Biochemistry Review

Questions
Status
1 What are proteins? How can the protein diversity of living beings be
explained?
Proteins are molecules made of sequences of amino acids bound by a peptide bond.
The genetic code codifies twenty different amino acids that can compose proteins.
So there are numerous combinations of amino acid which can form polypeptide
chains and for this reason protein molecules can be immensely diverse.

2 What is the importance of proteins for living beings?
Proteins play a fundamental role in nearly all biological processes. Due to their
diversity they can assume many different configurations and they can play varied
roles in cells and tissues.
Some protein functions are noteworthy: the structural function (cell membrane
proteins, cytoskeleton proteins, proteins of the connective tissue), the enzymatic
function (enzymes are proteins), the energy storage function (proteins can be
degraded into acetyl-CoA and cycle the Krebs cycle), the osmotic regulation function
(albumin), the transportation function (membrane channels, respiratory pigments), the
immune protection function (antibodies), the movement function (contractile proteins),
the endocrine integration function (hormones) and the informative function (membrane
receptors, intracellular signalers). There are also many proteins whose biological
functions are not yet known.

3 What is the primary structure of a protein? What is the importance of the
primary structure?
The primary protein structure is the linear sequence of amino acids that form the
molecule.
The primary structure is the basis of the protein identity. Modification of only
one amino acid of the primary structure creates a different protein. This different
protein can be inactive or can even have other biological functions.

4 What is the secondary structure of a protein?
The secondary protein structure is generated by the manner its amino acids interact
through the intermolecular bond. These interactions create a spatial conformation of the
polypeptide filament. The two most studied secondary conformations of proteins are the
alpha-helix and the beta-sheet.

5 What is the tertiary structure of a protein? What are the main types of tertiary
structure?
The tertiary protein structure is a spatial conformation additional to the secondary
structure in which the alpha-helix or the beta-sheet folds itself up. The forces that
keep the tertiary structure generally are interactions between the R groups of the

amino acids and between other parts of the protein and water molecules of the
solution.
The main types of tertiary structure of proteins are the globular proteins and the
fibrous proteins.
6 What is the quaternary structure of a protein? Do all proteins have quaternary
structure?
The quaternary protein structure is the spatial conformation due to interactions
among polypeptide chains that form the protein.
Only those proteins made of two or more polypeptide chains have quaternary
structure. Insulin (two chains), hemoglobin (four chains) and the immunoglobulins
(antibodies, four chains) are some examples of protein having quaternary structure.

7 What is protein denaturation? Is there any change in the primary structure
when a protein is denatured? What are some factors that can lead to protein
denaturation?
Secondary, tertiary and quaternary structures of proteins are spatial structures.
Denaturation is modification in any of these spatial structures that makes the
protein deficient or biologically inactive.
After denaturation the primary protein structure is not affected.
Protein denaturation can be caused by temperature variation, pH change, changes
in the concentration of surrounding solutes and by other processes. Most proteins
denature after certain elevation of temperature or when in very acid or very basic
solutions. This is one of the main reasons that it is necessary for the organisms to keep
stable temperature and pH.

8 What is the difference between essential and natural amino acids?
Essential amino acids are those that the organism is not able to synthesize and
that need to be ingested by the individual. Natural amino acids are those that are
produced by the organism.
There are living species that produce every amino acid they need, for example, the
bacteria Escherichia coli, that does not have essential amino acids. Other species, like
humans, need to obtain essential amino acids from the diet. Among the twenty
different known amino acids that form proteins humans can make twelve of them and
the remaining eight need to be taken from the proteins they ingest with food.
The essential amino acids for humans are phenylalanine, histidine, isoleucine, lysine,
methionine, threonine, tryptophane and valine.

9 Of what units are nucleic acids constituted? What are the chemical entities
that compose that unit?
Nucleic acids are formed by sequences of nucleotides.
Nucleotides are constituted by one molecule of sugar (deoxyribose in DNA and
ribose in RNA) bound to one molecule of phosphate and to onenitrogen-containing

base (adenine, uracil, cytosine or guanine, in RNA, and adenine, thymine, cytosine and
guanine, in DNA).
10 Into which two groups can the nitrogen-containing bases that form DNA and
RNA be classified? What is the criterion used in that classification?
The nitrogen-containing bases that form DNA and RNA are classified as pyrimidine and
purine bases.
By the analysis of the structural formulae of those nitrogen-containing bases it is
possible to realize that three of them, cytosine, thymine and uracil, have only one
nitrogenized carbon ring. The others, adenine and guanine, have two
nitrogenized associated carbon rings.

11 Concerning the nitrogen-containing bases that participate in nucleotides, what
is the difference between DNA and RNA?
In DNA nucleotides can be formed of adenine (A), thymine (T), cytosine (C) or
guanine (G). In RNA nucleotides can also contain adenine (A), cytosine (C) or
guanine (G), however, instead of thymine (T) there is uracil (U).

