SCIE2004 Biochemistry 1: Analysis of Biomolecules and Genetic Code

This report delves into key concepts in biochemistry, focusing on the structure and function of biomolecules, including carbohydrates, lipids, proteins, and nucleic acids. It explores the properties and reactions of various organic compounds like amines, esters, and amides, and discusses their roles in biological systems. The report also examines genetic expression, covering DNA organization, replication, RNA synthesis, processing, and metabolism. Furthermore, it investigates the structure of the cell membrane, associated transport mechanisms, and the roles of the cell membrane and cytoskeleton in metabolic processes, including protein synthesis and intercellular communication. The impact of cyanide on cellular respiration and a comparison of normal and sickle cell hemoglobin at the DNA and amino acid level are also analyzed. The report concludes by ranking organisms based on DNA sequence similarity and discussing the processes of transcription and translation.

Running head: REPORT 1
Report
Student’s Name
University Affiliation

REPORT 2
Questions and Answers
Introduction
The report involves questions and answers that discuss the structure and function of
biomolecules and identifies the basic features of amines, esters, and amides. The report also
discusses genetic expression and the mechanisms of DNA and RNA process in an organism.
PART A
Question One
Both hexamine and triethylamine have the same number of electrons and molecular weight but
their boiling point varies because of their differences in intermolecular hydrogen bonding.
Hexamine has higher boiling points than triethylamine because it has hydrogen bonds as well as
van der Waals dispersion forces whereas triethylamine has not.
Question Two
The boiling point of propanol is higher than that of propanal. The main reasons for this variation
are as a result of their differences in intermolecular forces and polarization. Propanal is an
aldehyde which has Oxygen which is highly polar and has no hydrogen bonds (Nelson, Cox, &
Lehninge, 2005). It has only dipole-dipole interactions which are weak intermolecular force
whereas propanol which is an alcohol has hydrogen bonds which have the strongest
intermolecular forces acting between hydrogen molecules thus their variation in their boiling
points.
Question Three
Both stearic and linoleic acid are all carboxylic acids with 18 carbon atoms but have differences
in their melting points. Their large differences in melting point are as a result of the saturation.
Stearic fatty acid is saturated fatty acid whereas linoleic acid is unsaturated fatty acid. The higher
the unsaturation, this is why linoleic has a lower melting point than stearic( Ko, et al., 2010).

REPORT 3
Question Four
The common characteristic that all amides with antibacterial activity have is nitro and Bromo
substituent on the phenyl ring. The nitro and Bromo substituents are the one that causes
antimicrobial activity. Their mechanism of action is that amide peptide causes membrane
permeation and metabolism disruption as well as interruption of protein and DNA functions of
bacteria. Amides are applied in pharmaceutical industries to make antibacterial and antifungal
agents against yeast, gram positive and gram negative bacteria (Nugent, 2010).
PART B
Carbohydrates are a molecular compound that is made up of carbon, hydrogen, and oxygen
elements. Carbohydrates are classified into three groups according to their structural features.
They include monosaccharides, disaccharides, and polysaccharides. Monosaccharides are the
simplest sugars and are made up of one polyhydroxy aldehyde or ketonic unit. Their number of
carbon mostly ranges from three to seven and are classified into their functional groups. An
aldose sugar is monosaccharides that has aldehyde group whereas a ketose sugar is the one that
has ketonic unit. Also, mono sugars can be classified depending on the number of carbons in the
sugar. For examples sugars with three carbons can be referred to as trioses, with five carbon
pentoses or with six carbon hexoses. Some examples of monosaccharides include glucose,
glyceraldehyde, ribose and dihydroxyacetone (Devlin, 2011).
Disaccharides involve more than one monosaccharide unit. The mono sugars are linked together
by glycosidic linkages. Some of the common disaccharides include fructose, maltose, and
lactose. On hydrolysis, disaccharides sugars yield monosaccharides units which may be similar
or dissimilar. On the other hand, polysaccharides consist of a large number of monosaccharides
units which may be branched or unbranched. When polysaccharides are hydrolyzed they mostly
yield similar monosaccharide units. Some examples of polysaccharides include chitin, gum,
mucilage, and pectic substances.
Cell membrane serves as a cell wall and cytoskeleton in some organelles. It is composed of a
mixture of different classes of molecules. The most common components are lipids and protein.

