LECTURE - 4 Biological Macromolecules – Proteins

Answers – High Fructose Corn Syrup

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 backbone 5 end 5C5C 3C3C 5C5C 3C3C 3 end (a) Polynucleotide, or nucleic acid (b) Nucleotide Phosphate group Sugar (pentose) Nucleoside Nitrogenous base 5C5C 3C3C 1C1C

#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-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding (b) Transfer RNA (a) DNA

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 hydrolysis of 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 the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration High blood sugar Normal blood sugar Insulin secreted Proteins - Hormones

Figure 5.15h 60  m Collagen Connective tissue Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Proteins - Structural

Figure 5.15b Storage proteins Ovalbumin Amino acids for embryo Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Proteins – Storage

Figure 5.15f Transport proteins Transport protein Cell membrane Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Proteins – Transport/Cell communicaton

Figure 5.15g Signaling molecules Receptor protein Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Proteins – Cell/Cell communication

Figure 5.15d Muscle tissue ActinMyosin 100  m Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Proteins - Movement

Figure 5.15e Defensive proteins Virus Antibodies Bacterium Function: Protection against disease Example: Antibodies inactivate and help destroy viruses 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) Amino group Carboxyl group  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 ( I le 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 peptide bond forming Side chains Back- bone Amino end (N-terminus) Peptide bond 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 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 5.20a Primary structure Amino acids 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 Structure  Helix

 Function follows form  A helices  DNA binding (transcription factors, hox proteins, chromatin proteins…)  Membrane spanning proteins

Proteins – Secondary Structure  Pleated Sheets

 Usually part of Protein/Protein interactions  Silk is an example of  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