Lecture 4 - Proteins and Nucleic Acids - Updated PDF

Review of biochemistry, carbs and fats Explain the importance of water and salts to body homeostasis. Define acid and base, and explain the concept of pH. Explain the role of dehydration synthesis and hydrolysis in forming and breaking down organic molecules. Describe and compare the bui...

Review of biochemistry, carbs and fats Explain the importance of water and salts to body homeostasis. Define acid and base, and explain the concept of pH. Explain the role of dehydration synthesis and hydrolysis in forming and breaking down organic molecules. Describe and compare the building blocks, general structures, and biological functions of carbohydrates. Describe the building blocks, general structures, and biological functions of lipids. 1 Human Anatomy & Physiology Sept 11 Proteins and Nucleic Acids Lecture 4 [email protected] Office Hours (2RC056) Mondays 11am to 1pm or by appointment 2 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Proteins Tortora 2.8 Proteins have a wide variety of functions, including structural, enzymatic and mechanical (muscles). Also known as polypeptides, proteins are polymers of __________, held together with covalent bonds. This bond between an amine group and an acidic carboxyl group is called a _________ bond. All human proteins are made from up to 20 different types of amino acids. Each amino acid has one amine group and one carboxyl group, and one of 20 different R group side chains. 3 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Amino acids Tortora 2.8 All amino acids contain an amino group (NH2), an acidic carboxyl group (COOH), and a side chain (R). Side chain Amino Carboxyl (base) (acid) group group Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. 4 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Amino acids Tortora 2.8 Different _____________________ give each amino acid its characteristics (size, polarity and pH). Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. 5 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Peptide bonds Tortora 2.8 Peptide Dehydration bond synthesis Hydrolysis Glycylalanine Glycine Alanine Water (a dipeptide) Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. 6 Human Anatomy & Physiology Sept 11 Primary protein structure Amino For proteins, primary acids structure is the linear sequence or order of amino acids in the polypeptide chain. Peptide bond Polypeptide chain 7 Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. Human Anatomy & Physiology Sept 11 OpenStax 2.5 Secondary protein structure Tortora 2.8 Secondary structure Alpha helix refers to shapes like alpha (α) helices or Hydrogen bond beta (β) pleated Hydrogen bond sheets that form when amino acids from the primary structure interact with each other through ___________ Beta pleated sheet ___________. 8 Adapted from © 2021 by John Wiley & Sons, Inc. All rights reserved. Human Anatomy & Physiology Sept 11 OpenStax 2.5 Tertiary protein structure Tortora 2.8 Tertiary structure is the three-dimensional shape of a single polypeptide chain. This shape arises from how the chain folds, based on regions of amino acids that Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. are hydrophilic (charged or polar side chains fold to the outside, to be near water) or hydrophobic (non- polar side chains fold to the inside, to get away from water), or disulphide bridges (covalent bonds between sulphurs from two cysteine amino acids). 9 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Quaternary protein structure Tortora 2.8 Quaternary structure occurs when two or more polypeptide chains join together to make one functional protein multimer. Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. The polypeptide chain subunits are stabilized together by the same types of interactions that stabilize protein tertiary structure in each chain. Not all proteins have quaternary structures. 10 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Fibrous and globular proteins Tortora 2.8 Fibrous proteins are extended, strand-like, insoluble molecules that provide mechanical support and tensile strength to tissues. Globular proteins are compact, spherical, water- soluble, and chemically active molecules (active sites) that oversee most cellular functions. Protein _________________ is a loss of the specific three-dimensional structure of a globular protein, leading to a potential loss of function, that may occur when globular proteins experience changes in environmental factors such as temperature or pH. 11 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Enzymes Tortora 2.8 Enzymes are globular proteins that act as biological catalysts to regulate and increase speed of chemical reactions without getting used up in the process. Enzymes lower the ____________________ needed to initiate a chemical reaction, which leads to an increase in the speed or rate of a reaction without requiring high temperatures. Names usually end in –ase and are often named for the reaction they catalyze. For example, a hydrolase will hydrolyze things, an oxidase will oxidize things. 