BIOCHEMISTRY LECTURE Amino Acid Absorption

Amino acids are absorbed in the small intestine, then transported to the liver
I. PROTEINS from the intestines via the portal vein.

Proteins- large molecules, made up of amino acids chain, sequence of In the liver, amino acids are: synthesize new proteins, Converted to energy,
amino acids is determined by DNA. glucose, or fat, Released to the bloodstream and transported to cells
throughout the body
Peptide Bonds Link Amino Acids
- Form when acid group (COOH) of one amino acid joins amine group (NH2) Amino Acid Metabolism
of a second amino acid Liver metabolizes amino acids, depending on bodily needs.
- through condensation Most amino acids are sent into the blood to be picked up and used by the
- broken through hydrolysis cells. Amino acid pool is limited but has many uses
Protein turnover – the continual degradation and synthesizing of protein
Structure of Proteins: classified by number of amino acids (carbon,
hydrogen, oxygen, and nitrogen) in a chain. Protein Synthesis
Transcription- a copy of code (m RNA) is made.
Peptides: fewer than 50 amino acids Translation- reading the code
Dipeptides: 2 amino acids Elongation- ribosome builds amino acids based on code of mRNA
Tripeptides: 3 amino acids
Polypeptides: more than 10 amino acids Metabolic Fate of Amino Acids
1. Protein turnover
Proteins: more than 50 amino acids 2. Gluconeogenesis
Typically 100 to 10,000 amino acids linked together 3. ATP production
4. Fat cells

PROTEIN NUTRITION

Essential- must be consumed in the diet

Nonessential- can be synthesized in the body
Conditionally essential- cannot be synthesized due to lack of protein

Denaturing: alteration of the protein’s

shape and function; through heat, acids,
bases, salts, mechanical agitation.
Note: Primary structure is unchanged by
denaturing

PROTEIN DIGESTION
Protein-energy malnutrition (PEM)- eating too little protein

1. Kwashiorkor (Severe protein defieciency)/manas

2. Marasmus (Results from a severe deficiency in
kilocal)/sobrang payat pero Malaki tyan
3. Marasmic Kwashiorkor (Chronic deficiency in
protein)/sobrang payat pero sobrang laki tyan at ulo.
 II. 3D STRUCTURE OF PROTEIN TERTIARY STRUCTURE
-Myoglobin is an example of this
PRIMARY STRUCTURE
- N-terminal end, and C-terminal end is present

SECONDARY STRUCTURE QUATERNARY STRUCTURE

- hydrogen bonded arrangement of backbone of the protein Fibrous proteins:
- 2 rotation: Bond between a-carbon and amino nitrogen; contain polypeptide
a-carbon and carboxyl carbon chains organized
- regular, repeated patterns of folding of the protein backbone. approximately parallel
- Alpha helix: coils around helix axis in clockwise along a single axis
- Beta sheet: antiparallel b-pleated sheet arrangement Globular proteins:
proteins which are folded
to a more or less
spherical shape

Hydrophobic and Hydrophilic

Supersecondary structure (combination of a-

and b-sections)

this concept has been described in the description of the formation of

liposomes.

Protein Folding Chaperones

- Chaperones aid in the correct and timely folding of many proteins
- hsp70 were the first chaperone proteins discovered
- it exist in organisms from prokaryotes to humans
 III. CARBOHYDRATES -Example: Aldose and Ketose; Fructose and
- (CH2O)n Galactose
-large group of organic compounds occurring in foods and Glyceraldehyde- contains a stereo center
living tissues, including sugars, starch, and cellulose. and exists as a pair of enantiomers
-formed by green plants from CO2 and water during the Enantiomers- Mirror-images stereoisomers
process of photosynthesis
- soluble in water 2. Disaccharides (Dimers) C12H22O11
Fiber- carbs that cannot be digested. - Double sugar
- Sucrose (eg. Table sugar)
Physical Properties - Glycosidic Bond (when two monosaccharides join
1. Stereoisomers- same structural formula but they differ I spatial Disaccharide. Same to condensation
configuration.
2. Optical Activity- rotation of plane polarized light forming + 3. Polysaccharides (Polymers)
glucose and – glucose. - 3 or more simple sugar
3. Distereo Isomers- the configuration changes with regard to C2, - Glycogen animal starch stored in liver & muscles
C3, and C4 in glucose. - Cellulose - indigestible in humans - forms cell walls
4. Annomersim- spatial configuration with respect to the first - Starches - used as energy storage
carbon in aldoses and second carbon in ketoses. - Classification:
o Storage (eg. starch:plants and glycogen:animals)
Chemical Properties o Structural (eg. cellulose:cell wallf of plants and
1. Osazone Formation – are carbohydrates derivatives when chitin:animals. It is the major structural
sugars are reacted with excess component of the exoskeletons of invertebrates,
1. of phenylhydrazine. such as insects and crustaceans; also occurs in
2. Benedict’s Test – are reducing sugars when heated in the cell walls of algae, fungi, and yeasts)
presence of alkali get converted to powerful reducing species - Types:
known as enediols. o Homopolysaccharides (single sugar monomer)
3. Oxidation – monosaccharides are reducing sugars if their o Heteropolysaccharides (two or more monomer)
carbonyl groups oxide give carboxylic acids.
4. Reduction to alcohols – products are known as alditols.
Dehydration Synthesis
Groups of CARBOHYDRATES Combining simple molecules to form a more complex one
with the removal of water

