BIOCHEMISTRY 5
strands.
Nucleic Acid
Friedrich Miescher – Swiss physiologist who discovered
nucleic acids.
2 Types of Nucleic Acid:
1. Deoxyribonucleic Acid (DNA) – found within the cell
nucleus; storage and transfer of genetic information;
passed from existing cells to new cells during cell
division.
2. Ribonucleic Acid (RNA) – occurs in all parts of a cell;
synthesis of proteins.
Nucleic Acid – an unbranched polymer containing monomer
units called nucleotides.
Nucleotide – three-subunit molecule in which a pentose sugar
is bonded to both a phosphate group and a nitrogen-containing
heterocyclic base.
- Building blocks for nucleic acids.
3 Components of Nucleotide:
1. Pentose Sugars
2. Nitrogen-Containing Heterocyclic Bases
3. Phosphate
Pentose ribose (RNA) and pentose 2’-deoxyribose (DNA) –
sugar unit of a nucleotide.
The three pyrimidine derivatives found in nucleotides are
thymine (T), cytosine (C), and Uracil (U).
The two purine derivatives found in nucleotides are adenine
(A) and guanine (G).
Nucleoside – two-subunit molecule in which a pentose sugar is
bonded to a nitrogen-containing heterocyclic base.
Ribonucleic Acid (RNA) – nucleotide polymer in which each of
the monomers contains ribose, a phosphate group, and one of
the heterocyclic bases adenine, cytosine, guanine, or uracil.
Deoxyribonucleic Acid (DNA) – nucleotide polymer in which
each of the monomers contains deoxyribose, a phosphate
group, and one of the heterocyclic bases adenine, cytosine,
guanine, or thymine.
Nucleic Acid backbone – alternating sugar-phosphate chain in
a nucleic acid structure.
Primary nucleic acid structure – the sequence in which
nucleotides are linked together in a nucleic acid.
Complementary bases – pairs of bases in a nucleic acid
structure that hydrogen-bond to each other.
Complementary DNA strands – strands of DNA in a double
helix with base pairing such that each base is located opposite
its complementary base.
In DNA, the two strands are connected by hydrogen bonds
between their bases.
DNA Replication – biochemical process by which DNA
molecules produce exact duplicates of themselves.
DNA helicase – the DNA double helix unwinds.
Replication fork – the point at which the DNA double helix is
unwinding.
Antimetabolites – drugs which are DNA-replication inhibitors.
Okazaki fragments – short segments formed in the other
Nicks – breaks or gaps in the daughter strand.
Leading strand – the strand that grows continuously.
Lagging strand – the strand that is synthesized in small
segments.
Chromosome – an individual DNA molecule bound to a group
of proteins.
5 Types of RNA Molecules:
1. Heterogeneous nuclear RNA (hnRNA) – RNA
formed directly by DNA transcription.
2. Messenger RNA (mRNA) – RNA that carries
instructions for protein synthesis to the sites for protein
synthesis.
3. Small nuclear RNA (snRNA) – RNA that facilitates
the conversion of heterogeneous nuclear RNA to
mRNA.
4. Ribosomal RNA (rRNA) – RNA that combines with
specific proteins to form ribosomes.
5. Transfer RNA (tRNA) – RNA that delivers amino
acids to the sites for protein synthesis.
Cytoplasm – a cell consists of a nucleus and an extranuclear
region.
Replication – process by which DNA molecules produce exact
duplicates of themselves.
Transcription – process by which DNA directs the synthesis of
the hnRNA/mRNA molecules that carry the coded information
needed for protein synthesis.
Gene – segment of a DNA strand that contains the base
sequence for the production of a specific hnRNA/mRNA
molecule.
Genome – all of the genetic material contained in the
chromosomes of an organism.
Template strand – the strand of DNA used for hnRNA/mRNA
synthesis.
Information strand – other DNA strand (non-template strand).
Exon – gene segment that conveys genetic information.
Intron – gene segment that does not convey genetic
information.
Splicing – process of removing introns from an hnRNA
molecule and joining the remaining exons together to form an
mRNA molecule.
Small nuclear ribonucleoprotein (snRNPs) – complex
formed from an snRNA molecule and several proteins.
Spliceosome – a large assembly of snRNA molecules and
proteins involved in the conversion of hnRNA molecules to
mRNA molecules.
Alternative splicing – process by which several different
proteins that are variations of a basic structural motif can be
produced from a single gene.
Transcriptome – all of the mRNA molecules that can be
generated from the genetic material in a genome.
Codon – three-nucleotide sequence in an mRNA molecule that
codes for a specific amino acid.
Genetic code – assignment of the 64 mRNA codons to specific
amino acids.
Synonyms – codons that specify the same amino acid.
Anticodon loop – the loop opposite the open of the cloverleaf.
Anticodon – three-nucleotide sequence on a tRNA molecule
that is complementary to a codon on an mRNA molecule.
Translation – process by which mRNA codons are deciphered
and a particular protein molecule is synthesized.
Ribosome – an rRNA-protein complex that serves as the site
for the translation phase of protein synthesis.
5 Steps to the Translation process:
1. Activation of tRNA
2. Initiation
3. Elongation
4. Termination
5. Post-translation processing
Translocation – part of translation in which a ribosome moves
down an mRNA molecule three base positions so that a new
codon can occupy the ribosomal A site.
Polyribosome – complex of mRNA and several ribosomes.
Mutation – an error in base sequence in a gene that is
reproduced during DNA replication.
2 Common type of Mutation:
1. Point mutation – mutation in which one base in a
DNA base sequence is replaced with another base.
2. Frameshift mutation – mutation that inserts or
deletes a base in a DNA molecule base sequence.
Mutagen – substance or agent that causes a change in the
structure of a gene.
Virus – small particle that contains DNA or RNA surrounded by
a coat of protein and that cannot reproduce without the aid of a
host cell.
Retrovirus – an RNA containing virus.
Vaccine – preparation containing an inactive or weakened form
of a virus or bacterium.
Genetic Engineering – process whereby an organism is
intentionally changed at the molecular level so that it exhibits
different traits.
Recombinant DNA – DNA that contains genetic material from
two different organisms.
Restriction enzyme – an enzyme that recognizes specific
base sequences in DNA and cleaves the DNA in a predictable
manner at these sequences.
Transformation – process of incorporating recombinant DNA
in a host cell.
Clones – cells with identical DNA that have descended from a
single cell.
Polymerase chain reaction (PCR) – a method for rapidly
producing multiple copies of a DNA nucleotide sequence.
DNA fingerprinting – work with DNA in the forensic area.
DNA polymerase – enzyme present in all living organisms; key
substance in the PCR process.
THE DIGESTIVE SYSTEM and BODY
METABOLISM
METABOLISM
Metabolism – sum total of all the biochemical reactions that
take place in a living organism.
Catabolism – all metabolic reactions in which large
biochemical molecules are broken down to small ones.
Anabolism – all metabolic reactions in which small biochemical
molecules are joined together to form larger ones.
Metabolic pathway – series of consecutive biochemical
reactions used to convert a starting material into an end
product.
Prokaryotic cells – have no nucleus and are found only in
bacteria.
Eukaryotic cell – cell in which all DNA is found in a
membrane—nucleus.
Nucleoid – single circular molecule found near the center of
