Get documents about "Biochemistry
Document Sample
Biochemistry
The Chemistry of Life
You are chemistry.
BIOCHEMISTRY: The study of the
molecular basis of life and its processes.
Biochemists have to understand both the
living and chemical world well.
KEY: Many biological processes are the
same in different organisms Their basic
building blocks and pathways are the
same.
BIOMOLECULES
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
CARBOHYDRATES
Bread
Pasta
Rice
Carbohydrates
―Hydrates of carbon‖ (C, H, & O)
Polyhydroxy aldehydes
(ALDOSES) or ketones
(KETOSES)
Usually Cx(H2O)y
―Sugars‖
Single unit: Monosaccharide
Two units: Disaccharide
Three units: Trisaccharide, etc.
Many units: Polysaccharide
Some Common Disaccharides
Sucrose: Table Sugar
Glucose+Fructose
Lactose: Milk sugar
Glucose+Galactose
Maltose: Malt/Barley sugar
Glucose+Glucose
Some Common Polysaccharides
Starch: glucose polymer (alpha)
Potato, rice, wheat, corn
Glycogen: branched glucose
polymer
Animal storage
Cellulose: glucose polymer (beta)
Plant structures, paper, cotton,
wood
Chitin: Modified glucose (N-Acetyl
Glucose)
Fungi cell wall, insect exoskeleton
http://www.bmb.psu.edu/courses/bisci004a/chemtutor/polysac2.jpg
http://www.bmb.psu.edu/courses/bisci004a/chemtutor/polysac1.jpg
CARBOHYDRATES
Extra carbohydrates is stored in the liver
and muscle tissues as glycogen
Large excess are converted to fat
Carbohydrates supply 4 kcal of energy per
gram
On the ―Sugarfree‖ Phenomenon
Saccharin
Oldestartificial
sweetener
Aspartame and
Acesulfame-K
Not carbohydrates
Sucralose
―Splenda‖
LIPIDS
Lipid – a cellular
constituent that is soluble
in organic solvents (e.g.
hexane); insoluble in water
Lipid family
Fatty acids (long chain
carboxylic acids)
Phospholipids - forms the cell
membrane
Steroids (e.g. cholesterol and
sex hormones)
Fat soluble vitamins
Fatty Acids
http://biology.clc.uc.edu/graphics/bio104/fat.jpg
Fatty Acids
http://biology.clc.uc.edu/graphics/bio104/fatty%20acid.jpg
Fatty Acids
http://biology.clc.uc.edu/graphics/bio104/cistrans.jpg
Phospholipids
Made from glycerol, two fatty acids, and
(in place of the third fatty acid) a
phosphate group with some other
molecule attached to its other end
Contains a ―hydrophobic‖ and
―hydrophillic‖ group
Hydrophobic – water hating, not soluble in
water
Hydrophilic – water loving, soluble in water
Phospholipids
http://biology.clc.uc.edu/graphics/bio104/lecithin.jpg
Phospholipids
http://www.sirinet.net/~jgjohnso/membranebilayer.jpg
Cell Membrane
http://www.sirinet.net/~jgjohnso/cellmembranes15.jpg
Steroids CH3 OH
Biological molecules CH3
that perform diverse
functions testosterone
O
Consists of four
fused rings
CH3 O
CH3
H3C CH3
CH3
CH3
CH3
cholesterol HO estrogen
HO
Functions of Fats
Used to build cells and parts of the cell (e.g.
brain cells, nerve tissues, cell membrane)
Stored in the body in adipose tissue
Adipose tissue are called fat depots
Surround vital organs (e.g. heart, kidney,
spleen) to serve as protective cushion
Stored under the skin for insulation
Fat reserves are converted to glycerol and fatty
acids ( 9 kcal per gram)
Glycerol is burned for energy or converted to glucose
Fats and Health
Lipoproteins
Group of proteins with a triglyceride or cholesterol
Very-low density lipoprotein (VLDL)
Transport triglycerides
Low density lipoprotein (LDL)
Transport cholesterol to cells
High density lipoprotein (HDL)
Transport cholesterol to liver
On Coconut Oil
C8 ...... 8.86 (Caprylic)
C10......6.17 (Capric)
C12......48.83 (Lauric)
C14......19.97 (Myristic)
C15......Traces (0.01)
C16.......7.84 (Palmitic)
C18.......3.06 (Stearic)
C18:2 ....0.76
C18:1.....4.44
C20........0.05 (Arachidic)
Regular Coconut Oil (RBD) vs.
VCO
• RBD
• Refined, bleached, deodorized
• From highly processed copra
• VCO
1. Quick drying of fresh coconut meat
which is then used to press out the
oil.
2. Wet-milling. "Coconut milk" is
expressed first by pressing. The oil
is then further separated from the
water. Methods which can be used
to separate the oil from the water
include boiling, fermentation,
refrigeration, enzymes, and
mechanical centrifuge.