12 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Characteristics of enzymes Tortora 2.8 Many functional enzymes consist of two parts, an apoenzyme (protein portion) and cofactors (helper molecules, typically metal ions) or coenzymes (organic molecules, often derived from vitamins). Apoenzymes together with the necessary cofactors or coenzymes are called holoenzymes. Enzymes are highly specific and efficient enough to catalyze reactions millions of times faster than the reaction would occur without the enzyme. Enzymes are easily regulated by the cell to control the chemical reactions taking place. 13 Human Anatomy & Physiology Sept 11 Enzyme mechanisms Substrates Active site Sucrose H 2O 1. Enzyme and substrate of enzyme Water come together at an active Enzyme Sucrase site, forming an enzyme- substrate complex. 1 2. Enzyme catalyzes the Products Glucose reaction and transforms Fructose substrate into products. 3. When the reaction is complete, the enzyme is 3 2 unchanged and free to Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. catalyse another reaction. 14 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Nucleic acids Tortora 2.9 Nucleic acid polymers are made up of monomers called ______________, each composed of nitrogen base, a pentose sugar, and a phosphate group. The two major classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is a double-stranded helical molecule (double helix) located in the cell nucleus. RNA is a single-stranded linear molecule that is active mostly outside of the nucleus. 15 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Deoxyribonucleic acid (DNA) Tortora 2.9 DNA encodes the genetic recipe for the synthesis of all of your proteins. Through these proteins, DNA controls how your cells develop and function. DNA nucleotides contain a deoxyribose sugar, phosphate group, and one of four nitrogen bases: Adenine (A) and guanine (G) are purines. Cytosine (C) and thymine (T) are pyrimidines. Each purine perfectly pairs with one pyrimidine through hydrogen bonding. 16 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Hydrogen bonds in base pairing Tortora 2.9 Bonding of nitrogen bases from strand to opposite strand is very specific and (almost) always follows complementary base-pairing rules: A always pairs with T and G always pairs with C. 17 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Adenine and thymine Tortora 2.9 18 Human Anatomy & Physiology Sept 11 OpenStax 2.5 The double helix of DNA Tortora 2.9 2’ 3’ 5’ 1’ 4’ 4’ 1’ 5’ 3’ 2’ 2’ 3’ 5’ 1’ 4’ 4’ 1’ 5’ 3’ 2’ Phosphate group Deoxyribose group = Adenine (a purine) Hydrogen bond = Guanine (a purine) = Thymine (a pyrimidine) = Cytosine (a pyrimidine) Copyright © 2021 by John Wiley & Sons, Inc. All rights reserved. 19 Human Anatomy & Physiology Sept 11 DNA and RNA strands are synthesized 5’ to 3’ Thymine Adenine A nucleotide can be added here 2’ 3’ 1’ 4’ 5’ 5’ 4’ 1’ 3’ 2’ 2’ 3’ 1’ 4’ 5’ 5’ 4’ 1’ 3’ 2’ Cytosine Guanine A nucleotide can be added here 20 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Ribonucleic acid (RNA) Tortora 2.9 RNA is used to take nucleotide sequence information from DNA and use it to make proteins. Chemically, RNA is slightly different from DNA. It contains a ribose sugar (not deoxyribose) and the DNA nucleotide thymine is replaced with ________. Uracil is a pyrimidine and binds with adenine. There are three varieties of RNA involved in gene expression: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). 21 Human Anatomy & Physiology Sept 11 OpenStax 2.5 Adenosine triphosphate (ATP) Tortora 2.10 The chemical energy released from breaking down glucose can be captured in adenosine triphosphate (ATP). ATP is an adenine-containing RNA nucleotide with two additional ______________ groups (three phosphates in total). We can hydrolyze one or two of those additional phosphates from ATP. The energy from a freed phosphate binding to another molecule, phosphorylating it, can power a chemical reaction. Think of an ATP molecule as a rechargeable battery.22  Sept 11 OpenStax 2.5 Structure of ATP Tortora 2.10 OpenStax Anatomy and Physiology OpenStax Anatomy andCC BYPhysiology 4.0 CC BY 4.0 23 Human Anatomy & Physiology Sept 11 OpenStax 2.5 ATP powers reactions in the cell Tortora 2.10 24 Human Anatomy & Physiology Sept 11 ATP synthesis ATP is useful for two main reasons: You can get energy from many different sources (e.g. carbs, fats, proteins). If you use all of these different chemicals to make ATP, you can use the ATP energy to power any of your enzymes. You can make ATP in one place in the cell (typically mitochondria) and use it somewhere else. ATP will diffuse throughout the cell, get used to power a reaction, then ADP will diffuse back to the mitochondria to recharge. 25 After today’s lecture, you should be able to: Describe the four levels of protein structure. Describe enzyme action. Compare and contrast DNA and RNA. Explain the role of ATP in cell metabolism. 26