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Welcome to BI 212, Summer 2010
Lecture 1 Outline (Ch. 3, 4, 5)
I.
Chemical Bonds and Shape
II.
Water Molecules
III. Chemical Reactions
IV. Organic Chemistry – Carbon-based molecules
V. Macromolecules
A.
B.
C.
D.
Carbohydrates
Lipids (NOT TRUE POLYMERS)
Proteins
Nucleic Acids
VI. Lecture Concepts
Chemical properties – all about shape
• water
• methane
Chemical Bonds - Covalent
• electronegativity: attraction of e- by atom
• non-polar = e- shared equally
• polar = e- unequal
• bonds can differ in polarity
Chemical Bonds - Ionic
• electronegativity so unequal, e- stripped
• Example: sodium chloride
Chemical Bonds - Hydrogen
• H atom (covalent bond), attracted to electronegative atom
• between like or unlike molecules
Water – chemical properties
75% water
70-95% water
Water – chemical properties
• Cohesion – tendency of molecules to stick to each other
• Adhesion – “ ” to stick to surrounding
H2O
Hg
• Surface tension
• Capillary action
Water – chemical properties δ-
δ+
δ+
- dissolve anything polar or ionic (salt, proteins)
• hydrophilic – attracted to water
- poor solvent for non-polar substances
(butter, cell membranes)
• hydrophobic –
repelled by water
Water – chemical properties
• less dense when solid (ice)
• high specific heat - insulating
Water – chemical reactions
Other chemical reactions
CO2 + H2O + light  C6H12O6 + O2
Carbon – history of organic compounds
• historically - compounds divided by burn/won’t burn
living – wood, fat, oil
non-living – water, rocks
• early 18th century living - organic
non-living - inorganic
• “vital force” – needed to make inorganic
organic
Carbon – history of organic compounds
• Friedrich Wölher - 1820s
- heated ammonium cyanate
-made urea
(organic compound
in urine)
• 19th century - chemists – increasingly complex molecules
• Stanley Miller - 1953
- amino acids from inorganic gasses
Carbon isomers
• Organic compounds all contain carbon
- vary atoms with which carbon bonds
- vary shape/structure of molecules
• Isomers = same molecular formula, different shape
C4H10
C4H10
butane
isobutane
Carbon isomers
Carbon – functional groups
• functional groups – common atom combinations, reactions
1. Hydroxyl (-OH)
4. Amino (-NH2)
2. Carboxyl (-COOH)
5. Sulfhydryl (-SH)
-
3. Phosphate (-PO42-)
6. Methyl (-CH3)
Self-Check
Which functional groups are present in the following molecule?
HO
O
C
C
4. Amino (-NH2)
2. Carboxyl
(-COOH)
5. Sulfhydryl
(-SH)
H
C OH
H C
H
1. Hydroxyl
(-OH)
H
N
H
Which are not present ?
-
3. Phosphate
(-PO42-)
6. Methyl
(-CH3)
Macromolecules
Macromolecules = giant molecules
Four biological classes:
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic acids
Synthesis –
Monomers (single units) joined into polymers (multi-unit)
Macromolecules
Dehydration synthesis =
remove H2O, new bond
Hydrolysis = add H2O, break bond
Carbohydrates
1. Carbohydrates – sugars and sugar polymers
Carbohydrates
1. Carbohydrates
• Monosaccharide – simplest sugar molecule
- multiple of CH2O
-hexose – 6 C
-Glucose
-pentose – 5
-Ribose
Carbohydrates
• In water, sugars = rings
glucose
• C @ each corner
Carbohydrates
• joined by dehydration synthesis
glycosidic bond
Carbohydrates
• Polysaccharide – 100s – 1000s of monosaccharides
Two purposes:
Storage:
- plants – starch
- animals – glycogen
Structure:
- plants – cellulose
- (animals – chitin)
Carbohydrates - storage
Animal storage glycogen
Plant storage starch
Carbohydrates - structure
Carbohydrates
α glucose
β glucose
starch
digestible (humans)
celluose
indigestible (humans)
Lipids
2. lipids – fats, phospholipids, steroids
• hydrophobic
• not made of monomers
i. fats – glycerol + fatty acid by dehydration – ester bond
fat molecule:
-one glycerol, 3 f.a.
aka triglyceride
Lipids
• saturated fats – all C bonded to
as many H as possible
• unsaturated fats – at
least one C with fewer H
Lipids
ii. phospholipids – glycerol + 2 f.a.
