Biochemistry Trivia

1. What is the name of the process by which proteins are made?

From Quiz Protein Synthesis Potpourri

Answer: Translation

In translation, the cell creates the protein from scratch, one amino acid at a time. This might seem like it would take forever to do, but translation can take only a matter of minutes! The other answers refer to steps in making DNA/RNA rather than proteins, which come before protein synthesis.

From Quiz Lipids in Biochemistry II

Answer: Generation of heat

Brown fat is abundant in newborns and is important in keeping them warm. The reason for the brown colouration is an abundance of mitochondria in the brown adipose cells. With almost all other cell types, protons leave the mitochondrial matrix during oxidative phosphorylation, and re-enter via the ATP synthase protein, which generates ATP. In brown adipose cells, however, there is an abundance of a protein called thermogenin in the mitochondria, which provides an alternate entry route into the matrix for the protons. Protons may therefore bypass the ATP synthase, and the energy released is converted to heat, rather than chemical, energy.

From Quiz Getting to Know Your Protein

Answer: X-ray crystallography

X-ray crystallography is pretty much unmatched in the detail with which it can analyse protein structures. Solving protein structures to atomic detail often allows the protein's mechanism of action to be deduced (as was the case for ATP synthase). There are several limitations to x-ray crystallography, however. Proteins must be crystallised prior to analysis and this is difficult for proteins which are large and/or dynamic. It is for this reason that the 26S proteasome, which is essential to our well-being, has proven difficult to analyse using this technique. Additionally, some argue that the crystallisation conditions are too far removed from physiological conditions and so the structures observed cannot be seen as wholly representative.

From Quiz Amino Acids - Why They Matter

Answer: It allows protein structure and function to be probed

Alanine is chemically simple and so by replacing other amino acids of a protein with alanine, it may be deduced what role these replaced residues play (either functionally or structurally). For example, glutamate, which usually exists as a negatively charged form, may be involved in a charge-charge interaction with a positively charged residue (arginine, for example). If there is indeed a charge-charge interaction, and if this interaction has any significance in either the structure or the function of the protein, this will be apparent following alanine mutagenesis, since alanine is incapable of mimicking the negative charge of glutamate. Alanine is also one of the most important amino acids in gluconeogenesis - the process of synthesising glucose from non-carbohydrate sources in times of starvation/intense exercise. In active muscles, pyruvate is released when glucose is metabolised. This pyruvate can be converted back to glucose in the liver, but is unable to travel in the blood. Pyruvate is therefore either converted in the muscle into lactate or alanine, which are then transported to the liver via the blood, where they are converted to glucose. When carried as lactate, this is known as the Cori cycle, and when carried as alanine, it is the alanine cycle.

From Quiz Lipids in Biochemistry I

Answer: Triacylglycerides

Triacylglycerides (triglycerides) are stored in adipose cells. Adipose tissue is what makes us appear "fat" in the eyes of others. It is commonly told that we have a set number of adipose cells, and that fluctuations in our body fat are due to variation in the amount of fat stored in each cell, rather than their number. These stores are used as energy reserves (more on this later), for warmth, and for protection (fat is a good shock absorber and lines vital organs). Lipids can perform more specialised functions also - for example, the waxy covering of some leaves makes them largely waterproof.

From Quiz Solving Levinthal's Paradox

Answer: Free energy

Proteins fold to reduce their Gibbs free energy (G), which can be done by either decreasing the protein's enthalpy (H), or by increasing the system's entropy (S). This is represented by the equation G = H - (S x T), where T is the temperature of the system. Gibbs free energy can be defined as thermodynamic potential, and the lower this is, the more stable the protein is. While temperature is usually constant (i.e. physiological temperature), enthalpy can be decreased by forming strong interactions between the different amino acids of the protein. Entropy is defined as the number of possible conformations the protein can adopt. It is entropy that lies at the heart of the Levinthal Paradox. Increasing the entropy of the system is one of the strongest explanations of how the Levinthal Paradox can be resolved.

From Quiz Keeping an Eye on Your Blood Sugar

Answer: Hyperglycemia

Carbohydrates are long chains of sugar units linked by glycosidic bonds. They are broken down by enzymes such as amylase to ultimately yield glucose - the primary fuel unit for most of our tissues.

From Quiz Biochemistry: The Next Level

Answer: albumin

Albumin is the most abundant protein in the blood plasma. It serves as a carrier protein for several water-insoluble substances. It also functions to retain water in the circulation by oncotic pressure. Hemoglobin, is more abundant than albumin. However, hemoglobin is bound within the red blood cells, and therefore not normally found in the blood plasma (in vivo).

From Quiz Chemical Structure of Amino Acids

Answer: Glycine

Glycine is the simplest of the amino acids, with only a hydrogen atom serving as its R group. It is a non-essential amino acid as it is synthesized in the body from serine, another amino acid. Glycine is unique among the 20 standardized amino acids in that it does not have a chiral center - a central carbon atom containing four different attached groups. This means glycine does not form enantiomers as the other 19 amino acids do. It can exist in both hydrophobic or hydrophilic conditions.

