Biological Macromolecules (Chapter 5: Part 2)

Draw the structure of a general amino acid. Label the carboxyl group, the amino group, and the variable ('R') group.

+NH2 is the amino group +CO2H is the carboxyl group +R is the variable group

Explain the three major structural differences between RNA and DNA.

-1. Different pentose 2. DNA consists of deoxyribose. RNA consists of ribose. 3. DNA has thymine. RNA has of uracil. 4. DNA has 2 strands. RNA has 1 strand. -DNA - double helix, pentose sugar = deoxyribose, uses thymine (T) RNA - single helix, pentose sugar = ribose, replaces T (thymine) with U (uracil) +DNA: thymine, 2 strands, deoxyribose sugar +RNA: Uracil, 1 strand, ribose sugar

How can the structure of a protein be changed ("denatured")?

-If a protein's conformation is altered, the function of the protein will be altered through environmental aspects like pH, salt concentration, or temperature -If a protein's environment changes, the protein can change shape or unfold completely. These are changes in pH, temperature, or ionic concentration of the surrounding solution. Denatured proteins are usually biologically inactive, particularly in enzymes. +interactions with intense heat, nonpolar substances, and aqueous environments can cause the unraveling of proteins

Why are proteins the most complex biological molecules?

-Proteins are the most complex biological molecules because they are made of five different elements: carbon, hydrogen, oxygen, nitrogen, and sulfur. -Because they have many different functions based on their structure. The structure of a protein depends on the sequence of amino acids and there are 20 different amino acids, which can be assembled in any order, so there are a lot of ways a protein can be folded. This is why proteins have many functions which are categorized into 7 main functions: defense, transport, support, enzyme catalysis, motion, regulation, and storage +Proteins are made of several different atoms (C, H, O, N, S) +Structure is dependent on amino acid sequence, which is dependent on R groups

Define each of the following levels of protein structure and explain the bonds that contribute to them: Secondary

-Regular, repeating 3D structures found in all polypeptide chains through hydrogen bonding between atoms in the CN backbone of the polypeptide -"local folding" The peptides (amino acids) from hydrogen bonds with each other. The CO group of one and HN group of another (groups come from the peptide backbone) form weak hydrogen bonds that help to support the structure of the peptide chain. These bonds/interactions determine whether the secondary structure. There are 2 kinds: a helix (coils, cylindrical) and B pleated sheets (planar). There can be a mix of these in one protein. +interactions within the carbon/nitrogen backbone lead to beta sheet folding and alpha helixes. 2D

How does the structure of the 'R' group affect the properties of a particular amino acid?

-The R group differs with each amino acid. The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid, thus affecting its functional role in a polypeptide. -The structure of the R group determines the unique properties of amino acids. The 20 amino acids are grouped into 5 chemical classes, based on their R group: 1. Nonpolar amino acids often have R groups containing CH2 or CH3 2. Polar uncharged amino acids often have R groups with oxygen or -OH 3. Charged amino acids have R groups that contain acids or bases that ionize. 4. Aromatic amino acids have R groups that contain an organic (carbon) ring with alternating single and double bonds. Also nonpolar 5. Amino acids that have special functions have unique properties. Ex: Methionine is usually the 1st amino acid in a chain. Proline causes kinks in chains. Cysteine links chains together. +it differs (with about 20/21 different r groups) in polarity, charge, and reactions with water. Thus, the resulting proteins will have different properties

Define each of the following levels of protein structure and explain the bonds that contribute to them: Primary

-The sequence of amino acids in one polypeptide chain through peptide bonds between amino acids -It's the sequence of amino acids. Dehydration synthesis creates peptide bonds (which are covalent btw) between two amino acids. The peptide bonds act as a partial double bond and inhibit free rotation, which affects the structural character of the coils and other shapes formed by chains of amino acids. +peptide bonds between amino acids which create a polypeptide chain

Define each of the following levels of protein structure and explain the bonds that contribute to them: Tertiary

-The specific 3D shape of a particular polypeptide chain. It forms through interactions between R-group atoms with other R-groups and the local environment of the cells. -""whole molecule folding" final 3D shape of the polypeptide. Determines how regions of secondary structure are further folded in space to form the final shape of the protein. Driven by: hydrophobic exclusion, ionic bonds between R groups, and disulfide bonds (covalent bonds between two cysteine R groups) lock particular regions together. Final folding is determined by primary structure and the chemical nature of its side groups Stabilized by: hydrogen bonding between R groups of different amino acids, electrostatic attraction between R groups of different charges (also called salt bridges), hydrophobic exclusion of nonpolar R groups, and covalent bonds in the form of disulfides. No holes in interior of proteins. unique shapes of R groups allow them to fit precisely. Van der Waals forces help stability -r group interactions based on polarity, charge, and water interactions cause unorganized folding/coiling. 3D

Define each of the following levels of protein structure and explain the bonds that contribute to them: Quaternary

-The specific 3D shape of any protein that is made of more than one polypeptide chain -The arrangement of polypeptide subunits. Only found in proteins with multiple polypeptides. Interfaces where the subunits touch our often nonpolar and are important for transmitting information between the subunits about individual subunit activities. There are hydrophobic interactions that also help to determine structure. -multiple polypeptides interaction and connected together

Things to make sure you understand

How the structure of proteins and nucleic acids allow for their biological functions. How both protein structure and nucleic acid structure illustrate the concepts of emergence and combinatorial complexity. Why directionality and sequence are crucial for the structure and function of proteins and nucleic acids. How nucleic acids and proteins function in storage and expression of biological information.