Crisco and Olestra (by P&G)
1911: Shortening
―To eat, or not to eat - fat is the question.”
- from the Introduction of Mary Enig, Know your Fats: The
Complete Primer for Understanding the Nutrition of Fats, Oils,
and Cholesterol, Bethesda Press, USA, 2000.
Olestra
1998, Proctor and Gamble introduced a
new fat/oil substitute called Olestra (brand
name Olean®
material replaces fats in snack foods such
as potato chips
claimed that food using Olestra in place of
digestible fats provide less calories since
the Olestra is not digested and passes
through the body unchanged
Some side effects include abdominal
cramping and loose stools
Olestra
How does Olestra work?
http://www.cnn.com/HEALTH/9802/10/fakefat.olestra/olestra.large.jpg
Olean®
Olean®
http://static.howstuffworks.com/gif/question526-fat-chips.jpg
http://static.howstuffworks.com/gif/question526-olestra-chips.jpg
Proteins
Made up of amino acids
The side groups are
what make each amino
acid different from the
others. Of the 20 used to
make proteins, there are
three groups. The three
groups are ionic, polar
and non-polar.
Amino Acid Peptide
Polypeptide Protein
SIDE
CHAIN R O
+
H3 N C C
-
H O
R1 O R1 O
+
H2N C C H3N C C
-
H OH H O
AMINO ACID ZWITTERION
AMINO ACIDS ARE ZWITTERIONS
Synthesis of Proteins
R1 O R2 O
+ +
H3 N C C
-
+ H3 N C C
-
H O H O
peptide
R1 O bond
+
H3N C C R2 O
H NH C C + H2O
-
H O
Synthesis of Proteins
R1 O R2 O R3 O
+ +
H3 N C C NH C C + H 3N C C
- -
H H O H O
R1 O R2 O
+ R3
H3N C C NH C C O
H H NH C C
-
H O
Synthesis of Proteins
R1 O R2 O
+ R3 O R4 O
H3N C C NH C C
+
H H NH C C + H 3N C C
- -
H O H O
R1 O R2 O
+ R3
H 3N C C NH C C O
NH C C R4 O
H H
H NH C C
N-Terminal End -
H O
C-Terminal End
Synthesis of Proteins
R1 O R2 O R3 O R4 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
≠
=
R4 O R2 O R3 O R1 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
Synthesis of Proteins
R1 O R2 O R3 O R4 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
≠
=
R1 O R3 O R2 O R4 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
Synthesis of Proteins
R1 O R2 O R3 O R4 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
≠
R4 O R2 O R3 O R1 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
≠
R1 O R3 O R2 O R4 O
+
H3N C C NH C C NH C C NH C C
-
H H H H O
Proteins
http://chemed.chem.purdue.edu/genchem/topicreview/bp/1biochem/graphics/20.gif
Why
is
sinigang
tasty?
Structure of Proteins
Primary Structure
sequence of the amino acids in the protein
Secondary Structure
polypeptide chain folds back on itself to form a secondary
structure
Tertiary Structure
interactions between amino acid side chains that leads to
the three-dimensional structure of the polypeptide chain
Quaternary Structure
interactions between individual polypeptide chains
Protein Structure
25.3
Proteins
Protein Structure
Hydrogen Bonds in Parallel and Antiparallel b-pleated Sheets
25.3
Protein Structure
Intermolecular Forces in a Protein Molecule
ionic forces
hydrogen
bonds dispersion
forces
dispersion ionic forces
forces
dispersion dipole-dipole
forces forces
CYSTEINE bonds and Hair rebonding
25.3
Sickle cell anemia
HEMOGLOBIN of a HEMOGLOBIN of a person
HEALTHY PERSON w/ SICKLE CELL
ANEMIA
http://www.concord.org/~barbara/workbench_web/unitIV_mini/images/normHB.jpeg
http://www.concord.org/~barbara/workbench_web/unitIV_mini/images/sickleHB.jpg
Sickle cell anemiaO
HO
OH
O NH2
Aspartic Acid (E)
to
CH3 O
H3 C OH
NH2
Valine (V)
http://www.pueblo.gsa.gov/cic_text/health/sicklecell/sickle.gif
THE ENZYME GLYCOSIDASE
Q: WHAT IS AN ENZYME?
A: They are proteins which act as biological catalysts that enhance
reaction rates as they provide an alternative reaction pathway that
requires less energy than an uncatalyzed reaction.
*Catalysis can happen at mild temperatures
*Very specific to the reactions they catalyze
*SUBSTRATES
*ACTIVE SITE
ENZYME CATALYSIS
FROM: http://www.nd.edu/~aostafin/CRCD/index7.htm
ENZYME CATALYSIS
FROM: http://www.nd.edu/~aostafin/CRCD/index7.htm
GLYCOSIDASE ACTION
GLYCOSIDE Eg.