the cell in a region.
Cytoplasm – water-based material of a eukaryotic cell that lies
between the nucleus and the outer membrane of the cell.
Organelles – minute structure within the cytoplasm of a cell
that carries out a specific cellular function.
Cytosol – water-based fluid part of the cytoplasm of a cell.
3 Types of Organelles:
1. Ribosome – site where protein synthesis occurs.
2. Lysosome – an organelle that contains hydrolytic
enzymes needed for cellular rebuilding, repair, and
degradation.
3. Mitochondria (mitochondrion) – an organelle that is
responsible for the generation of most of the energy
for a cell.
Cristae – folds of the inner membrane that protrude into the
matrix.
ATP synthase complexes – small spherical knobs attached to
the cristae.
Phosphoester bond – phosphate-ribose bond.
Phosphoanhydride bond – the chemical bond formed when
two phosphate groups react with each other and a water
molecule is produced.
Strained bonds – bases for the net energy production that
accompanies hydrolysis.
Uridine triphosphate (UTP) – involved in carbohydrate
metabolism.
Guanosine triphosphate (GTP) – participates in protein and
carbohydrate metabolism.
Cytidine triphosphate (CTP) – involved in lipid metabolism.
Flavin Adenine Dinucleotide (FAD, FADH2) – coenzyme
required in numerous metabolic redox reactions.
Coenzyme A (CoA) – derivative of the vitamin B pantothenic
acid.
Acetyl group – portion of an acetic acid molecule that remains
after the –OH group is removed from the carboxyl carbon atom.
High-energy Compound – compound that has a greater free
energy of hydrolysis than that of a typical compound.
Common metabolic pathway – sum total of the biochemical
reactions of the citric acid cycle, the electron transport chain,
and oxidative phosphorylation.
Citric acid cycle – series of biochemical reactions in which the
acetyl portion of acetyl CoA is oxidized to carbon dioxide and
the reduced coenzymes FADH2 and NADH are produced.
Hans Adolf Krebs – discovered the Krebs cycle.
Electron transport chain – series of biochemical reactions in
which electrons and hydrogen ions from NADH and FADH 2 are
passed to intermediate carriers and then ultimately react with
molecular oxygen to produce water.
Cytochrome – heme-containing protein in which reversible
oxidation and reduction of an iron atom occur.
Oxidative phosphorylation – biochemical process by which
ATP is synthesized from ADP as a result of the transfer of
electrons and hydrogen ions from MADH or FADH2 to O2
through the electron carriers involved in the electron transport
chain.
Coupled reactions – pairs of biochemical reactions that occur
concurrently in which energy released by one reaction is used
in the other reaction.
Chemiosmotic coupling – explanation for the coupling of ATP
synthesis with electron transport chain reactions that requires a
proton gradient across the inner mitochondrial membrane.
Phytochemical – nonnutrient compound found in plant-derived
foods that has a positive effect on human health.
CARBOHYDATE METABOLISM
Digestion – biochemical process by which food molecules,
through hydrolysis, are broken down into simpler chemical units
that can be used by cells for their metabolic needs.
- Involves the use of Hydrolases.
The three major breakdown products from carbohydrate
digestion are glucose, galactose, and fructose.
Carbohydrate metabolism process begins in the mouth,
esophagus, stomach, and small intestines.
Saliva – moistens the food and makes swallowing easier.
- approximately 99.5% water, the remaining 0.5%
consists of mucin.
- has a pH range of 5.75 – 7.0 optimum at pH 6.6.
Mucin – glycoprotein that acts as a lubricant, inorganic salts,
buffers and enzymes that catalyzes hydrolysis reaction.
Esophagus – hollow tube beginning at the very back of the
pharynx and ending at the stomach.
- Transport swallowed food and liquid from the
throat, through the chest into the stomach.
Stomach – large, hollow organ and holds the food we eat.
- Secretes acid and some digestive enzymes which
help begin the processes of digestion.
Zymogen pepsinogen – contacts with HCl to convert
pepsinogen into pepsin that catalyzes hydrolysis of protein to
polypeptides.
Small Intestines – major site for the digestion and absorption
of nutrients so they can be used by the body.
- About 10 feet long
- Consist of duodenum, jejunum, and ilium
Colon (Large intestine) – receives water and undigested food
products from the small intestines.
Villi – the folds of the intestinal wall are lined with fingerlike
projections.
Glycolysis – metabolic pathway by which glucose is converted
into two molecules of pyruvate, a chemical energy in the form of
ATP is produced, and NADH-reduced coenzymes are
produced.
Anaerobic pathway – metabolic pathways in which molecular
oxygen is not a participant.
Anaerobic pathway – pathways that require molecular oxygen.
Energy-consuming stage – the six-carbon stage of glycolysis.
Energy-generating stage – the three-carbon stage of
glycolysis.
Substrate-level phosphorylation – biochemical process
whereby ATP is produced from ADP by hydrolysis of a high-
energy compound.
Fermentation – biochemical process by which NADH is
oxidized to NAD+ without the need for oxygen.
Lactate Fermentation – enzymatic anaerobic reduction of
pyruvate to lactate.
Ethanol Fermentation – enzymatic anaerobic conversion of
pyruvate to ethanol and carbon dioxide.
Glycogenesis – metabolic pathway by which glycogen is
synthesized from glucose 6-phosphate.
Glycogenolysis – metabolic pathway by which glucose 6-
phosphate is produced from glycogen.
Gluconeogenesis – metabolic pathway by which glucose is
synthesized from noncarbohydrate materials.
Cori cycle – cyclic biochemical process in which glucose is
converted to lactate muscle tissue, the lactate is reconverted to
glucose in the liver, and the glucose is returned to the muscle
tissue.
Pentose phosphate pathway – metabolic pathway by which
glucose 6-phosphate is used to produce NADPH, ribose 5-
phosphate, and numerous other sugar phosphates.
Insulin – produced by the beta cells of the pancreas.
Glucagon – polypeptide hormone produced in the pancreas by
alpha cells.
Epinephrine (adrenaline) – released by the adrenal glands in
response to anger, fear, or excitement.
LIPID METABOLISM
Chyme – thick semi-liquid material made up of small
triacylglycerol globules, other partially digested food, and
gastric secretions.
Cholecystokinin – release of bile stored in the gallbladder.
Fatty acid micelle – micelle in which fatty acids and/or
monoacylglycerols and some bile are present.
Chylomicron – lipoprotein that transports triacylglycerols from
intestinal cells, via the lymphatic system, to the bloodstream.
Adipocyte – triacylglycerol-storing cell.
Adipose tissue – tissue that contains large numbers of
adipocyte cells.
Fatty acids and Glycerol – major products of complete
hydrolysis of lipid digestion.
Monoglycerides – major product of incomplete hydrolysis of
lipid digestion.
Glucogenic amino acid – amino acid that has a carbon-
containing degradation product that can be used to produce
glucose via gluconeogenesis.
Ketogenic amino acid – amino acid that has a carbon-
containing degradation product that can be used to produce
ketone bodies.
Bile pigment – colored tetrapyrrole degradation product
present in bile.
Jaundice – condition that occurs when this balance is upset
such that bilirubin concentrations in the blood becomes higher
than normal.

