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LECTURE - 4
Biological Macromolecules – Proteins
Answers – High Fructose Corn Syruphttps://www.sciencenews.org/article/sweet-confusion
Answers – Trans fats
Most naturally occurring fats have their hydrogen atoms arrainged in a cis configuration.
Some debate as to whether or not they are any worse than naturally occurring saturated fats
Un-saturated fats are easier to breakdown and metabolize. (the double bonds help facilitate oxidization)
Trans fat synthesis requires extremely high heat and high temperatures that can not be replicated in a home kitchen
Outline
Nucleic Acids Cont. Form follows function Amino Acids Protein Structure Protein Folding
#3 Nucleic Acid - refresh
Polymers called polynucleotides A single nucleotide consists of:
Nitrogenous base A pentose sugar One or more phosphate groups
Figure 5.26ab
Sugar-phosphate backbone5 end
5C
3C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Phosphategroup Sugar
(pentose)
Nucleoside
Nitrogenousbase
5C
3C
1C
#3 Nucleic Acids
There are two families of nitrogenous bases Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring Purines (adenine and guanine) have a six-
membered ring fused to a five-membered ring
In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose
Nucleotide = nucleoside + phosphate group
Figure 5.26c
Nitrogenous bases
Cytosine (C)
Thymine (T, in DNA)
Uracil (U, in RNA)
Adenine (A) Guanine (G)
Sugars
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components
Pyrimidines
Purines
#3 Nucleic Acids
Nucleotides are joined by covalent bonds that form between the —OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next
#3 Nucleic Acids
These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
#3 Nucleic Acids
The sequence of bases along a DNA or mRNA polymer is unique for each gene
#3 Nucleic Acids
RNA -single polypeptide chains
DNA - double helix
Two backbones run in opposite 5→ 3 direction - antiparallel
#3 Nucleic Acids
Complementary base pairing
#3 Nucleic Acids
Can also occur between two RNA molecules or between parts of the same molecule
In RNA, thymine is replaced by uracil (U) so A and U pair
#3 Nucleic Acids
One DNA molecule includes many genes ~40,000 genes in the human genome 23 chromosome pairs Each chromosome is a DNA polypeptide 60 – 150 million base pairs per chromosome.
Figure 5.27
Sugar-phosphatebackbones
Hydrogen bonds
Base pair joinedby hydrogen bonding
Base pair joinedby hydrogen
bonding
(b) Transfer RNA(a) DNA
5 3
53
Review - Macromolecules
Nucleic Acids DNA & RNA
Lipids Fatty Acids Phospholipids Steroids
Carbohydrates Monosaccharides and Disaccharides Starch/Glycogen Cellulose/chitin
Proteins
Account for more than 50% of the dry mass of most cells
Functions include: Enzymes Structural support Storage Hormones Transport Cellular communications Movement Defense against foreign substances
Proteins - Enzymes
Enzymes - a type of protein that acts as a catalyst to speed up chemical reactions Can perform their functions repeatedly. They carry out the processes of life.
Enzymatic proteins
Enzyme
Example: Digestive enzymes catalyze the hydrolysisof bonds in food molecules.
Function: Selective acceleration of chemical reactions
Figure 5.15a
Proteins - Enzymes
Figure 5.15c
Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration
Highblood sugar
Normalblood sugar
Insulinsecreted
Proteins - Hormones
Figure 5.15h
60 m
Collagen
Connectivetissue
Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues.
Proteins - Structural
Figure 5.15b
Storage proteins
Ovalbumin Amino acidsfor embryo
Function: Storage of amino acidsExamples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo.
Proteins – Storage
Figure 5.15f
Transport proteins
Transportprotein
Cell membrane
Function: Transport of substancesExamples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes.
Proteins – Transport/Cell communicaton
Figure 5.15g
Signalingmolecules
Receptorprotein
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells.