REPORT 4
Lipids are a class of molecules that hat shows a wide diversity in terms of biological function
and structure. The main role of lipids is in the formation of permeability of barrier cells in form
of a lipid bilayer. The percentage of lipids in the cell membrane can be 20 to 80 percent
depending on the location and the function of the membrane in the body.
The main component in membrane is phospolipid which forms a lipid bilayer in the cell
membrane. This lipid bilayer has two units namely; hydrophilic and hydrophobic units. The
hydrophobic side repels water and points away from intracellular fluids whereas hydrophilic unit
is attractive to water thus it face intracellular fluids. The hydrophobic tail is able to repel water
and faces away from the intracellular and extracellular fluid. The phospholipids organize
themselves such that they expose the hydrophilic regions to water and hydrophobic regions away
from water (Yeagle, 2011). The arrangement is spontaneous and does not need any energy. This
arrangement of phospholipid forms a layer that represents a wall between the inner and outer
side of the cell thus playing a crucial role in maintaining the structure of cell membrane. The
lipid bilayer is also semi-permeable which makes it allow specific substances to diffuse across
the cell membrane.
The other important lipid component in the cell membrane is cholesterol. It plays a critical role
in making the cell membrane to be rigid thus maintaining the structure of cell membrane. The
third lipid component of the cell membrane which helps in maintaining the structure of the cell is
glycolipid. Glycolipid consists of the sugar chain and helps the cell to be able to recognize other
cells of the body.
A protein structure is organized into four different levels namely; primary, secondary, tertiary
and quaternary structures. The primary structure provides the description of the specific order
arrangements of amino acids which are bonded together to make a chain of the protein referred
to as a polypeptide chain (Alipanahi et al., 2015). The primary structure of this polypeptide chain
is identified starting at the amino acid which is located at the N-terminus of the polypeptide
chain. In regard to this, each amino acid is identified using its abbreviation. A good example of a
protein with primary structure is insulin hormone. Insulin is a relatively small protein which
consists of fifty-one amino acids. It is composed of two polypeptide chains where polypeptide A
consists of twenty-one amino acids and polypeptide B chain thirty amino acids (Li, et al., 2015).

REPORT 5
The second level of protein structure is a secondary structure. It is made up by the spatial
rearrangement of amino acid that is adjacent to the primary structure Secondary structure is a
common occurring structure in most proteins and is formed via hydrogen linkages. Some
examples of secondary structure proteins include Beta pleated sheet and an alpha helix. Long
chains of the polypeptide will have some parts that either in form of a twist or pleated sheet or
alpha helices shape to form secondary structures.
The further folding and twists of secondary structure of proteins forms what is called tertiary
structure. It is a compact structure which has hydrophilic groups on the surface of the protein
molecule and hydrophobic heads which are in the interior. It is the tertiary structure that
determines the functional activity of the protein. Examples of tertiary proteins include fibrous
and globular proteins.
On the other hand, quaternary structure is composed of more than one polypeptide chain which is
in a specific orientation with respect to each other. Examples of proteins with tertiary structures
include myoglobin and heme (Barrett, 2012).
PART C
Question One
Cyanide affects cellular respiration by inhibiting the key enzyme involved in cellular respiration.
It reversibly binds to iron iii ions in the hem group found in the cytochrome oxidase within the
mitochondria. This inhibits the electron transport chain blocking the reduction of oxygen to
water and ATP (Ochiai, 2012).
Question Two
DNA Sequence 3’- TACGAATCAGCTGTA-5’
Complementary DNA Sequence 5’- ATGCTTAGTCGACAT-3’
MRNA seq 5- AUGCUUAGUCGACAU

