changes

        What breaks hydrogen bonds? - -pH and salt changes (Disulfide bonds broken by reducing agent)

        What breaks hydrophobic bonds? - Heat

        Types of bonds from strongest to weakest - -disulfide bond -ionic bond -hydrogen bond -hydrophobic bond

        Which bond is weakest, but have most influence on protein structure because of how many there are? - Hydrophobic bond

        Quaternary Structure - -only some proteins will get here -2 or more subunits -proteins -Polypeptides (Example= myoglobin and hemoglobin)

        Hydrolysis - Broken peptide bonds

        Chaperones - Help fold proteins

        Denature - -have an environmental change that causes a protein to misfold or unfold. -breaking side change &amp secondary structure bonds -disulfide=reducing agent -ionic=pH or salt change -hydrophobic=heat change

        Degradation - Break peptide bonds (Hydrolysis)

        Aggregation - -proteins clump together in abnormal way (d/t hydrophobic interactions)

        Enzymes - -functional proteins -catalysts -reusable (can be recycled!) -specific -induced fit -work like assembly line (enzyme pathway)

        Feedback inhibition - -stop the enzyme &quotassembly line&quot because we have too much &quotproduct&quot -happens naturally to maintain homeostasis

        Competitive inhibition - -medicine/drugs -competitive inhibitor will bind to active site to prevent substrate from binding -(overcome inhibition by adding more substrate)

        Non-competitive inhibition - -more effective -bind to allosteric site of enzyme -changes the shape of the protein

        DNA - -phosphate + deoxyribose sugar + A/T/C/G -contains 2 strands -the strands are anti-parallel (opposite each other) : 5'-3' 3'-5'

        RNA - -phosphate + ribose sugar + A/U/C/G

        -binds to hgb on the heme &amp blocks O2 from binding -has 200 x higher affinity -a competitive inhibitor -puts hgb into the R state (makes hgb want to bind hgb even more) -this is why it is so dangerous, our hgb picks it up instead of O2)

        2, 3, BPG - -produced in our body naturally -similar function to H+ (stabilizes the T state) -produced in 2 cases (high altitudes &amp pregnancy)

        Hemoglobins role I'm CO poisoning - Hgb binds to CO with a higher affinity than O2 &amp stabilizes the R state

        What facilitates the transition of hgb from the R state to the T state? - An increase in the concentration of H+

        Carbohydrate metabolism - 1. Glycolysis 2. Citric acid cycle (aerobic) 3. Electron transport chain (aerobic) 4. Firmentation (anaerobic) 5. Gluconeogenesis (anaerobic)

        What occurs during aerobic respiration? - NADH &amp FADH2 are produced from NAD &amp FAD during citric acid cycles. -NADH &amp FADH2 donate electrons to the ETC, re-engineering NAD &amp FAD. -O2 accepts electrons, producing water

        What directly provides the energy necessary for the conversion of ADP to ATP by ATP synthase?

        • Protons moving down a concentration gradient from the intermembrane space to the mitochondrial matrix.

        Cori Cycle - -muscle cells produce lactate which is then converted to glucose in the liver

        Exonuclease - During DNA replication, if an error is detected, DNA polymerase removes the nucleotides and replaces them with correct ones.

        Insulin - -increase glucose in blood -fed state(after we eat, increase glucose=pancreas releases insulin)

        -lets glucose into cells -signals for GluT4 to go to cell membrane

        Glycolysis - -break glucose -make ATP (useable energy)

        Glycogenesis - -store glucose as glycogen (short term storage) -in liver

        Fatty acid synthesis - - make fat from acetyl CoA -fats stored in triglycerides (3 fatty acids) -adipose tissue (long term storage)

        Glycogenolysis - Break glucose out of glycogen

        Gluconeogenesis - -make new glucose(from lactate) -acetyl CoA pyruvate glucose -glycerol (from triglycerides) -amino acids(last resort!)

        Beta oxidation - Break fats into acetyl CoA

        Fatty acid structures - -made up of carbonyl groups

        Saturated fatty acids - -no double bonds -maximum Hs

        Unsaturated fatty acid - -(not saturated with Hs) -at least 1 double bond -lose 2 Hs per double bond

        Essential - -we have to eat it (our bodies cannot make it) -omega 3 -omega 6

        Unsaturated fats - -natural (veg oils) -1 double bond

        Trans-unsaturated - -treat saturated with chemicals to switch hydrogen to other side -not natural! Build up in our body d/t doesn't recognize them.

        Fluidity - -more double bonds=always more fluid! -if same # double bonds, but shorter chain, will be MORE fluid!


        Pros And Cons Of Genetic Engineering

        This is the restriction enzyme and acts as “molecular scissors” cuts the two DNA chains at a specific area in the genome so that sections of DNA can be supplemented or detached. A piece of RNA known as guide RNA is the second key molecule. This consists of pre-designed RNA quite small in length sequence, consisting of about 20 bases, positioned within a longer RNA scaffold. The scaffold binds to DNA and the pre-designed sequence ‘guides’ Cas9 to the right part of the genome. ensuring that the Cas9 enzyme intersects at the right point in the genome.