+ phosphate + choline
• lipid bilayer
Lipids
iii. steroids (some) – C skeleton 4 fused rings
cholesterol
estradiol
testosterone
cortisol
Proteins
3. proteins – string of amino acids
• very diverse group of macromolecules
3) Energy Storage
(e.g. albumin)
1) Catalyze Chemical
Reactions (e.g. amylase)
2) Structure
(e.g. keratin)
5) Hormones
4) Transport
(e.g. insulin)
6) Poisons
(e.g. hemoglobin)
(e.g. venom)
7) Movement
(e.g. muscle fibers)
Proteins
• monomer – amino acid
• polymer – polypeptide
• joined by dehydration
• peptide bond
Proteins – amino acids (a.a.)
Amino (-NH2)
Carboxyl (-COOH)
Proteins
Structure of an amino acid
Alpha C
Amino group
Carboxyl group
“R” group – changes
amino
terminus (N)
carboxy
terminus (C)
Proteins – amino acids (a.a.)
20 different a.a.
“R” group different
Classes:
• non-polar
• polar
• charged
Amino (-NH2)
?
Carboxyl (-COOH)
Proteins
mature proteins processed, folded
Proteins
N
Four levels of protein structure:
i.
Primary – unique sequence of a.a.
*determined by peptide bonds
ii. Secondary – coiled and folded (sheet or helix)
*determined by amino-carboxyl H-bonds
C
Proteins
Four levels of protein structure:
iii. Tertiary – regions linked
*determined by R-group H-bonds
iv. Quaternary – >1 protein
*determined by proteinprotein interaction
Proteins
Alterations to protein structure:
• mutations –
Ex. sickle cell anemia
• environment – pH, temp,
chemicals
Ex. hair perm
sickle cell
• denatured – unfolded proteins
- Sometimes reversible, usually not
normal cell
Biomolecules
Self-Check
Specific
Molecule
Which Biomolecule
Group?
Building blocks/
Monomers?
Joining
Bond?
CELLULOSE
FAT
STARCH
STEROID
GLYCOGEN
PHOSPHOLIPID
PROTEIN
DNA
RNA
-----
Biological
Function?
Self-Check
Which term includes all others in the list?
a. Monosaccharide
b. Glycogen
c.
Starch
d. Carbohydrate
e. Polysaccharide
Which of the following is NOT a protein?
a. Hemoglobin
b. Cholesterol
c.
A keratin molecule
d. An enzyme
e. Insulin
Relationship of DNA to RNA, Proteins
DNA
RNA
Proteins
Relationship of DNA to RNA, Proteins
DNA – macromolecule; 4. Nucleic Acids
• Two types:
i. DNA – deoxyribonucleic acid
ii. RNA – ribonucleic acid
· DNA – nucleus, contains genes
· RNA – copy of gene,
directions for protein synthesis
Nucleic acid - structure
Nucleic acids
• Monomer – nucleotide
a. pentose sugar
b. nitrogenous base
c. phosphate group
• Polymer –
nucleic acid
• Ends different,
5’ end –
PO42- on C#5
3’ end –
OH group on C#3
Nucleic acid - formation
Nucleic acids
H
OH
• Monomers - dehydration
• Bond formed – phosphodiester bond
Nucleic acid - components
Nitrogenous bases:
- two types – pyrimidines & purines
DNA
RNA
**(C) - adenine
**(A)
- cytosine
**(G)
- thymine* (T) - guanine
- uracil*(U)
U
U
Pentose sugars:
- deoxyribose* & ribose*
(DNA)
(RNA)
Nucleic acid - comparisons
5’ 3’
• “backbone” - PO4 and sugars
• nitrogenous bases - on sugar
• polymer = nucleic acid strand
DNA – two strands
RNA – one strand
• DNA - antiparallel
3’ 5’
Nucleic acids
• double helix
• Covalent bonds
- sugars to phosphates
- bases to sugars
• Hydrogen bonds
– base to paired base
Self-Check
Nucleic acid – Comparisons
DNA
# strands • double stranded
RNA
• single strand
Sugar name •
•
Bases used •
•
Function •
•
Backbone •
•
H-bonds? •
•
Covalent bond •
locations?
•
Lecture 1 Concepts
-
Discuss properties of water and explain using its structure
-
Define the term ‘organic’ according to biochemistry
-
Name the six functional groups and draw each one
-
Recognize and explain dehydration synthesis and hydrolysis
-
Compare and contrast glycogen, starch, and cellulose
-
Explain how fats/oils, phospholipids, & steroids are different
-
List and recognize the four levels of protein structure – explain
what determines each level
-
Draw a generalized amino acid (example p.78) & explain how
protein primary structure is determined
-
Draw a generalized nucleotide – this makes up what molecule(s)?
Discuss how the two ends of a DNA strand are different and what is
meant by ‘antiparallel’
-
List four types of macromolecules, including monomer, polymer,
examples, bond type
-
Write out a list of new terminology and provide descriptions