From Quiz Back to Basics - Food Molecules

Answer: Monosaccarides

All three (glucose, fructose and galactose) contain 6 oxygen atoms, 6 carbon atoms and 12 hydrogen atoms. However, all are arranged differently and have different shapes. All three are soluble in water.

From Quiz One- and Three-Letter Codes of Amino Acids

Answer: 21

While 22 amino acids are proteinogenic (i.e. can be used to build proteins), only 20 are encoded by DNA. The other two are selenocysteine and pyrrolysine. Selenocysteine requires an additional RNA sequence in order to be produced, and pyrrolysine is not found in humans. One option was 64, which is the theoretical number of amino acids that the 3 bases per amino acid codes for: There are 4 different bases in DNA, A, T, G and C, and they code for amino acids in triplets. 4 to the power of 3 is 64, but the code is redundant in many places, i.e. most amino acids are coded for by two or more codes. For example: the amino acid lysine is coded for by the triplets AAA and AAG.

From Quiz Basic Biochemistry

Answer: Ribose

Glucose and fructose are both 6-carbon sugars, while sucrose is glucose and fructose bonded together. Ribose is the sugar in RNA.

From Quiz Back to school with enzymes.

Answer: Site

It's the active site that binds to molecules so that enzymes can go about their business.

From Quiz Keeping an Eye on Your Blood Sugar

Answer: Beta cells

The pancreas is a multi-functional organ, releasing hormones and enzymes which generally influence metabolism. Glucose enters the pancreatic beta cells and is metabolised, releasing ATP. This ATP actually acts as a signal and causes an influx of calcium into the cell, inducing it to secrete insulin.

From Quiz Chemical Structure of Amino Acids

Answer: Cysteine

Cysteine is one of two amino acids which contain sulfur - the other is methionine. However, unlike in methionine, the sulfur atom in cysteine is very chemically reactive, and can be oxidized to form disulfide bonds which are important in protein structures, particularly tertiary structures. Cysteine is nonpolar, uncharged, and hydrophobic. It is non-essential, however may be essential in rare cases, for example in infants, the elderly, and people with absorption problems. Cysteine is potentially toxic, thus is oxidized to a dimer of two cysteine atoms called cystine, which is non-toxic.

From Quiz Back to Basics - Food Molecules

Answer: Condensation reaction

In a condensation reaction, water is removed and a peptide bond forms between the amino group of one amino acid and the carboxyl group of another. It is the order of amino acids which determines the structure and function of the protein. Carbohydrates and triglycerides also arise from the joining of molecules via condensation reactions.

From Quiz Biochem Basics of Carbohydrates

Answer: C6 H12 O6

Glucose is a 6-carbon sugar. CO2 is carbon dioxide. C12 H22 O11 is a disaccharide. C H3 OH is methanol or methyl alcohol.

From Quiz Basic Biochemistry

Answer: C, H, & O

Carbohydrates are composed of carbon, hydrogen, and oxygen atoms. Proteins are composed primarily of carbon, hydrogen, oxygen, as well as nitrogen.

From Quiz Back to school with enzymes.

Answer: Conditions are too acidic

Enzymes are held together by attraction between oppositely charged molecules, a bit like the poles on magnets. When acid is introduced into the stomach and pH drops, there are loads of positive charges floating around which mess up the charges in the enzyme, so it breaks down.

From Quiz Biomolecules I

Answer: Metalloprotein

Ceruloplasmin is a type of conjugated protein found in the plasma of blood, which has copper as the non-protein component. It is a metalloprotein as it contains a metallic ion as the prosthetic group. Prosthetic group is nothing but the non-protein component. Phosphoproteins have a phosphate unit as the prosthetic group, lipoproteins have a lipid as the prosthetic group and glycoproteins have a carbohydrate as the prosthetic group.

From Quiz Biochemistry

Answer: lipids

Lipids hold the distinction of having monomers called fatty acids that aggregate into fats, composed of three fatty acids and a glycerol molecule. CHO's, proteins and NA's all lose a water molecule to form a disaccharide/dipeptide/DNA molecules.

From Quiz Protein Synthesis Potpourri

Answer: Messenger RNA (mRNA)

DNA is not used directly in the synthesis of proteins. Instead, messenger RNA is made from the DNA in the process of transcription. Transfer RNA is responsible for holding the amino acids in place during synthesis.

From Quiz Lipids in Biochemistry II

Answer: They are packaged in proteins known as lipoproteins

Lipoproteins form a kind of hydrophilic shell around the hydrophobic lipid core, and therefore provide an energetically stable vehicle for lipid transport around the body. The size of this entity, as well as the proteins involved and the type of lipid carried, defines the lipoprotein. Dietary lipids are transported in what are known as chylomicrons, which are taken to the liver for further processing. Lipids can also be carried as very low-density lipoproteins (VLDL) or low-density lipoproteins (LDL), together known as "bad cholesterol", or as high-density lipoproteins (HDL), or "good cholesterol".