Proteins – Cell/Cell communication
Figure 5.15d
Muscle tissue
Actin Myosin
100 m
Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible for theundulations of cilia and flagella. Actin and myosinproteins are responsible for the contraction ofmuscles.
Proteins - Movement
Figure 5.15e
Defensive proteins
Virus
Antibodies
Bacterium
Function: Protection against diseaseExample: Antibodies inactivate and help destroyviruses and bacteria.
Proteins - Defense
Proteins - Polypeptides
Proteins are Polypeptides (biologically functional)
Polypeptides: unbranched polymers built from the same set of 20 amino acids(Amino acids are linked by peptide bonds)
Range in length from a few to more than a thousand monomers
Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)
Amino acids
Organic molecules with carboxyl and amino groups
Amino acids differ in their properties due to differing side chains, called R groups
Side chain (R group)
Aminogroup
Carboxylgroup
carbon
Figure 5.16a
Nonpolar side chains; hydrophobic
Side chain
Glycine(Gly or G)
Alanine(Ala or A)
Valine(Val or V)
Leucine(Leu or L)
Isoleucine(Ile or I)
Methionine(Met or M)
Phenylalanine(Phe or F)
Tryptophan(Trp or W)
Proline(Pro or P)
Figure 5.16b
Polar side chains; hydrophilic
Serine(Ser or S)
Threonine(Thr or T)
Cysteine(Cys or C)
Tyrosine(Tyr or Y)
Asparagine(Asn or N)
Glutamine(Gln or Q)
Figure 5.16c
Electrically charged side chains; hydrophilic
Acidic (negatively charged)
Basic (positively charged)
Aspartic acid(Asp or D)
Glutamic acid(Glu or E)
Lysine(Lys or K)
Arginine(Arg or R)
Histidine(His or H)
Condensation reaction results in peptide bond Peptide bond
New peptidebond forming
Sidechains
Back-bone
Amino end(N-terminus)
Peptidebond
Carboxyl end(C-terminus)
Proteins = AA polymers
Proteins – Form and Function
A functional protein – A polypeptide that is properly twisted, folded, and coiled into its unique shape
AA sequence determines the three-dimensional structure
Structure determines the function
(a) A ribbon model (b) A space-filling model
Groove
Groove
Protein – Form and Function
Antibody protein Protein from flu virus
Protein – Form and Function
Proteins - Form
Three levels of protein structure Primary Structure – The unique sequence of
amino acids. Secondary structure - Coils and folds in the
polypeptide chain. Tertiary structure - Determined by
interactions among various side chains (R groups).
Some have a fourth level Quaternary structure - Results when a
protein consists of multiple polypeptide chains.
Proteins – Form – Primary Structure
The sequence of amino acids in a protein. Kinda like the order of letters in a long word Read left to right
Starts with amino group – N-terminus Ends with carboxy group – C-
terminus
Figure 5.20aPrimary structure
Aminoacids
Amino end
Carboxyl end
Primary structure of transthyretin
Proteins – Form – Secondary Structure
Secondary structure – Regular, repeated folds and twists
Stabilized by hydrogen bonds Determined by aa sequence (primary
structure) Two main Secondary Structures:
helix – Coils pleated sheet- folds
Proteins – Secondary Structurea Helix
Proteins – Secondary Structurea Helix
Function follows form A helices
DNA binding (transcription factors, hox proteins, chromatin proteins…)
Membrane spanning proteins
Proteins – Secondary Structureb Pleated Sheets
Proteins – Secondary Structureb Pleated Sheets
Usually part of Protein/Protein interactions Silk is an example of b pleated sheets
Made up of multiple polypeptides packed together Amyloid Proteins
Implicated in Alzheimer's, Parkinson’s & Huntington’s disease
Mad Cow’s disease (Transmissible spongiform encephalopathy)
Rheumatoid arthritis Chronic traumatic encephalopathy
Accumulation of Tau Protein & Beta Amyloid plaques
Proteins – Tertiary Structure
The 3 dimensional shape of the whole protein