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