12 Which are the nucleotides portions that bind in the formation of nucleic
acids? What is meant by the 5 and 3 extremities of nucleic acids?
The phosphate group of one nucleotide binds to the pentose of the other nucleotide
and so on to make the polynucleotide chain.
Each extremity of a DNA or RNA chain can be distinguished from the other extremity
according to their terminal chemical entity. The phosphate-ended extremity is called
5-extremity and the pentose-ended extremity is called 3-extremity. So DNA or
RNA chains can be run along the 5-3 way or along the 3-5 way. These ways are
important in several biological functions of DNA and RNA since some reactions
specifically occur following one way or the other way.

13 What is the rule for the pairing of nitrogen-containing bases in the DNA
molecule? And in the RNA? Is this last question appropriate?
The rule for the pairing of nitrogen-containing bases of the polynucleotide chains that
form the DNA molecule is pyrimidine base binds to purine base, under the condition
that thymine (T) binds to adenine (A) and cytosine (C) binds to guanine (G).
In RNA there is no binding between nitrogen-containing bases. That is because
RNA is formed of only one polynucleotide chain; differently, DNA is formed of two
chains. It is therefore not correct to question base pairing in RNA.


14 Concerning their biological function what is the difference between DNA and
RNA?
DNA is the source of information for RNA production (transcription) and thus for
protein synthesis. DNA is still the basis of heredity due to its replication capability.
The messenger RNA is the template for protein synthesis (translation). In this

process tRNA and rRNA also participate since the first carries amino acids for the
polypeptide chain formation and the second is a structural constituent of ribosomes (the
organelles where proteins are made).

15 What are the main types of lipids?
What is meant by saturation or unsaturation of oils and fats?
The main types of lipids are triglycerides (fats and oils), phospholipids, waxes
and steroids.
When it is said that a triglyceride is saturated it means that in its molecule the carbon
chain is bound in its maximum capacity to hydrogens, i.e., there are no double
or triple bonds between carbons. These saturated molecules are generally solid fats
at normal temperature.
Unsaturated triglyceride molecules are those in which there are double or triple
bonds between carbons and so they do not accomplish their maximum capacity of
hydrogenation. These unsaturated molecules in general are oils, liquid at normal
temperature.
The terms saturated or unsaturated refer then to the saturation of the carbonic chain by
hydrogen atoms.

16 What are phospholipids?
Phospholipids are molecules made of glycerol bound to two long molecules
of fatty acids and to one phosphate group. Therefore, phospholipids are
amphipathic molecules, i.e., they have a non-polar portion, due to the long fatty acid
chains, and a polar portion, due to the group phosphate.
Phospholipids are the main component of cell membranes. Sphingomyelin, the
substance that forms the myelin sheath of axons in the nervous system, is a
phospholipid too.

17 What are steroids? What are some examples of steroids with a biological
function?
Steroids are lipids based in an angular combination of four carbon rings, three of
them made of six carbons and one ring made of five carbons in the extremity. The
union of each ring to the adjacent ring is made by the sharing of two adjacent carbons
belonging to both rings.
Bile salts, cholesterol, the sexual hormones estrogen, progesterone and
testosterone, the corticosteroids and the pro-vitamin D are examples ofsteroids.


18 What are monosaccharides, oligosaccharides and polysaccharides?
Monosaccharides are simple molecules of carbohydrates that cannot be broken
into smaller molecules of other carbohydrates. Oligosaccharides are
carbohydrates made by union of a maximum of 10 monosaccharides.
Polysaccharides are polymers of monosaccharides made of more than 10 units

of such monomers. The most important polysaccharides are cellulose, starch, glycogen
and chitin.
19 What is the difference between monosaccharides and disaccharides? What are
some examples of disaccharides and of monosaccharides that form them?
Monosaccharides are simple molecules of carbohydrates that cannot be broken
into other carbohydrates. Glucose and fructose are examples of monosaccharides.
Disaccharides are carbohydrates made of two monosaccharides and with the loss
of one molecule of water (dehydration). The chemical bond between two
monosaccharides is known as a glycosidic bond.
Sucrose (table sugar) is a disaccharide made by the union of one molecule of glucose
with one molecule of fructose. Maltose is a disaccharide made by two glucose
molecules. Lactose (milk sugar) is another disaccharide and it is created by the union
of one molecule of galactose with one molecule of glucose.


20 What are hexoses? What are some examples of hexoses with important
biological functions?
Hexoses are carbohydrates made of six carbons. Glucose, fructose and
galactose are examples of hexoses. Hexoses have an important biological role as
energy sources for the metabolism.

