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Pinciples - biochmistry > Biomolecules and reactions > Flashcards

Flashcards in Biomolecules and reactions Deck (44):

What does a general atom consist of (including any charges or mass numbers)?

Nucleus contains protons (positive charge and mass of 1) and neutrons (charge of zero and mass of 1). Orbiting the nucleus is an electron(s) (charge of negative one and negligible mass).


What does the atomic number reveal about an element?

It reveals the number of electrons an element has orbiting its nucleus.


How would the electron arrangement of an atom be if it was referred to as being 'stable'?

You will find that on the outermost shell, all of the possible orbitals will be fully occupied by electrons, e.g. the noble gases.


If in a shell of an atom, some of the orbitals are not fully occupied b electrons, what would you describe the atom as being?



What type of bonding causes electrons to be shared EQUALLY?

Non-polar covalent bonding.


What is the definition of 'bond energy'?

It is the amount of energy required to separate two bonded or interacting atoms under physiological conditions.


What is van der waal's interactions described as being?

Interaction of electrons of non-polar substances.


How many covalent bonds can an atom of carbon make?

Carbon can make four covalent bonds. This leads to the formation of a tetrahedral structure.


What does the term 'electronegativity' mean?

It is the attractive force that an atomic nucleus exerts on its electrons, i.e. it is a measure of the amount of energy required to separate an electron from its nucleus (due to how attracted it is to keeping it in essence).


What causes an increase in electronegativity?

The more stable an atom is, the greater the attraction there will be between the nucleus and the electron. Therefore, a high degree of stability will cause an increase in electronegativity.


Name four types of common reactions

Phosphorylation (and de-phosphorylation), acylation, carboxylation and esterification.


What is a condensation reaction?

In a condensation reaction, water is removed and two substances are, as a consequence, joined.


Give an example of a condensation reaction.

Esterification is an example of a condensation reaction,.


What is the opposite to a condensation reaction?

Hydrolysis is the opposite as water is used to split up a molecule into smaller molecules.


What is a 'redox' reaction?

A 'redox' reaction is a reaction that you will see electrons being transferred from one molecule to another. Therefore oxidation occurs in one and reduction occurs in another.


What is an 'oxidising agent' in a redox reaction?

An oxidising agent is a molecule which is reduced itself and promotes oxidation in another by accepting the transfer of electrons itself (i.e. it gains electrons).


What is the final product of catabolism?

Carbon dioxide (being the final oxidation state of carbon) is the final product of catabolism.


Give four examples of common arrangements of atoms in biological molecules.

Methyl group, amino groups, amides. and carboxyl groups.


What are the five functions of biomolecules?

Information storage (DNA), structural (teeth, bones, cartilage), energy generation (glycolysis etc), energy currency/storage (ATP), recognition/communication/specificity (receptors, hormones, enzymes).


There are four major classes of biomolecules. What are they?

Peptides and proteins (consist of amino acids), lipids (triglycerides, phospholipids, steroids), nucleic acids (DNA, RNA), and carbohydrates (mono-, di-, polysaccharides).


What a carbohydrates composed of?

A singular, or multiple units of glucose for example. A monosaccharide is a singular glucose.


What is the first law of thermodynamics?

Matter and energy can neither by created nor destroyed. When energy is converted from one form to another, the total energy before and after the conversion is the same.


The second law of thermodynamics is?

When energy is converted from one form to another, some of that energy becomes unavailable to do work, i.e. no energy transformation is 100% efficient.


What is enthalpy a measure of?

Enthalpy is a measure of the energy within a thermodynamic system - more specifically it is related to heat i.e. whether a reaction is exothermic or endothermic depending on if the resultant enthalpy value is positive or negative (enthalpy is delta H).


What is an 'entropy' value?

The entropy of a substance is a measure of disorder within that system - the larger the value of entropy, the greater the amount of disorder there is within the system (entropy = S).


If a reaction is endothermic, what is most likely to happen to the entropy value for the reaction?

If a reaction is taking in energy, it is most likely imposing order on the system, and therefore the entropy value is probably decreasing.


What does the symbol delta G represent and what calculation is it apart of?

Delta G represents the standard free energy change seen within a reaction, and the calculation is: delta G = delta H - T (delta S).


What other calculation can be used to calculate the free energy of a reaction (delta G)?

Another way to calculate the free energy of a reaction is by taking away the energy of the reactants from the products.


A reaction in which the total free energy change of the product(s) is less than the total free energy of the reactant(s) is an example of what type of reaction?

This is an example of an exothermic reaction as delta G will be negative - these reactions will always be feasible.


What type of reaction can occur spontaneously?

Exothermic reactions can occur spontaneously as they don't require any input of energy.


Describe what the total free energy would be like in a reaction which is endothermic.

The total free energy of the products is more than the total free energy of the reactants and as a result endothermic reactions will have a positive delta G value. Therefore these reactions are not feasible unless a certain level of energy input is reached.


What does deltaGo' stand for?

it is the change in free energy under standard conditions.


Why is deltaG related to equilibrium ?

The further towards completion the point of equilibrium is, the more free energy is released.


What does it mean when deltaG is zero?

If deltaG is zero, it is a characteristic of a readily reversible reaction.


What type of reaction is the most favourable?

Exothermic reactions are the most favourable.


As endothermic reactions aren't favourable, how do they occur in the body?

They are driven by coupling to highly favourable processes - they will exert energy which afterward they can use to stimulate their own reaction.


Does the formation of ATP have a positive or negative deltaG?

It has a very negative deltaG value which is what makes it such a good energy currency in the body. Often involved in coupling to drive many cellular responses (active processes).


Is ATP more or less stable than ADP? Explain.

ATP is less stable than ADP as the negative charges close together in ATP put an electrostatic strain (repulsion) on the molecule - this is why it can readily remove a phosphate group releasing energy between the high energy anhydride bond (this removes the strain).


Do cells contain a high or low storage of ATP?

They store a low amount of ATP: concentration < 10mM.


Give two examples of where in the body we use the most amount of ATP.

The brain and muscle cells use ATP at a high rate. So we must be good at regenerating ATP.


Define metabolism.

Metabolism is all the reactions taking place in the body.


What is metabolism divided into?

Metabolism is divided into anabolism and catabolism.


What is meant by catabolism?

Catabolism is the breaking down of complex molecules into smaller ones all the while releasing energy. E.g. glycolysis. Note some catabolic reactions do require energy.


What is anabolism?

Anabolism is the synthesizing of complex molecules out of smaller ones in energy-consuming reactions. E.g. gluconeogenesis (making new glucose from non-carbohydrate precursors like pyruvate)