Triacylglycerol mobilization – hydrolysis of triacylglycerols

stored in adipose tissue, followed by release into the
bloodstream of the fatty acids and glycerol so produced.
POWERPOINT
β-oxidation pathway – repetitive series of four biochemical Nucleic Acid – are molecules that store the patterns of life and
reactions that degrade acyl CoA to acetyl CoA by removing two these patterns are passed from one generation to the next.
carbon atoms at a time, with FADH2 and NADH also being - found in cells as nucleoproteins.
produced.
A polymer in which the monomer unit is nucleotides.
Ketone body – one of three substances produced from acetyl
CoA when an excess of acetyl CoA from fatty acid degradation Nucleotides are joined together by phosphodiester bonds.
accumulates because of triacylglycerol-carbohydrate metabolic
imbalances. 2 Types of Nucleic Acids:
Ketogenesis – metabolic pathway by which ketone bodies are 1. DNA: Deoxyribonucleic Acid
synthesized from acetyl CoA. - found within cell nucleus
- storage and transfer of genetic information
Ketonemia – excess accumulation of ketone bodies in blood. - passed from one cell to other during cell division
Ketosis – body condition in which high levels of ketone bodies
are present in both the blood and urine. 2. RNA: Ribonucleic Acid
- occurs in all parts of cell
Lipogenesis – metabolic pathway by which fatty acids are - primary function is to synthesize the proteins.
synthesized from acetyl CoA.
3 Components of Nucleotode:
1. Pentose Sugar – monosaccharide
2. N-bases – heterocyclic amines derived from purine
PROTEIN METABOLISM and pyrimidine.
3. Phosphate Group

Amino acids – major product of protein digestion. Nitrogen-Containing Heterocyclic Bases