Hydrolysis or Chemical Digestion

Addition of WATER to a compound to SPLIT it into smaller
subunits

Hemiacetal Cyclization of sugars

Fischer
projections bonds
are written in a two
dimensional
representation
showing the
configuration of
tetrahedral
stereocenters

Haworth projections five- and six-membered hemiacetals

are represented as planar pentagons
1. Monosaccharides (Monomers) C6H12O6
-Simple sugar Glycoprotein contains carbohydrate residues in addition to
-Single ring structure the polypeptide chain which involve in the immune
-Cannot be hydrolyzed to simpler carbs response like antibodies which bind to and immobilized in
-Building blocks of all carbs antigens. Oligosaccharide

Protein Glycosylation a process by which carbohydrate

components are covalently added to proteins to form
glycoproteins
 IV. LIPIDS
-non polar (hydrophobic) compounds, soluble in organic solvents.
- Amphipathic in nature, having a non-polar end and a polar end.
-most common monomer of lipid is triglycerides
- Found in plant: seeds, animals: adipose and connective tissue
- 95% lipids in every food
-Sphingolipids Contain sphingosine, a long-chain amino alcohol
sphingosine. Found in Plants and Animals, and majority in Nervous
System. Similar to Phospholipids.
- Glycolipids a compound in which a carbohydrate is bound to an -
OH of the lipid
- Gangliosides Glycolipids with complex carbohydrate moiety that
contains more than 3 sugars

Types of Lipids
Vitamins are divided into two classes: lipid-soluble and water-soluble
1. Fatty Acids unbranched-chain carboxylic acid, most commonly of
12 - 20 carbons, derived from hydrolysis of animal fats, vegetable
oils, or phosphodiacylglycerols of biological membranes
- Building blocks for triglycerides and phospholipids
- may vary at Length (affects absorption) Saturation (chem structure)
- Unsaturated fatty acids have lower melting points than their
saturated counterparts.

2. Fats and Oils formed from glycerol and fatty acids

- function: gives energy a. (9 kcals/g= 60% energy needs at rest),
b.stored as adipose tissue, insulation & protection, cell membrane
and constituents.
3. Triglycerides predominate form of fat in foods and major storage
form of fat in the body (composed of 3 fatty acids+glycerol)
- ester of glycerol with three fatty acids.
- Saponification the reactions of glyceryl ester with sodium or
potassium hydroxide to produce a soap, which is the corresponding
salt of the long-chain fatty acid.
- Shape as Letter E.
4. Waxes esters of fatty acids with long chain monohydric alcohols
- may also contain hydrocarbons
- Found as protective coatings for plants and animals
- Carnuba wax is valued for its toughness and water resistance
- Steroids: a group of lipids that have fused-ring structure of 3 six-
membered rings, and 1 five-membered ring.
-Vitamin A (retinol) occurs only in the animal world
-Vitamin A is found in the plant world in the form of a provitamin in a
group of pigments called carotenes
-the most abundant form in the circulatory system is vitamin D3
- The most active of vitamin E is a-tocopherol
Prostaglandins: a family of compounds that have the 20-carbon
skeleton of prostanoic acid. 1st detected in prostate: seminal fluid
Leukotrienes: Found in white blood cells. Derived from arachidonic
acid
Hormonal Control of Appetite Certain regulatory pathways control
one’s desire to eat

5. Phospholipids hydrophilic on one end; hydrophobic on the other

- Make up the phospholipid bilayer in the cell membrane (Lecithin-
used an emulsifier in foods)
-Made by the liver
- Kinks in Hydrocarbon chain=effects of double bonds

6. Sterols more complex than phospholipids or triglycerides

- Do not provide energy
- Cholesterol is the best known sterol
-Phytosterols major plant sterols
-Important part of : sex hormones – testosterone, Vitamin D, Bile
(aids fat digestion), Adrenal hormones – cortisol
 V. NUCLEIC ACIDS

Friedrich Miescher- called nuclein from the nuclei of pus cells. It has
acidic property called nucleic acid

-genetic material: stores information (genes, DNA-> RNA->

Proteins) AND transfer information (blueprint for new cells &
offsprings)

DNA: is found in the nucleus with small amounts in mitochondria and

chloroplasts.
RNA: all throughout the cell.