From Quiz Gastronomy Meets Biochemistry

Answer: The body metabolises phenethylamine in chocolate before it can exert its effect on the brain

Phenethylamine is rapidly metabolised by enzymes called MAOA and MAOB. These are monoamine oxidases, and so catalyse the oxidative removal of amine groups from molecules. This means that phenethylamine no longer has the "amine" and can no longer exert feelings of love on the brain. MAOA and MAOB really are the party-poopers of the body, also metabolising dopamine and other such chemicals which are linked to the feeling of excitement and reward. There may still be truth in finding happiness in a bar of chocolate, however. Chocolate contains tryptophan - an amino acid which our body cannot produce and so which must be required from our diets. Tryptophan is metabolised in our bodies into different chemicals, one of which is serotonin, also known as the "happiness molecule". However, like with phenethylamine, there is disagreement between scientists over whether the relatively low amount of tryptophan obtained from eating chocolate is sufficient to induce any significant physiological effects.

From Quiz Amino Acids - Why They Matter

Answer: Because histidine can act as both an acid and a base

The Bronsted-Lowry definition of an acid is a proton donor. The equivalent definition of a base is a proton acceptor. Histidine can act as both. But aren't acids and bases polar opposites? The vague and perhaps disappointing answer is that it is all relative. To be more specific, it is all relative to physiological pH (around 7). Amino acid side chains can be assigned a value known as a pKa, which tells us about whether they act as an acid or as a base. If the pKa of an amino acid side chain is higher than the physiological pH, it is a base. If the pKa of an amino acid side chain is lower than the physiological pH, it is an acid. Histidine's side chain has a pKa value close to physiological pH, meaning that it is granted flexibility in its proton donation and acceptance. Proton exchange is a common feature of the chemistry that takes place at the active sites of many enzymes and so, therefore, is histidine. A second interesting feature of histidine (and one that has been invaluable to biological research) is its ability to bind metals, particularly zinc. Various research groups are interested in one type of protein only, and so may wish to isolate their pet protein in order to study it more closely. One way of doing this is to alter the gene which codes for the protein with an aim of incorporating several histidine residues at the terminus of the protein. For reasons that are self-explanatory, this is called a poly-histidine tail. Cells producing this protein will also produce many other proteins. These cells can be broken open and the lysate passed over a column to which zinc is attached. Due to zinc's affinity for histidine, the target protein will remain in the column whilst other proteins wash out.

From Quiz Lipids in Biochemistry I

Answer: Mitochondria

In the cytosol, fatty acids (also known as acyl chains) are "activated" by having a coenzyme A attached to them. This makes the fatty acid (now referred to as acyl CoA) a suitable candidate for the carnatine shuttle system, which transports it from the cytosol to the mitochondria. This acyl CoA is here converted to acetyl CoA - this is beta oxidation - which can then enter the citric acid cycle, eventually yielding energy.

From Quiz Solving Levinthal's Paradox

Answer: The theory of hierarchical folding

The idea that proteins fold by only acquiring native interactions (i.e. interactions that exist in their correctly folded state) seemed promising. With each native contact made, the number of possible conformations dramatically decreases and so does the time taken to search for the correctly folded state. These folding dynamics can be visualised by "folding funnels". These visual representations show a three-dimensional energy surface representing the energies of the differently folded states of a single protein. There is a high energy plateau which represents the numerous high energy (unstable) folded conformations, with a gradual slope leading to a central trough representative of the lowest energy folded state (usually taken to be the native conformation). This theory is often accompanied by the "blind golfer analogy" - if a blind golfer were to hit golf balls, it would take an unimaginably long time to make a hole in one. However, if the green were arranged so that the hole lay in a central trough, the ball hit by the golfer would simply roll down the hill into the hole regardless of where the ball landed. Here, the golf ball's progress to the hole can be described as being guided. This theory contributed to solving the Levinthal Paradox, but was still insufficient to explain the speed of protein folding. Moreover, the discovery of proteins which acquired non-native interactions as part of their normal folding process (e.g. beta-lactalbumin) showed that this explanation was not universal.

From Quiz Chemical Structure of Amino Acids

Answer: Glutamic acid

Glutamic acid is one of two acidic amino acids (the other is aspartic acid). The carboxylated form (shown in the question, which is the form glutamic acid takes at physiological pH) is very important in taste sensation, contributing to the taste known as umami. MSG, found in many foods, is monosodium glutamate. Glutamic acid is non-essential.

From Quiz Back to Basics - Food Molecules

Answer: At least one C=C double bond

If a fat/lipid contains at least on C=C double bond, it is classified as an unsaturated fat, and will usually be liquid at room temperature. Triglyceride molecules consist of one molecule of glycerol bonded to three fatty acids by ester bonds. Each fatty acid contains an "R" group which is a hydrocarbon chain which determines whether the fat is saturated or unsaturated.

From Quiz One- and Three-Letter Codes of Amino Acids

Answer: Proteins

The answer is proteins. Proteins are long linear chains of amino acids which are joined together by peptide bonds. They are synthesized in the ribosome, which can be attached to the smooth endoplasmic reticulum (smooth ER) or floating free in the cytoplasm. There are an estimated 100 billion different proteins; the highest number of different proteins within any one organism is an estimate of 60000!

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