1. Pyrimidine Bases
Amino acid pool – total supply of free amino acids available - Thymine (T), Cytosine (C), and Uracil (U)
for use in the human body.
2. Purine Bases
Protein turnover – repetitive process in which proteins are - Adenine (A) and Guanine (G)
degraded and resynthesized within the human body.
*Adenine (A), Guanine (G), and Cytosine (C) are found in both
Nitrogen balance – state that results when the amount of DNA and RNA.
nitrogen taken into the human body as protein equals the
amount of nitrogen excreted from the body in waste materials. *Uracil (U) is found only in RNA.
*Thymine (T) is found only in DNA.
Negative nitrogen balance – accompanies a state of “tissue
wasting”. Phosphate – third component of a nucleotide, is derived from
phosphoric acid (H3PO4).
Positive nitrogen balance – indicates the rate of protein
anabolism exceeds that of protein catabolism. Nucleoside – a two-sub-unit molecule in which a pentose
sugar is bonded to a nitrogen-containing heterocyclic base.
Transamination reaction – biochemical reaction that involves
the interchange of the amino group of an α-amino acid with the Nucleotides – adenosine 5-triphosphate (ATP) serves as a
keto group of an α-keto group. common currency into which energy gained from food is
converted and stored.
Aminotransferase – needed enzyme for a transamination
reaction. Differences between DNA and RNA
DNA RNA
Oxidative deamination reaction – biochemical reaction in Structure Double stranded Single stranded
which an α-amino acid is converted into an α-keto acid with Sugar Deoxyribose Ribose
release of an ammonium ion. N-bases A, G, C, T A, G, C, U
Function Stores genetic Transmit genetic
Urea cycle – cyclic biochemical pathway in which urea is information information
produced, for excretion, using ammonium ions and aspartate
molecules as nitrogen sources. Primary Nucleic Acid Structure – a sequence that contains
nucleotides linked to a nucleic acid.
Primary Level of DNA structure – describes the sequence
and relative contents or % composition of the DNA molecule.
Important features of all polynucleotides:
a. A polynucleotide has a sense of directionality.
b. A polynucleotide has individuality, determined by the
sequence of its bases.
Secondary Structure – involves two polynucleotide chains
coiled around each other in a helical fashion.
- The polynucleotides run anti-parallel to each other,
i.e., 5’-3’ and 3’ and 5’.
DNA Sequence – the sequence of bases on one
polynucleotide is complementary to the other polynucleotide.
Complementary DNA strands – strands of DNA in a double
helix with base pairing such that each base is located opposite
its complementary base.
Tertiary Structure – the 3-D structure that involves a higher-
order folding of elements of regular secondary structure.
- the supercoiling of the DNA.
Histones – small proteins that participate in forming the
nucleosomal structure of the chromatin.
Quaternary Structure – involves the interaction of the DNA
with other macromolecules, specifically proteins.
- this organizational structure allows long stretches of
DNA to be tightly packed in a space of about 2 µm in diameter.
Central Dogma of Genetics – summarizes the mechanisms
for transfer of genetic information.
Replication – process by which DNA molecules produce exact
duplicates of themselves.
- old strands act as templates for the synthesis of new
strands.
- the newly synthesized DNA has one new DNA strand
and old DNA strand.
Proteins – responsible for the formation of skin, hair, enzymes,
hormones, and so on.
2 phases of Protein Synthesis
1. Transcription – a process by which DNA directs the
synthesis of mRNA molecules.
2. Translation – a process in which mRNA is deciphered
to synthesize a protein molecule.
DNA -------Transcription-- RNA -------Translation-- Protein
Messenger RNA (mRNA) – the product of DNA transcription.
- carries instructions for protein synthesis from DNA.
- contains a sequence of three bases specifying for an
amino acid. This sequence is called a codon.
- single-stranded and has a random conformation.
*The base sequence in mRNA determines the amino acid
sequence for protein synthesized.
*The base sequence of an mRNA molecule involved only 4
different bases – A, C, G, and U.
Codon – a three-nucleotide sequence in an mRNA molecule
that codes for a specific amino acid.
*Based on all possible combination of bases A, C, G, and U,
there are 64 possible codes.
Genetic Code – the assignment of the 64 mRNA codons to
specific amino acids.
- 3 of the 64 codons are termination codons (“stop”
signals)
Gene – a segment of a DN base sequence responsible for the
production of a specific hnRNA/mRNA molecule.
Characteristics of Genetic Code
 The genetic code is almost universal.
 The same codon specifies the same amino acid
whether the cell is a bacterial cell, a corn plant cell, or
a human cell.
*The codon – coding for the amino acid methionine (AUG)
functions as initiation codon.
*STOP codons – UAG, UAA, and UGA
-terminate protein synthesis.
Transfer RNA (tRNA) – the only RNA with a specific shape
2-D structure: cloverleaf
3-D structure: L-shaped
- act as intermediaries to deliver amino acids to mRNA
- the adaptor molecule that recognizes the codon in
mRNA and transfers the amino acid corresponding to the codon
- contains the anticodon loop
- a sequence of three bases complementary to the
codon
*During protein synthesis, amino acids do not directly interact
with the codons of an mRNA molecule.
2 features of the tRNA structure
 The 3’ end of the tRNA is where an amino acid is
covalently bonded to the tRNA.
 The loop opposite to the open end of tRNA, called the
anticodon, comprises seven unpaired bases.
tRNA
- each tRNA is specific for only one amino acid.
- each cell carries at least 20 specific enzymes, each specific
for one amino acid.
- each enzyme recognizes only one tRNA.
- the enzyme bonds the activated amino acid to the 3’
terminal –OH group of the appropriate tRNA by an ester bond.
- all the opposite end of the tRNA molecule is a codon
recognition site.
- the codon recognition site is a sequence of three bases
called an anticodon.
- this triplet of bases aligns itself in a complementary fashion
to the codon triplet on mRNA.
Ribosomal RNA (rRNA) – allows the bonding of mRNA in the
ribosomes.
- complexes with proteins to form structures called
ribosomes, the site of protein biosynthesis.
Ribosome – an rRNA-protein complex
- serves as the site of protein synthesis.
Mutation – an error in base sequence reproduced during DNA
replication.
- errors in genetic information is passed on during
transcription.
- the altered information can cause changes in amino
acid sequence during protein synthesis and thereby alter proten
function.
- involves a change in shape, structure or nucleotide
sequence of the DNA.
- may be due to ultraviolet, ionizing radiation,
alkylating agents, and intercalating agents.
*Such changes have a profound effect on an organism.
Mutagens – substance or agent that causes a change in the
structure of a gene.
The Digestive System and Body Metabolism
Digestion – breakdown of ingested food.
 - breakdown of food molecules, through hydrolysis, 3. Glycogenolysis – breakdown of glycogen into
into simpler chemical units that can be used by cells for their glucose units.
metabolic needs. 4. Amino acid catabolism
- Involves the use of hydrolases 5. Catabolism of Nucleotides
6. Catabolism of Heme
Saliva – approximately 99.5% water, while the remaining 0.5%
consists of mucin, a glycoprotein that acts as lubricant, Glycolysis – series of 10 enzyme-catalyzed reactions that
inorganic salts, buffers and enzymes that catalyze hydrolysis break down a glucose molecule into two pyruvate molecules.
reaction.
- has a pH range of 5.75-7.0 optimums at pH 6.6 Anabolic Processes:
Process of Digestion 1. Gluconeogenesis – process by which glucose is
1. Mouth synthesized from non-carbohydrate precursors such
as glycerol, lactate, and some amino acids.
2. Esophagus – hollow tube beginning at the very back 2. Glycogenesis – the synthesis of glycogen
of the pharynx (throat) and ending at the stomach. 3. Pentose phosphate pathway or Hexose
- its function is to transport swallowed food and monophosphate shunt
liquid from the throat, through the chest into the stomach. 4. Ketogenesis – the synthesis of ketone bodies.
- it is not active in the breakdown or absorption. 5. Synthesis of purines and pyrimidines
Flavin Adenine Dinucleotide (FAD) – coenzyme required in
3. Stomach – large, hollow organ and holds the food we numerous metabolic redoz reactions
eat.
- functions as a reservoir. FAD: oxidized form
- secretes acid and some digestive enzymes FADH2: reduced form
which help begin the processes of digestion.
- acts a churn to mix up food Nicotinamide Adenine Dinucleotide (NAD+, NADH) – a
typical cellular reaction in which NAD+ serves as the oxidizing
4. Small Intestines – major site for the digestion and agent is the oxidation of a secondary alcohol to give a ketone.
absorption of nutrients so they can be used by the
body. NAD+: coenzyme
- about 10 feet long. NADH: reduced form
- divided into 3 parts namely: duodenum,
jejunum and ileum. Coenzyme A – a derivative of vitamin B
- active form is the sulfhydryl group (-SH group) in the
5. Colon or Large Intestine – receives water and ethanethiol subunit of the coenzyme.
undigested food products form the small intestine.
Oxidative Phosphorylation – the synthesis of ATP driven by
electron transport.
*Gastric Juice (HCl) contains zymogen pepsinogen, contacts - takes place in the mitochondria.
with HCl to convert pepsinogen into pepsin that catalyzes
hydrolysis of protein to polypeptides. Substrate Level Phosphorylation – the transfer of a high-
energy phosphate group to ADP driven by the breakdown of a
Villi – minute hair-like structure on the linings that brushes the more energy-rich substrate.
nutrients unto the bloodstream.
Cellular Respiration – central catabolic pathway for all
Carbohydrates  Monosaccharides organisms.
Fats and Lipids  Fatty acids and Glycerol
Proteins  Amino acids 3 Phases
1. Glycolysis
Absorption – passage of nutrients into the blood. 2. Intermediate phase
3. Kreb’s Cycle or Citric Acid Cycle
Metabolism – totality of the chemical reactions that occur in an
organism
- chemical reactions carried out by living cells Role of other Nucleotide Triphosphates in Metabolism:
 Uridine triphosphate (UTP) – involved in
Pathways – the sequences of the reactions carbohydrate metabolism
 Guanosine triphosphate (GTP) – involved in protein
Catabolism – pathways or processes that breakdown larger and carbohydrate metabolism
molecule into smaller ones with the release of energy in the  Cytidine triphosphate (CTP) – involved in lipid
form of ATP, GTP and reduced coenzyme. metabolism

