Biochemistry Review

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Questions
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?
Make up about (15%?) of the cell
Have many functions in the cell
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

What is the secondary structure of a protein?

!lpha"heli# and beta"sheet conformations are the two main types of secondary structure of a
protein molecule. !ccording to the primary protein structure its secondary structure can be of
one type or the other.
$n the alpha"heli# structure the polypeptide curls longitudinally by the action of hydrogen
bonds forming a spiral% or heli#. $n the beta"sheet conformation the protein is more distended
and the hydrogen bonds form a &ig"&ag"shaped protein structure called '"strand. Many
assembled beta"strands ma(e a beta"sheet.
)
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"heli# or the beta"sheet folds itself up. The forces that (eep the tertiary
structure generally are interactions between the *+ 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.
.
,
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.
-nly those proteins made of two or more polypeptide chains have quaternary structure.
$nsulin .two chains/% hemoglobin .four chains/ and the immunoglobulins .antibodies% four
chains/ are some e#amples of protein having quaternary structure.
0
What is protein denaturation? Is there any change in the primary structure
when a protein is denatured? What are some factors that can lead to protein
denaturation?
Secondary% tertiary and quaternary structures of proteins are spatial structures. 1enaturation
is modification in any of these spatial structures that ma(es the protein deficient or
biologically inactive.
!fter denaturation the primary protein structure is not affected.
Protein denaturation can be caused by temperature variation% p2 change% changes in the
concentration of surrounding solutes and by other processes. Most proteins denature after
certain elevation of temperature or when in very acid or very basic solutions. This is one of
the main reasons that it is necessary for the organisms to (eep stable temperature and p2.
the process of unfolding
Can be down with heat, pH or chemical compounds
In the chemical compound, can remove and have the protein renature or refold
3
What is the difference between essential and natural amino acids?
Essential amino acids are those that the oranism is not able to synthesi!e and that need to
be inested by the individual. "atural amino acids are those that are produced by the
oranism.
#here are livin species that produce every amino acid they need$ for e%ample$ the bacteria
Escherichia coli that does not have essential amino acids. &ther species$ like humans$ need
to obtain essential amino acids from the diet. 'mon the t(enty different kno(n amino acids
that form proteins$ humans can make t(elve of them and the remainin eiht needs to be
taken from the proteins they inest (ith food.
#he essential amino acids for humans are phenylalanine$ histidine$ isoleucine$ lysine$
methionine$ threonine$ tryptophane and valine.
4
Of what units are nucleic acids constituted? What are the chemical entities that
compose that unit?
5ucleic acids are formed by sequences of nucleotides.
5ucleotides are constituted by one molecule of sugar .deo#yribose in 15! and ribose in
+5!/ bound to one molecule of phosphate and to one nitrogen"containing base .adenine%
uracil% cytosine or guanine% in +5!% and adenine% thymine% cytosine and guanine% in 15!/.
16
Into which two groups can the nitrogen-containing bases that form D! and
"! be classified? What is the criterion used in that classification?
#he nitroen)containin bases that form *"' and +"' are classified as pyrimidine and
purine bases.
,y the analysis of the structural formulae of those nitroen)containin bases it is possible to
reali!e that three of them$ cytosine$ thymine and uracil$ have only one nitroeni!ed carbon
rin. #he others$ adenine and uanine$ have t(o nitroeni!ed associated carbon rins.
11
#oncerning the nitrogen-containing bases that participate in nucleotides$ what
is the difference between D! and "!?
+e7ect 81
12
Which are the nucleotides %portions& that bind in the formation of nucleic
acids? What is meant by the '( and )( extremities of nucleic acids?
The phosphate group of one nucleotide binds to the pentose of the other nucleotide and so on
to ma(e the polynucleotide chain.
9ach e#tremity of a 15! or +5! chain can be distinguished from the other e#tremity
according to their terminal chemical entity. The phosphate"ended e#tremity is called ):"
e#tremity and the pentose"ended e#tremity is called 3:"e#tremity. So 15! or +5! chains
can be run along the ):"3: way or along the 3:"): way. These ways are important in several
biological functions of 15! and +5! 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 D!
molecule? !nd in the "!? Is this last question appropriate?