REPORT 6
Codon seq= AUG –CUU-AGU-CGA-CAU
Amino acid seq= Met-Leu-Ser-Arg-His
Question Three
The normal Haemoglobin DNA consists of a DNA template made up of CAC-GTG-GAC-TGA-
GGA-CTC-CTC-TTC. This DNA template undergoes transcription to form a mRNA
complementary to the DNA template mRNA Chain; GUG-CAC-CUG-ACU-CCU-GAG-GAG-
AAG
By using the messenger RNA chain of normal hemoglobin, the amino acid will be Val-His-Leu-
Thr-Pro-Glu
Sickle cell hemoglobin DNA template is; CAC-GTA-GAC-TGA-GGA-CAC
Then the massager RNA Sickle cell hemoglobin m-RNA = GUG-CAU-CUG-ACU-CCU-GUG
The amino acid sequence of sickle cell hemoglobin will be Val-His-Leu-Thr-Pro-Val
The difference between normal hemoglobin and sickle cell hemoglobin occurs only in a single
amino acid at codon six whereby codon six of normal hemoglobin is Glu and Val in sickle cell
hemoglobin. Sickle cell hemoglobin and normal hemoglobin vary from each other in just one
amino acid. This distinction in one amino acid causes a lot of differences in the properties of
these two kinds of hemoglobin. This difference will also affect the role of hemoglobin an
oxygen-carrying protein
Question Four
a) Adenine- Found in both RNA and DNA

REPORT 7
b) Guanine-Found in both RNA and in DNA
c) 2-deoxy-D-ribose- Found in DNA
d) Cytosine-Found in both RNA and in DNA
e) Thymine-Found in DNA
f) D-ribose-Found in RNA
g) Uracil-Found in RNA only
Question Five
Depending on the similarity of the sequence, the organism can be ranked as Human, Rhesus
monkey, Bullfrog, Tuna, chicken and the furthest organism from the human is silkworm. I think
this ranking does not give definite information on how further apart the organism is in evolution.
This is because it does not involve crucial information such as features of these organisms.
Question Six
a) The template strand is in the bottom one with the direction 3’ to 5’. This is supported by the
fact that messenger RNA is transcribed in 5’ to 3’ direction. On the other hand, the coding strand
is the first which has the direction of 5’-3’ (Meister, 2012).
b) The sequence of messanger RNA is AUGGACGGUUGA
c) AUG= Met
GAC= Asp
GGU= Gly
UGA= Thr
d) Translation of the mRNA: UAC CUG CCA ACU

REPORT 8
UAC= Tyr
CUG= Asp
CCA= Pro
ACU= Thr
Conclusion
In conclusion, the assessment has played a lot in understanding crucial concepts in biochemistry
which are related to health science. I can now exhibit my knowledge by applying the principles
and concepts in biochemistry which ranges from structure and function of biomolecules to
genetic expression, DNA organization, and replication, RNA synthesis, processing, and
metabolism.
.

REPORT 9
References
Alipanahi, B., Delong, A., Weirauch, M. T., & Frey, B. J. (2015). Predicting the sequence
specificities of DNA-and RNA-binding proteins by deep learning. Nature
biotechnology, 33(8), 831.
Barrett, G. (Ed.). (2012). Chemistry and biochemistry of the amino acids. Springer Science &
Business Media.
Devlin, T. M. (2011). Textbook of biochemistry. John Wiley & Sons,.
Ko, S. H., Su, M., Zhang, C., Ribbe, A. E., Jiang, W., & Mao, C. (2010). Synergistic self-
assembly of RNA and DNA molecules. Nature chemistry, 2(12), 1050.
Li, M., Wang, I. X., Li, Y., Bruzel, A., Richards, A. L., Toung, J. M., & Cheung, V. G. (2011).
Widespread RNA and DNA sequence differences in the human transcriptome. science,
1207018.
Meister, A. (2012). Biochemistry of the amino acids. Elsevier.
Nelson, D. L., Cox, M. M., & Lehninger, A. L. (2005). Principles of biochemistry. WH Freeman
and Company, New York, fourth edition edition, 1(1.1), 2.
Nugent, T. C. (Ed.). (2010). Chiral amine synthesis: methods, developments and applications.
John Wiley & Sons.
Ochiai, E. I. (2012). General principles of biochemistry of the elements (Vol. 7). Springer
Science & Business Media.
Rees, D. C., Williams, T. N., & Gladwin, M. T. (2010). Sickle-cell disease. The
Lancet, 376(9757), 2018-2031.
Saenger, W. (2013). Principles of nucleic acid structure. Springer Science & Business Media.
Yeagle, P. L. (2011). The structure of biological membranes. CRC press.