Anabolism - pathways that put smaller molecules together to
synthesize larger molecules.
- pathways which harness the release energy to
synthesize molecules needed for cell manufacture, growth, and
reproduction.
Catabolic Processes:
1. Cellular Respiration – main energy-producing
pathways of the cell.
- process in which cellular energy is
generated through the oxidation of nutrient
molecules with O2 as the ultimate electron
acceptor.
2. Lipolysis and β-oxidation – lipolysis is the
breakdown of fats or lipids
*In cellular reactions, ATP functions as both a source of a
phosphate group and a source of energy.
Important Intermediate Compounds in Metabolic Pathways:
 Adenosine phosphates
 Adenosine Monophosphate (AMP) – one phosphate
group
 Adenosine Diphosphosphate (ADP) – two
phosphate groups
 Adenosine Triphosphate (ATP) – three phosphate
groups
 Cyclic monophosphate (cAMP) – cyclic structure of
phosphate
Energy Count
 For every Acetyl CoA: Ketone Bodies – one of the substances (acetone, β-
3 NADH (x3 ATPs) = 9 ATPs hydroxybutyrate, and acetoacetate) that are formed principally
1 FADH2 (x2 ATPs) = 2 ATPs in liver mitochondria.
1 GTP = 1 ATP
Total = 12 ATPs *Formation occurs when the amount of acetyl CoA produced is
excessive compared to the amount of oxaloacetate available to
* +2 cytoplasmic NADH from glycolysis react with it and take it into the Citric Acid Cycle.