21 What are pentoses? What are the roles of pentoses in DNA and RNA
molecules?
Pentoses are carbohydrates made of five carbons.
The DNA molecule is made of a sequence of molecules called nucleotides. Each
nucleotide is formed by the association of one pentose called deoxyribose with a
phosphoric acid and a nitrogen-containing base (A, T, C or G). RNA is also formed by a
sequence of nucleotides. The RNA nucleotides are made by association of one ribose
(a pentose) with one phosphoric acid and one nitrogen-containing base (A, U, C or G).
So pentoses are fundamental components of DNA and RNA.

22 What are the main biological functions of the polysaccharides?
Polysaccharides have an energy storage function and a structural function.
Polysaccharides incorporated by living beings along the food chain are important
sources of carbohydrates for the energetic metabolismof organisms of the next trophic
levels.
Starch is the polysaccharide used for energy store by plants. Glycogen is a
macromolecule responsible for the storage of glucose in the liver and muscles. Chitin is
a polysaccharide with structural functions that constitutes the exoskeleton of the
arthropods and the cell wall in fungi.


23 What are the basic constituents of the cell membrane?
The cell membrane is formed of lipids, proteins and carbohydrates.
The membrane lipids are phospholipids, a special type of lipid to which one extremity a
phosphate group is bound thus assigning electrical charge to this region of the
molecule. Since phospholipids have one electrically charged extremity and a long
neutral organic chain they can organize themselves in two layers of associated
molecules: the hydrophilic portion (polar) of each layer faces outwards in contact with
water (a polar molecule too) of the extracellular and the intracellular space and the
hydrophobic chains (non polar) face inwards isolated from the water. Because this type
of membrane is made of two phospolipid layers it is also called a bilipid membrane.
Membrane proteins are embedded and dispersed in the compact bilipid structure.
Carbohydrates appear in the outer surface of the membrane associated to some of
those proteins under the form of glycoproteins or bound to phospholipids forming
glycolipids. The membrane carbohydrates form the glycocalix of the membrane.
This description (with further explanations) is known as the fluid mosaic model about
the structure of the cell membrane.


24 What are the respective functions of phospholipids, proteins and
carbohydrates of the cell membrane?
Membrane phospholipids have a structural function, they form the bilipidmembrane that
constitutes the cell membrane itself.
Membrane proteins have several specialized functions. Some of them are channels for
substances to pass through the membrane, others are receptors and signalers of
information, others are enzymes, others are cell identifiers (cellular labels) and there
are still those that participate in the adhesion complexes between cells or between the
internal surface of themembrane and the cytosketeleton.
Membrane carbohydrates, associated to proteins or to lipids, are found in the outer
surface of the cell membrane and they have in general labeling functions for recognition
of the cell by other cells and substances (for example, they differentiate red blood cells
in relation to the ABO blood group system), immune modulation functions, pathogen
sensitization functions, etc.

25 What is the relationship between concentration gradient and active and
passive transport?
Passive transport is the movement of substances across membranes in favor of
their concentration gradient, i.e., from a more concentrated region to a less
concentrated region. Active transport, on the other hand, is the transport of substances
across membranes against their concentration gradient, from a less concentrated to a
more concentrated region. In passive transport, because it is spontaneous, there is no
energy spent; the active transport however requires energy (work) to occur.
Active transport works to maintain or increase the concentration gradient of a
substance between two regions while passive transport acts in a manner to reduce the
concentration gradient.

26 What do facilitated diffusion and active transport have in common? What are
the differences between them?
Facilitated diffusion can be confused with active transport because in both processes
there is participation of membrane proteins.
In active transport however the transported substance moves against its
concentration gradient and with energy spent. Facilitated diffusion is a passive
transport in favor of the concentration gradient and it does not require energy.

27 How does the sodium-potassium pump present in the cell membrane work?
What is the importance of this protein for the cell?
The sodium-potassium pump is the transport protein that maintains the concentration
gradient of these ions between the intra and the extracellular spaces. This protein is
phosphorylated in each pumping cycle and then it pumps three sodium ions outside the
cell and puts two potassium ions inwards. The phosphorylation is made by the binding
of a phosphate donated by one ATP molecule that then is converted into ADP
(adenosine diphosphate).
The job of the sodium-potassium pump, also known as sodium-potassium ATPase, is
fundamental to keep the characteristic negative electrical charge in the intracellular side
of the membrane of the resting cell and to create adequate conditions of sodium and
potassium concentrations inside and outside the cell to maintain the cellular
metabolism.


28 What is the metabolic pathway?
The sum total of the chemical processes that occur in living organisms, resulting
in growth, production of energy, elimination of waste material, etc

29 Which metabolic pathway is a common pathway to both anaerobic and aerobic
metabolism?
Glycolysis.

Glycolysis is a metabolic pathway that is found in the cytoplasm of cells in all
living organisms and is anaerobic, or does not require oxygen. The process converts
one molecule of glucose into two molecules of pyruvate.


30 What are basic steps in cellular respiration?
1- Glycolysis
2- Acetyl CoA Formation
3- Krebs Cycle
4- Electron Transport System