Cloning- The process of making identical copies of DNA

-Recombinant DNA- DNA molecules that contain covalently linked
segments derived from 2 or more DNA sources
-Sticky Ends can be used to construct Recombinant DNA
-DNA Ligase- seals nicks in the covalent structure
-Plasmid- small circular DNA that is not part of the main circular
DNA chromosome of the bacterium.

Genetic Engineering- when an organism is intentionally altered at

the molecular level to exhibit different traits

Gene therapy- cells of specific tissues in a living person are altered

in a way that alleviates the affects of a disease

DNA Library- a collection of clones of an entire genome

Polymerase Chain Reaction- a method of amplification for

possibility to increase the amount of a given DNA many times over
without cloning the DNA

DNA Fingerprinting- a technique that shows the genetic makeup of

living things. It is a method of finding the difference between the
satellite DNA regions in the genome.

It has 3 parts: Dideoxy nucleotides- used to terminate DNA synthesis.

 nitrogen base (C-N ring) NUCLEIC ACID DISORDERS

 pentose sugar (5C)
o ribose in RNA  Lesch Nyhan Syndrome- Children with this have excess
o deoxyribose in DNA uric acid in urine
 phosphate (PO4) group  SCIDS- ADA Deficiency

 PNP Deficiency- Impairment of T-cell function

Nucleic Polymer- backbone bonded by phosphodiester bond  Gout- Characterized by hyperuricemia
Replication- 2 strands of DNA helix are complementary;  Orotic Aciduria- Causes abnormal growth, megaloblastic
cell reproduction: mitosis; gamete production: meiosis anemia, and excretion of large amount of orotic acid in
- DNA in the chromosomes replicates itself every cell urine. Lack of 2 enzymes
division
- Maintains correct genetic information
- Two strands of DNA unwind
 VI. METABOLISM
set of chemical reactions that occur in living organisms in
order to maintain life. It has 2 parts which combine, it
maintains life:
-Anabolism: the energy- requiring process
-Catabolism: the energy- releasing process
Metabolites the intermediates and products of metabolism.
Primary involved in the normal growth, development and
reproduction.
Secondary not involved in those processes but usually has
important ecological function like antibiotics.
Metabolome complete set of small molecule metabolites
found within a biological sample.
Metabolomics study of metabolome.
Metabolic Pathway is a sequence of reactions that has a
specific purpose.
STAGES OF METABOLISM
Catabolism
• STAGE 1: Breakdown of macromolecules (proteins,
carbohydrates and lipids to respective building blocks.
• STAGE 2: Amino acids, fatty acids and glucose are
oxidized to common metabolite (acetyl CoA)
• STAGE 3: Acetyl CoA is oxidized in citric acid cycle to
CO2 and water. As result reduced cofactor, NADH2
and FADH2, are formed which give up their electrons.
Electrons are transported via the tissue respiration
chain and released energy is coupled directly to ATP
synthesis.
Anabolism- characterize by divergence.
• STAGE 1: Monosaccharide synthesis begin with
CO2, oxaloacetate, pyruvate or lactate.
Amino acids are synthesized from acetyl CoA,
pyruvate or keto acids of Krebs cycle.
Fatty acids are constructed from acetyl CoA.
• STAGE 2: monosaccharides, amino acids and fatty
acids are used for the synthesis of polysaccharides,
proteins and fats.
Dark Reactions or Carbon-fixation reactions: ATP and
NADPH produced from the light reactions serve as the source
energy and reducing power to drive the conversion of CO2 to
sugars.
Glycolysis- series of chemical reactions that occurs in the
fluid part of cytoplasm.
- first stage of glucose metabolism.

G protein or Guanine nucleotide binding proteins- a family

of proteins that act as molecular switches inside cells
-involved in transmitting signals from a variety of stimuli
outside a cell to its interior.
o Stimulating G protein (Gs)– activates adenylate
cyclase
o Inhibitory G protein (Gi)- stops/inhibit adenylate
cyclase
Allosteric enzymes- can adopt to two or more slightly
different conformations, and a shift from one to another caused
by the binding of a ligand can alter their activity.
o Active Site recognizes the substrates
o Regulatory Site recognizes a regulatory molecule