#he rule for the pairin of nitroen)containin bases of the polynucleotide chains that form
the *"' molecule is pyrimidine base binds to purine base$ under the condition that thymine
(#) binds to adenine (')$ and cytosine (-) binds to uanine (.).
/n +"'$ there is no bindin bet(een nitroen)containin bases. #hat is because +"' is
formed of only one polynucleotide chain0 differently$ *"' is formed of t(o chains. /t is not
correct so to 1uestion about base pairin in +"'.
"ucleic 'cid +evie( ) /mae *iversity2 *"' base parin
1
#oncerning their biological function what is the difference between D! and
"!?
*"' is the source of information for +"' production (transcription) and thus for protein
synthesis. *"' is still the basis of heredity due to its replication capability.
#he messener +"' is the template for protein synthesis (translation). /n this process$ t+"'
and r+"' also participate since the first carries amino acids for the polypeptide chain
formation and the second is a structural constituent of ribosomes (the oranelles (here
proteins are made).
1)
What are the main types of lipids?
What is meant by saturation or unsaturation of oils and fats?
1,
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 a#ons in the nervous system% is a phospholipid too.
10
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 si# carbons and one ring made of five carbons in the e#tremity. The union of each ring to
the ad7acent ring is made by the sharing of two ad7acent carbons belonging to both rings.
'ile salts% cholesterol% the se#ual hormones estrogen% progesterone and testosterone% the
corticosteroids and the pro"vitamin 1 are e#amples of steroids.
13
What are monosaccharides$ oligosaccharides and polysaccharides?
* + , to *- + over *-
14
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 bro(en into other
carbohydrates. ;lucose and fructose are e#amples of monosaccharides. 1isaccharides are
carbohydrates made of two monosaccharides and with the loss of one molecule of water
.dehydration/. The chemical bond between two monosaccharides is (nown 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. <actose
.mil( sugar/ is another disaccharide and it is created by the union of one molecule of
galactose with one molecule of glucose.
26
What are hexoses? What are some examples of hexoses with important
biological functions?
2e#oses are carbohydrates made of si# carbons. ;lucose% fructose and galactose are
e#amples of he#oses. 2e#oses have an important biological role as energy sources for the
metabolism
21
What are pentoses? What are the roles of pentoses in D! and "! molecules?
Pentoses are carbohydrates made of five carbons.
The 15! molecule is made of a sequence of molecules called nucleotides. 9ach nucleotide
is formed by the association of one pentose called deo#yribose with a phosphoric acid and a
nitrogen"containing base .!% T% = or ;/. +5! is also formed by a sequence of nucleotides.
The +5! nucleotides are made by association of one ribose .a pentose/ with one phosphoric
acid and one nitrogen"containing base .!% >% = or ;/.
So pentoses are fundamental components of 15! and +5!.
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 metabolism of organisms of the ne#t trophic levels.
Starch is the polysaccharide used for energy store by plants. ;lycogen is a macromolecule
responsible for the storage of glucose in the liver and muscles. =hitin is a polysaccharide
with structural functions that constitutes the e#os(eleton of the arthropods and the cell wall in
fungi
23
What are the basic constituents of the cell membrane?
#he cell membrane is formed of lipids$ proteins and carbohydrates.
#he membrane lipids are phospholipids$ a special type of lipid to (hich one e%tremity a
phosphate roup is bound thus assinin electrical chare to this reion of the molecule.
3ince phospholipids have one electrically chared e%tremity and a lon neutral oranic
chain they can orani!e themselves in t(o layers of associated molecules2 the hydrophilic
portion (polar) of each layer faces out(ards in contact (ith (ater (a polar molecule too) of
the e%tracellular and the intracellular space and the hydrophobic chains (non polar) face
in(ards isolated from the (ater. ,ecause this type of membrane is made of t(o phospolipid
layers it is also called a bilipid membrane.