Shuttle systems for Cytoplasmic NADH: Ketogenesis – involves the production of ketone bodies from
1. Glycerol-3-phosphate shuttle acetyl CoA.
- active in muscle tissues
- the receiver of electrons is FAD Acetyl CoA ---ketogenesis-- Ketone bodies
- 2 ATPs produced
*Synthesis of ketone bodies from acetyl CoA primarily in liver
2. Malate Aspartate shuttle mitochondria, diffused into blood stream and transported to
- mainly operational in liver cells peripheral tissues.
- the receiver of electrons is NAD+
- 3 ATPs produced *During starvation or uncontrolled diabetes, ketone bodies
accumulate in the blood and excess is secreted in the urine.
Energy Count
For 1 glucose molecule: 32 ATPs Ketonemia – excess accumulation of ketone bodies in blood.

Glycerol phosphate shuttle Malate Aspartate shuttle Ketonuria – ketone bodies are excreted in the urine.
32 ATPs 32 ATPs
+ 4 ATPs + 6 ATPs Ketosis – overall accumulation of ketone bodies in the blood
36 ATPs 38 ATPs and urine.

Lipogenesis – metabolic pathway by which fatty acids are

70-100 mg/100 mL of blood – normal fasting blood sugar synthesized from acetyl CoA.
- conversion of glucose to fats or acetyl CoA to fatty
Hypoglycemia – blood sugar below 70 acids at the liver and adipose tissue.

Hyperglycemia – blood sugar over 100 Lipid Storage

 Fatty acids are stored in adipocytes as triglycerides in
*The pancreas secretes insulin in response to glucose levels in the cells cytoplasm.
the blood.  When energy is needed, hydrolysis converts TAGs to
fatty acids which are transported to the matrix or
Glycogenesis – removal and conversion of excess glucose abundant mitochondria where they are oxidized.
and glycogen by the liver when glucose level rises after
digestion of a meal. *Fat in excess of the body’s requirement is stored as Adipose
tissue.
Glycosuria – presence of glucose in the urine.
Obesity – a condition resulting from glandular disorder or
Glycogenolysis – process of converting and breaking down of simply caused by overeating.
glycogen back to glucose by the liver. - if more than a normal amount of fat is deposited in
the adipose tissue.
Gluconeogenesis – formation of glucose from
non-carbohydrate sources. Stored fat serves as a:
 Reserve supply of food
Fatty Acid vs. Glucose Oxidation:  Support for the internal organs shock
 Spiral fatty acid oxidation produce net 95 ATP  Absorber for the intestinal organs
molecules by oxidation of 12 carbon atom fatty acid  Insulator for the body.
(lauric acid)
 1 Glucose molecule (6 carbon atoms) produces 36-38 Cholesterol – found in all cells of the body but particularly in
ATP molecules. the never tissue.

Oxaloacetate – produced from malate and also produced by *All carbon atoms of cholesterol come from the acetyl group of
the carboxylation of phosphoenolpyruvate (glycolysis). acetyl CoA.

*Pyruvate can be converted to oxaloacetate by pyruvate *Normally eliminated in the bile but when it is settles in the
carboxylase. gallbladder, gallstones are formed.

*Low glucose supply also slows down the citric acid cycle.
*Under low supply of oxaloacetate, the acetyl CoA will be in
excess (increased concentration).
*As a consequence, the excess acetyl CoA is converted to
ketone bodies.
*When there is adequate balance between lipid and
carbohydrate metabolism, most of the acetyl CoA produced
from the β-oxidation pathway is further processed through the
citric acid cycle.
*If it deposits on the walls of the arteries, Atherosclerosis
occur.
*Amino acids formed through digestion process enter the amino
acid pool in the body.
Amino Acid Pool – the total supply of free amino acids
available for use in the human body.
*The body cannot store protein. All protein in the body is
constantly being degraded and then re-synthesized.
*The stat that results when the amount of nitrogen taken into
the human body as protein equals the amount of nitrogen
excreted from the body in waste materials.
*A person who excretes as much as nitrogen daily as he/she
takes in is said to be in nitrogen balance.
The breakdown of amino acid carbon skeleton follows 2
pathways:
1. Glucogenic Amino Acids – those whose carbon
skeletons are degraded to pyruvate or oxaloacetate,
both of which may then be converted to glucose by
gluconeogenesis.

*Children have positive nitrogen balance because they need
extra protein for growth and to excrete less.
*Malnutrition and prolonged fever may lead to a negative
nitrogen balance.
Kwashiorkor – protein deficiency disease.
2. Ketogenic Amino Acids – those whose carbon
skeletons are degraded to acetyl CoA or acetoacetyl
CoA, both of which may then be converted to ketone
bodies.
Pyruvate is most commonly metabolized in one of three ways,
depending on the type of organism and the presence or
absence of O2.

Essential Amino acid – amino acid that the body cannot

synthesize and that must be supplied in the food.

