Housekeeping Matters

Submission of groupwork

20 November 2012
Bi 9 C, Dr Harvy Joy Liwanag

Grading system emailed to beadle Quiz on Nov 27 (Tue next week) about the lecture today and on Thursday Continue to read Ch 3-4 for Nov 22 3(Thurs)

Lipids
Fats and fatlike substances Group of compounds related by certain physical properties
Insoluble in water Soluble in nonpolar solvents (e.g. ether, chloroform, acetone)

Amphipathic has hydrophilic and hydrophobic parts

Functions
Major source of energy Provide hyrdophobic barrier Serve as co-enzymes, regulators coHormones Mediators of inflammation

Generally compartmentalized to protect themselves from the watery environment of cells *Micelles *Phospholipid bilayer

Classification
Neutral fats Phospholipids Steroids

Neutral / Fatty Acids

Are major fuels for animals Directly from dietary fat or indirectly from conversion of dietary carbohydrates Esters: combination of alcohol (glycerol) and an acid Commonly 14-24 carbons long 14-

Classified according to degree of saturation

Saturated: contain no double bond Monounsaturated: contain 1 double bond Polyunsaturated: contain > 2 double bonds

Unsaturated Fatty Acids

Unsaturated Fatty Acids

Geometric isomerism:
Cis: on the same side of the double bond Cis: Trans: on opposite sides of the double bond

TransTrans- and saturated fatty acids are associated with increased risk for cardiovascular disease. Mono- cis) Mono- (cis) and polyunsaturated fatty acids are thought to be protective

Fluidity decreases with (i.e. more likely to solidify)

Increasing chain length = more C atoms Increasing saturation = less double bonds

Fats
Fatty acid(s) attached to glycerol Triglycerides are most common
Fig. 3-12, p.40 Fig. 3-12a, p.40

y2

Phospholipids
Main components of cell membranes

Steroids
Complex alcohols Structurally unlike fats but have fatlike properties Rigid backbone of four fusedfused-together carbon rings e.g. cholesterol, vitamin D, adrenocortical hormones, sex hormones Cholesterol - most common type in animals
Fig. 3-14, p.41

Proteins
Most abundant and functionally diverse molecules in living systems Linear polymers of amino acids
Linked by peptide bonds

Why are proteins important?

Enzymes that regulate metabolism Neurotransmitters Contractile proteins of muscles Connective tissue framework Transport of molecules in blood Components of the immune system Development of drugs Normal fluid hemostasis

More than 300 amino acids have been described, but only 20 are commonly found in mammalian proteins These are the only amino acids coded by the DNA

Structures of Amino Acids

Except for Proline, each amino acid has: Proline,
1 carboxyl group (-COOH) (1 amino group (-NH2) (1 unique side chain (R-group) (R-

All three are bonded to a central -carbon The R-group dictates the function of the Ramino acid in a protein

Slide 19 y2 add figure3.13a

David, 10/19/2005

Amino Acid Structure

Properties of Amino Acids

Determined by the R group Amino acids may be:

carboxyl group amino group

NonNon-polar Uncharged, polar

R group

Positively charged, polar Negatively charged, polar

Protein Structure
4 Levels:
Primary Structure Secondary Structure Tertiary Structure Quarternary Structure

Primary Structure
Linear sequence of a proteins amino acids Peptide bonds
Attach amino group on one amino acid to the carboxyl group of another amino acid

Primary Structure
Unique for each protein Two linked amino acids = dipeptide Three or more = polypeptide Backbone of polypeptide has N atoms:
-N-C-C-N-C-C-N-C-C-N-

one peptide group

Properties of Peptide Bonds

Partial double bond character makes the bond rigid and planar Trans configuration Polar bond that can form hydrogen bonds in secondary structures Very stable, can only be disrupted by hydrolysis at:
Strong acid High temperature

Primary Structure & Protein Shape

Primary structure influences shape in two main ways:
Allows hydrogen bonds to form between different amino acids along length of chain Puts R groups in positions that allow them to interact