Membrane proteins are embedded and dispersed in the compact bilipid structure.
-arbohydrates appear in the outer surface of the membrane associated to some of those
proteins under the form of lycoproteins or bound to phospholipids formin lycolipids. #he
membrane carbohydrates form the lycocali% of the membrane.
#his description ((ith further e%planations) is kno(n as the fluid mosaic model about the
structure of the cell membrane.
2
What are the respective functions of phospholipids$ proteins and carbohydrates
of the cell membrane?
Membrane phospholipids have a structural function$ they form the bilipid membrane that
constitutes the cell membrane itself.
Membrane proteins have several speciali!ed functions. 3ome of them are channels for
substances to pass throuh the membrane$ others are receptors and sinalers of information$
others are en!ymes$ others are cell identifiers (cellular labels) and there are still those that
participate in the adhesion comple%es bet(een cells or bet(een the internal surface of the
membrane 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 eneral labelin functions for reconition of the cell
by other cells and substances (for e%ample$ they differentiate red blood cells in relation to the
',& blood roup system)$ immune modulation functions$ pathoen sensiti!ation functions$
etc.

2)
What is the relationship between concentration gradient and active and passive
transport?
4assive transport is the movement of substances across membranes in favor of their
concentration radient$ i.e.$ from a more concentrated reion to a less concentrated reion.
'ctive transport$ on the other hand$ is the transport of substances across membranes aainst
their concentration radient$ from a less concentrated to a more concentrated reion. /n
passive transport$ because it is spontaneous$ there is no enery spent0 the active transport
ho(ever re1uires enery ((ork) to occur.
'ctive transport (orks to maintain or increase the concentration radient of a substance
bet(een t(o reions (hile passive transport acts in a manner to reduce the concentration
radient.
2,
What do facilitated diffusion and active transport have in common? What are
the differences between them?
3imple diffusion is the direct passae of substances across the membrane in favor of their
concentration radient. /n facilitated diffusion the movement of substances is also in favor of
their concentration radient but the substances move bound to specific molecules that act as
5permeabili!ers6$ i.e.$ facilitators of their passae throuh the membrane.
20
How does the sodium-potassium pump present in the cell membrane wor.?
What is the importance of this protein for the cell?
#he sodium)potassium pump is the transport protein that maintains the concentration
radient of these ions bet(een the intra and the e%tracellular spaces. #his protein is
phosphorylated in each pumpin cycle and then it pumps three sodium ions outside the cell
and puts t(o potassium ions in(ards. #he phosphorylation is made by the bindin of a
phosphate donated by one '#4 molecule that then is converted into '*4 (adenosine
diphosphate).
#he 7ob of the sodium)potassium pump$ also kno(n as sodium)potassium '#4ase$ is
fundamental to keep the characteristic neative electrical chare in the intracellular side of
the membrane of the restin cell and to create ade1uate conditions of sodium and potassium
concentrations inside and outside the cell to maintain the cellular metabolism.
23
What is the metabolic pathway?
metabolic pathways are series of chemical reactions occurring within a cell. $n each
pathway% a principal chemical is modified by a series of chemical reactions. 9n&ymes
cataly&e these reactions% and often require dietary minerals% vitamins% and other cofactors in
order to function properly. 'ecause of the many chemicals .a.(.a. ?metabolites?/ that may be
involved% metabolic pathways can be quite elaborate. $n addition% numerous distinct pathways
co"e#ist within a cell
24
Which metabolic pathway is a common pathway to both anaerobic and aerobic
metabolism?
.lycolysis is a metabolic path(ay that is found in the cytoplasm of cells in all livin
oranisms and is anaerobic$ or does not re1uire o%yen. #he process converts one molecule
of lucose into t(o molecules of pyruvate.
36
What are basic steps in cellular respiration?
Glycolysis
Acetyl CoA Formation
Protein Biochemistry, IB, !A"
#rebs Cycle
$lectron ransport "ystem