Incomplete protein – a protein that does not contain all the Fates of Pyruvate
essential amino acid. Aerobic conditions
Pyruvate Acetyl CoA Citric Acid
plants and animals
*A normal adult requires 46 to 56 g of protein per day. Cycle
Anaerobic conditions
*When the body has depleted glycogen (starving), it can use Pyruvate Lactate
Contracting muscles
amino acids for fuel.
Anaerobic conditions
Degradation takes place in the two stages: Pyruvate Ethanol + CO2
Fermentation in yeast
1. Removal of the amino group.
2. Degradation of the carbon skeleton.

Transamination – removal of the α-amino group.

- requires pyridoxal phosphate, a coenzyme derived
from vitamin B6.

*Transamination is catalyzed enzymes called transaminases

or amino transferases.

Deamination (Oxidative Deamination) – catabolism reaction

whereby the α0amino group of an amino acid is removed,
forming a α-keto acid and ammonia which occur primarily in the
liver and the kidneys under the catalysis of the enzyme amino
acid oxidase.

3 Stages of Nitrogen Catabolism

1. Transamination – transfer of amino groups to alpha
α-ketoglurate.
2. Oxidative Deamination – ammonium ion (NH4) group
is liberated from the glutamate amino acid formed from
transamination.
3. Urea Cycle – series of biochemical reactions in which
urea is produced from ammonium ions and CO2.

*Nitrogens to be excreted are collected in glutamate, which is

oxidized to α-ketoglutarate and NH4+.

*NH4+ then enters the urea cycle.

*The ammonium ion produced by oxidative deamination is a

toxic substance, so it is quickly converted to carbomoyl
phosphate and then to urea via the urea cycle.

Urea Cycle – the pathway to eliminate ammonium ion.

Urea – excreted in the urine.

Hyperammonemia – failure of enzymes in the urea cycle.

- in severe cases, this leads to early death from toxic
ammonium ion buildup. It can also lead to retardation,
convulsions, and vomiting.

*Oxidative deamination produces large amounts of ammonium

ion which is toxic.
 19. Passageway of food molecules.
- Esophagus

20. Nutrient absorption occurs primarily in what organ?

- Small Intestine

QUIZ 1 QUIZ 2

1. The sequences of the reactions are called

1. A substance or agent that causes a change in the structure
- Pathways
of a gene.
- Mutagen 2. The reaction involved in the conversion of glucose to
glucose 6-phosphate in glycolysis
2. Monomer unit of nucleic acid. - Phosporylation
- Nucleotide
3. The reaction involved in the conversion of glucose-6
3. Product of DNA transcription. phosphate to fructose 6-phosphate.
- mRNA - Isomerism

4. Site of protein synthesis. 4. How many NADH are produced from 1 acetyl CoA entering
- Ribosome the Citric acid Cycle?
- 3 NADH
5. Sequence of 3 bases specifying for an amino acid.
- Codon 5. What is the starting material for Citric acid Cycle?
- Acetyl CoA
6. Terminate protein synthesis.
- Stop codons 6. What is the end product of glycolysis?
- 2 Pyruvate
7. DNA of eukaryotic cell is found in the _____.
- Nucleus 7. When glucose undergoes complete oxidation via cellular
respiration pathway through the malate-aspartate shuttle,
8. Main function is to store and transfer genetic information. the net number of ATP produced is
- DNA - 38 ATPs

9. Process by which DNA molecules produce exact duplicates 8. In the transport mechanism which operates in the muscle,
of themselves. how many ATP molecules are produced for each NADH?
- Replication - 2 ATPs

10. An error in base sequence reproduce during DNA 9. In what organelle of the cell does the Citric acid Cycle take
replication. place?
- Mutation - Mitochondria

11. It serves as a common currency into which energy gained 10. Net ATP produced in the glycolysis for molecule of
from food is converted and stored. galactose
- ATP - 2 ATPs

12. Types of RNA that delivers amino acids to the sites of 11. Total number of ATP produced in the Citric acid Cycle per
protein synthesis. acetyl CoA
- tRNA - 12 ATPs

13. Product of protein synthesis. 12. Main energy-producing pathways of the cell
- Amino acid - Cellular Respiration

14. Acid present in the stomach. 13. Catabolic process refers to breakdown of glycogen into
- Hydrochloric acid (HCl) glucose unit.
- Glycogenolysis
15. Function of bile in the digestion of fats.
- Emulsifying agent 14. A process by which glucose is synthesized from
non-carbohydrate precursor
16. First site of protein digestion. - Gluconeogenesis
- Stomach
15. Process by which excess glucose is converted into glycogen
17. Enzyme found in the stomach. - Glycogenesis
- Pepsin
QUIZ 3
18. Absorbs water and undigested food.
- Large intestines (colon) Test I.
1. Glucose  pyruvate = Glycolysis
 2. Acetyl CoA  NADH, FADH2, GTP = Citric Acid Cycle 6. Amino acid whose carbon skeleton can be converted to
3. Ammonia  urea = Urea Cycle glucose by gluconeogenesis.
4. Fats/Lipids  Fatty acid and glycerol = Lipolysis - Glucogenic
5. Fatty acids  Acetyl CoA = Beta-Oxidation pathway
6. Glycogen  Glucose = Glycogenolysis 7. A hormone used to lower blood glucose levels.
7. Glucose  glycogen = Glycogenesis - Insulin
8. Acetyl CoA  ketone bodies = Ketogenesis
9. Glucose  fats = Lipogenesis 8. Biochemical reaction in which ammonium ion is liberated
10. Non-carbohydrate (lactate, glycerol, amino acids)  from the amino acid formed from transamination.
glucose = Gluconeogenesis - Oxidative deamination
Test II.
1. What is the starting material of lactate fermentation or 9. Amino acids whose carbon skeletons are degraded to
formation of lactate in the muscles? pyruvate or oxaloacetate, both of which may then be
- Pyruvate converted to glucose by gluconeogenesis.
- Glucogenic
2. When glucose undergoes complete oxidation via cellular
respiration pathway through the glycerol phosphate 10. Overall accumulation of ketone bodies in the blood and
shuttle, the net ATP produced is urine.
- 36 ATPs - Ketosis