GLUCOSE
XYLOSE
MOLECULE O SUGAR ARABINOSE
GALACTOSE
RHAMNOSE, etc.
(may be inactive)
Hydrolysis by Enzyme
MOLECULE OH HO SUGAR
PROTEINS
Humans can synthesize all amino acids
except
Isoleucine,leucine, lysine, methionine,
phenylalanine, threonine, tryptophan, valine
Humans have to eat food with proteins to
get the amino acids
Sources of proteins
Corn protein – lacks lysine and tryptophan
Rice protein – lacks lysine and threonine
Wheat protein – lacks lysine
Soy protein – lacks methionine
Lean meat, milk, fish, eggs, cheese –
adequate proteins
Proteins and Health
Can combine different vegetables and grains to
have all essential amino acids
Grains(lacks tryptophan and lysine but with
methionine)
Legumes (enough tryptophan and lysine but no
methionine)
Extreme vegetarianism
May lack vitamin B12, calcium, iron, riboflavin, vitamin
D
Modified vegetarianism
Eg. No red meat
NUCLEIC ACIDS
―We wish to suggest a
structure for the salt of
deoxyribonucleic acid (DNA)‖
– 1953
―DNA Technology is the most
awesome skill acquired by
man since the splitting of the
atom.‖-1983
2000: Human Genome Project
completed. 30K genes now
expected unlike the 80K
before.
1860‘s: Gregor Mendel proposed heredity is
based on the transfer of several ―factors‖
between parents and offspring
Early 1900‘s: T.H. Morgan et.al. proved eye
color (as in fruit flies) depends on the transfer of
a single chromosome from parent to offspring.
―Factors‖ and chromosomes are one and the
same.
CHROMOSOMES: ―Colored-bodies‖
James Watson, Francis Crick, with experimental
data from Rosalind Franklin and Maurice Wilkins
Nucleic Acids
Carry genetic information.
DNA (deoxyribonucleic acids) have molecular
weights around 6 - 16 106 amu and are found
inside the nucleus of the cell.
RNA (ribonucleic acids) have molecular weights
around 20,000 to 40,000 amu and are found in
the cytoplasm outside the nucleus of the cell.
Nucleic acids are made up of nucleotides.
There are three important parts to a nucleic acid:
phosphoric acid unit,
five carbon sugar (e.g. deoxyribose), and
nitrogen containing organic base (e.g. adenine).
Nucleic Acids
NH2
OH N Organic
Phosphoric N
Acid - Base
O P O Unit
Unit N N
O CH2
O
HC CH
CH CH2 Deoxyribose
Unit
OH
Nitrogen Bases in Nucleic Acids
O
NH2
N
N NH
N
NH N NH2
NH N
Adenine Guanine
O
O NH2
H3C NH
NH N
NH O
NH O NH O
Thymine Uracil Cytosine
Nucleic Acids
DNA consists of two deoxyribonucleic
acid strands wound together in a
double helix.
The phosphate chains are wrapped
around the outside of the DNA
molecule.
Complementary base pairs are formed
from bases which optimize H-bonding:
T and A or C and G.
The complementary base pairs are
held together by hydrogen bonding.
During cell division, the DNA double
helix unwinds.
Base-Pair Formation by Adenine and Thymine and by
Cytosine and Guanine
Chargaff‘s rules
25.4
DNA & RNA Differences
Sugar: DNA-
deoxyribose
RNA-ribose
Uracil replaces
thymine in RNA
RNA can exist
stably as a single
strand)
Strand direction
The phosphate group
is connected at
carbon 5 of the sugar,
while the oxygen at
carbon 3 forms a
bond with the
phosphate group of
the next nucleotide.
Nucleotides are liked,
therefore, by
phosphodiester
bonds.
Watson-Crick DNA model (B-DNA)
1. 2 polynucleotide chains
twisted into a right-
handed double-helix;
diameter of 2.4nm;
each helical turn occurs
at 3.4nm; 10.4bp per
turn
2. Base-pairing
3. Antiparallel chains
4. Bases on inside,
phosphate-sugar on
outside
Variations on DNA structure
B-DNA: Base pairs at
right angles; 10.4bp/turn;
2.4nm diameter; sodium
salt of DNA, humid
conditions
A-DNA: bp tilt 20 degrees
from horizontal, 11bp per
turn, helical turn at
2.5nm, 2.6nm diameter;
dehydrated DNA
Z-DNA: bp in zigzag; left-
handed helix; 12bp per
turn, turn at 4.5nm; 1.8nm
diameter
Higher-order structures
Cruciforms: cross-like
structures that are likely
when DNA sequence has
a palindrome (similar in
principle to a hairpin
structure)
H-DNA: triple helix; bet.