        What is the difference between transcription and translation?

        (Insert diagram of the central dogma DNA -> RNA -> Protein)Transcription is the process of converting DNA to RNA. First, within the nucleus, DNA helicase breaks hydrogen bonds between base pairs to unwind the DNA. Then, complimentary free RNA nucleotides bind to exposed bases on the template strand. RNA polymerase then forms the sugar phosphate backbone. Introns and exons are repeatedly transcribed to make pre-mRNA which terminates at the stop codon. The pre-mRNA is then spliced to remove the introns and form mRNA.Translation follows this by converting RNA to protein. the mRNA leaves the nucleus via a nuclear pore into the cytoplasm. A ribosome binds to the mRNA. tRNA carrying an amino acid binds its anti- codon to the complimentary codon on the mRNA. A second tRNA binds adjacent to this first codon, carrying another specific amino acid. Peptide bonds form between the amino acids and another specific tRNA- amino acid complex binds adjacently, forming a polypeptide chain. When the ribosome reaches a stop codon on the mRNA, it disengages. this because there are no tRNA anti- codons complimentary to stop codons.


        Markscheme

        gene is a sequence of DNA bases
        DNA/gene codes for a specific sequence of amino acids/polypeptide
        enzymes are proteins/composed of polypetides
        sequence of amino acids determines tertiary structure/folding/shape of active site
        change in the gene/mutation will affect the active site/function of an enzyme
        enzymes are involved in replication/transcription of genes
        enzymes are involved in synthesis of polypeptides

        metabolic pathways can be a sequence/chain of reactions
        they can be cycles of reactions
        different enzymes control each reaction in the sequence/cycle
        accumulation of an end-product can inhibit the first enzyme of the sequence/ pathway
        (an end-product inhibitor) joins an allosteric site/a site separate from active site
        attachment at the allosteric site changes the shape of the active site
        preventing the binding of substrate
        until the level of the end-product is reduced (and the inhibition removed)
        this is an example of negative feedback


        a. phloem transports organic compounds/sucrose

        b. from sources/leaves/where produced to sinks/roots/where used

        c. through sieve tubes/columns of cells with sieve plates/perforated end walls

        d. loading of organic compounds/sucrose into /H + ions out of phloem/sieve tubes by active transport/using ATP

        e. high solute concentration causes water to enter by osmosis (at source)

        f. high (hydrostatic) pressure causes flow (from source to sink)

        g. companion cells help with loading / plasmodesmata provide a path between sieve tubes and companion cell

        a. meiosis / production of male and female gametes

        b. pollination / transfer of pollen from anther to stigma

        c. fertilization happens after pollination / fertilisation is joining of gametes

        d. seed dispersal / spread of seeds to new locations

        a. helicase unwinds the double helix

        b. gyrase/topoisomerase relieves strains during uncoiling

        c. helicase separates the two strands of DNA/breaks hydrogen bonds

        Accept unzips here but not for mark point a.

        d. each single strand acts as a template for a new strand / process is semi-conservative

        e. DNA polymerase III can only add nucleotides to the end of an existing chain/to a primer

        f. (DNA) primase adds RNA primer/short length of RNA nucleotides

        g. DNA polymerase (III) adds nucleotides in a 5&rsquo to 3&rsquo direction

        h. complementary base pairing / adenine to thymine and cytosine to guanine

        i. DNA polymerase (III) moves towards the replication fork on one strand and away from it on the other strand

        j. continuous on the leading strand and discontinuous/fragments formed on the lagging strand


        Translation may occur in either the cytoplasm or the rough endoplasmic reticulum. Two molecular factors that play a key role in translation are transfer RNAs.

        QUESTION No 1 How eggs and sperms are produced? Explain in detail the mechanism of fusion of Egg and sperm in human? ANSWER: Gametogenesis is the formation.

        With the developed technology and the phylogenetic tree method, scientists are now able to investigate genes and cells individually to distinguish whether pr.

        Gel electrophoresis is a laboratory method used to separate macromolecules. Also, used in the production of recombinant DNA and DNA cloning restriction fragm.

        Next, short strands of RNA, called the RNA primers, are synthesized by an enzyme called primase. This provides a 3’ OH group for enzyme called DNA polymerase.

        This particular copy is called messenger RNA (mRNA) molecule. What this messenger RNA would do is, it would leave the nucleus because DNA it not allow to lea.

        Our immune system is reliable for killing harmful things that cause diseases. Immune systems with cancer cells are lacking cells with genes and no faults, so.

        Construction of DNA, RNA, And Protein By Building Models Introduction Nucleic acids are made of nucleotides. When these nucleic acids form sequences they c.

        A case on cancer cell By Shamik D. Majumdar What does cancer cell mean? Normal cells can repair themselves if any part g.

        β’ jaw, β’ downstream clamp, etc.) that surround the DNA binding channel and stabilize DNA binding interactions. The core enzyme can bind DNA nonspecifically.


        Watch the video: Your Bodys Molecular Machines (September 2022).


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