3. In the transport chain mechanism which operates in the

liver, how many ATP molecules are produced for each
NADH. Nucleic Acid:
- 3 ATPs
DNA Informal strand: 5’ C G C T G T A G T T G G A T T 3’
4. Net ATP produced from one molecule of glycerol in the
muscle. DNA Template strand: 3’ G C G A C A T C A A C C T A A 5’
- 20 ATPs
mRNA: 5’ C G C U G U A G U U G G A U U 3’
5. Reaction pertains to transfer of an amino group from one
molecule to another. Amino acid sequence: Arg Cys Ser Trp Ile
- Transamination

Computation of ATP:

For Lauric Acid (12:0)

Equivalent no. of ATPs Answer
No. of acetyl CoA 6 x 12 = 72
No. of NADH 5 x 3 = 15
No. of FADH2 5 x 2 = 10
Total number of ATP = 97
No. of ATP consumed (activation) = -2
Net ATP produced = 95

For Myristic Acid (14:0)

Equivalent no. of ATPs Answer
No. of acetyl CoA 7 x 12 = 84
No. of NADH 6 x 3 = 18
No. of FADH2 6 x 2 = 12
Total number of ATP = 114
No. of ATP consumed (activation) = -2
Net ATP produced = 112

For Palmitic Acid (16:0)

Equivalent no. of ATPs Answer
No. of acetyl CoA 8 x 12 = 96
No. of NADH 7 x 3 = 21
No. of FADH2 7 x 2 = 14
Total number of ATP = 131
No. of ATP consumed (activation) = -2
Net ATP produced = 129

For Stearic Acid (18:0)

Equivalent no. of ATPs Answer
No. of acetyl CoA 9 x 12 = 108
No. of NADH 8 x 3 = 24
No. of FADH2 8 x 2 = 16
Total number of ATP = 148
No. of ATP consumed (activation) = -2
Net ATP produced = 146

For Arachidic Acid (20:0)

Equivalent no. of ATPs Answer
No. of acetyl CoA 10 x 12 = 120
No. of NADH 9 x 3 = 27
No. of FADH2 9 x 2 = 18
Total number of ATP = 165
No. of ATP consumed (activation) = -2
Net ATP produced = 163

Total ATP produced from 3 fatty acids (95 + 112 + 129 + 146 + 163) = 645

Total ATP produced from glycerol (muscle) = 20

Total ATP produced from compete oxidation = 625

Metabolic pathways

Glycolysis
Reaction involved:
STEP 1: Glucose  Glucose 6-phospate = Phosporylation
STEP 2: Glucose 6-phosphate  Fructose 6-phosphate =
Isomerization
STEP 3: Fructose 6-phosphate  Fructose 1,6-biphosphate = Β-Oxidation
Phosphorylation Reaction involved:
STEP 4: Fructose 1,6-biphosphate  Dihydroxyacetone phosphate STEP 1: Acetyl Coa  Trans-enoyl CoA = Dehydrogenation
and Two glyceraldehyde 3-phosphates = Cleavage STEP 2: Trans-enoyl CoA  L-β-Hydroxyacyl CoA = Hydration
STEP 5: Dihydroxyacetone phosphate  two glyceraldehyde 3- STEP 3: L-β-Hydroxyacyl CoA  β-Ketoacyl CoA = Hydrogenation
phosphates = Isomerization STEP 4: β-Ketoacyl CoA  Acetyl CoA & New Acyl CoA = Thiolysis
STEP 6: Two glyceraldehyde 3-phospahtes  two 1,3-
biphosphoglycerates = Oxidation & Phosphorylation
STEP 7: Two 1,3-biphosphoglycerates  Two 3-phosphoglycerates =
Phosphorylation
STEP 8: Two 3-phosphoglycerates  Two 2-phosphoglycerates =
Isomerization
STEP 9: Two 2-phosphoglycerates  Two phosphoglycerates =
Dehydration
STEP 10: Two phosphoenolpyruvates  Two pyruvates =
Phosphorylation

Citric Acid Cycle

Reaction involved:
STEP 1: Oxaloacetate  Citrate = Condensation
STEP 2: Citrate  Isocitrate = Isomerization
STEP 3: Isocitrate  α-ketoglutarate = Oxidation & Decarboxylation
STEP 4: α-ketoglutarate  Succinyl CoA = Oxidation &
Decarboxylation
STEP 5: Succinyl CoA  Succinate = Phosphorylation
STEP 6: Succinate  Fumarate = Oxidation
STEP 7: Fumarate  Malate = Hydration
STEP 8: Malate  Oxaloacetate = Oxidation

Urea Cycle

STEP 1: Carbamoyl Phosphate  Citrulline = Transfer

STEP 2: Citrulline  Argininosuccinate = Condensation
STEP 3: Argininosuccinate  Arginine = Cleavage
STEP 4: Arginine  Ornithine = Hydrolysis