Polypurine strand and
Polypyrimidine strand;
non-conventional base-
pairing
Supercoiling: packages
DNA into a compact form
PROBLEM
Determine the complementary DNA and
RNA sequence of the following
sequences:
A. 5‘ACCTTGAGTAACCAGATACCAGA3‘
B. 3‘GGCATCGGACTAGCAAGCCAGA5‘
PROBLEM
Examine these two DNA strands. Imagining
that they are paired to their
complementary strand, one can tell which
will have the higher BP. Which one is it?
A.AGTTGAGATGCCGCTGATGCCGATGC
CCGTCGCTCGGCGCTAAGCACCATGC
B.ATATCTAATCGATTCTATTATTTCTATAT
AGGCTAGCTAGCTATGCTTAGCTAGGC
The Genetic Code
GENOME – ENGLISH analogy
Nitrogenous Bases (ATCG) Letters (a,s,f,t,r,e,…)
Codons Words
Gene Sentences
Chromosome Chapters
Genome Book
The Central Dogma
replication
DNA Protein
transcription translation
mRNA
RNA polymerase Ribosome
tRNA
USING THE CODE
Messages from mRNA read from 5‘->3‘
Problem 1
What is the peptide encoded by the
following mRNA?
3‘-AGAAUAUCGAAGCAGGGGUAGUGA-5‘
Answer 1
What is the peptide encoded by the following
mRNA?
3‘-AG//AAU/AUC/GAA/GCA/GGG/GUA//GUGA-5‘
Met-Gly-Thr-Lys-Leu
Problem
The following is the parent DNA strand. Assuming
that splicing does not occur after transcription, give
the peptide it expresses.
5’-CTATAGAATCCCCCAATGACCACGCAT-3’
Answer 2
The following is the parent DNA strand. Assuming
that splicing does not occur after transcription, give
the peptide it expresses.
DNA: 5’-CTATAGAATCCCCCAATGACCACGCAT-3’
mRNA: 3’-GAUAUCUUAGGGGGUUACUGGUGCGUA-5’
READ mRNA from 5’ -> 3’
Met-Arg-Gly-His-Trp-Gly-Ile-Leu
On Cancer and Genetic Control
Cancer: Problem of cell persistence
Common: CLONALITY, AUTONOMY (proliferation), ANAPLASIA
(loss of function), METASTASIS/INVASION
Cancer cells do not die a natural death. (Apoptosis)
They build up and ―steal‖ nutrients normal healthy cells should
have
As they increase in number, they may also impinge on other
normal processes
On Cancer and Genetic Control
• We still cannot pinpoint exactly WHY one gets cancer.
• One way of explaining it is by MUTATIONS that occur in
one‘s genetic code.
• We all have proto-oncogenes. What matters is if these
are ―turned on‖ by some mutations.
• However, we know genetics and environment both play
a role — different factors contribute (Bullets analogy)
• Diet
• Vices
• Chemical exposure
• Radiation exposure
• Heredity
• Treatment: Stop their division, kill the cells
• Cut off nutrients/life supply
• Chemicals
• Radiation
• Induce programmed cell death (apoptosis)
Some interesting genetics: Scent Compatibility
From the 2006 Natural Products Lecture Class of Dr. Fabian Dayrit
Some interesting genetics: Scent Compatibility
From the 2006 Natural Products Lecture Class of Dr. Fabian Dayrit
Some interesting genetics: Nature vs. Nurture
―Epigenetics‖: The DNA is not the only important thing. What is
―around it‖ is also important. (eg. Twin study) it is not just the genes
that influence the traits and functions of an organism but also
‗epigenetic‘ or non-gene factors.
These epigenetic factors are features within the cell that can be
inherited when cells divide but they don‘t change the genes
themselves
Chimps and Humans are 99% similar genetically.
Humans have similar DNA (We have same general characteristics).
The only difference: 1 in 1000 nucleic acids!
We take note of the ENVIRONMENT and PROTEINS, along with
their functions
GENOMICS PROTEOMICS,
METABOLOMICS
Newborn Screening
The presence or levels of some
markers (genes or proteins) are
determined to check for possible
diseases.
Disease effects are established,
not just correlations.
Already being done here.
Hopefully routine in the
Philippines. (500-800 pesos)
Is the extreme presented in
GATTACA possible? ?
Chemistry In Action: DNA Fingerprinting
―The capacity to blunder slightly is the real marvel of DNA.
Without this special attribute, we would still be anaerobic
bacteria and there would be no music.‖
– Lewis Thomas
―In the transmission of human culture, people always
attempt to replicate, to pass on to the next generation
the skills and values of the parents, but the attempt
always fails because cultural transmission is geared to
learning, not DNA.‖
-Gregory Bateson
―There is no gene for the human spirit.‖
-GATTACA