Secondary Structures
Regular arrangements of amino acids that are located near each other in the linear sequence into geometrically ordered units Formed through hydrogen bonding between peptide bonds

2 main kinds of secondary structures

-helix
Most common R-handed spiral with polypeptide backbone core

-pleated sheets
Surfaces appear flat and pleated 2 or more peptide chains parallel (or antiantiparallel) to each other

Tertiary Structures
Overall 3-dimensional shape of the protein 3Globular vs Fibrous proteins

Final folding of domains and their final arrangement in the protein

Protein Shapes
Fibrous proteins Polypeptide chains arranged as strands or sheets E.g. collagen Globular proteins Polypeptide chains folded into compact, rounded shapes E.g. hemoglobin

Tertiary Structures
Stabilized by the following: Covalent bonds disulfide bonds NonNon-covalent bonds
Hydrophobic interactions Hydrogen bonds Ionic bonds

Tertiary Structure
heme group

Quaternary Structure
Some proteins are made up of more than one polypeptide chain

Folding as a result of interactions between R groups

coiled and twisted polypeptide chain of one globin molecule

Hemoglobin

heme

alpha globin

alpha globin

Polypeptides with Attached Organic Compounds

Lipoproteins
Proteins combined with cholesterol, triglycerides, phospholipids

Glycoproteins
beta globin beta globin
Fig. 3-17, p.44

Proteins combined with oligosaccharides

a Normal amino acid sequence at the start of a beta change for hemoglobin

b One amino acid substitution results in the abnormal beta chain in HbS molecules. During protein synthesis, valine was added instead of glutamate at the sixth position of the growing polypeptide chain.

VALINE VALINE HISTIDINE GLUTAMATE LEUCINE THREONINE PROLINE GLUTAMATE

HISTIDINE

LEUCINE THREONINE PROLINE

VALINE GLUTAMATE

Fig. 3-18a, p.45

Fig. 3-18b, p.45

Clumping of cells in bloodstream Circulatory problems, damage to brain, lungs, heart, skeletal muscles, gut, and kidneys Heart failure, paralysis, pneumonia, rheumatism, gut pain, kidney failure

c Glutamate has an overall negative charge; valine has no net charge. The difference gives rise to rod-shaped clumps that distort normally rounded red blood cells into sickle shapes. (A sickle is a farm tool that has a crescentshaped blade.)

sickle cell

Spleen concentrates sickle cells Spleen enlargement Immune system compromised Rapid destruction of sickle cells

normal cell

Anemia, causing weakness,fatigue, impaired development,heart chamber dilation Impaired brain function, heart failure
Fig. 3-18d, p.45

Fig. 3-18c, p.45

NUCLEIC ACIDS

Nucleotide Structure
Sugar
Ribose or deoxyribose

Nucleotide Functions
Energy carriers Coenzymes Chemical messengers Building blocks for nucleic acids

At least one phosphate group Base

NitrogenNitrogen-containing Single or double ring structure

ATP - A Nucleotide
base three phosphate groups

Nucleotides
The monomer units of building blocks of nucleic acids Functions:
Form part of many coenzymes Serve as donors of phosphoryl groups Regulatory nucleotides (second messengers, allosteric regulators) Synthetic analogues of drugs

sugar

Nucleic Acids
Cytosine Adenine

Purines and Pyrimidines

NitrogenNitrogen-containing heterocycles, cyclic heterocycles, compounds whose rings contain both carbon and other elements

Composed of nucleotides Single- doubleSingle- or double-stranded SugarSugar-phosphate backbone

Their planar characteristics facilitates stacking

Purines Adenine and Guanine Pyrimidines Cytosine, Uracil, and Uracil, Thymine

Bonding Between Bases in Nucleic Acids

THYMINE (T) base with a single-ring structure

DNA
DoubleDouble-stranded Consists of four types of nucleotides A bound to T C bound to G

CYTOSINE (C) base with a single-ring structure

Fig. 3-20, p.46

RNA
Usually single strands Four types of nucleotides Unlike DNA, contains the base uracil in place of thymine Three types are key players in protein synthesis

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