Cell Bio Chapter 3 Protein Structure and Function Protein polymers of amino acids function Molecular Structure of Protein Composed of amino acids and their specific order gives the protein its specific structure and Amino acids linked by peptide bonds which form by the dehydration reaction loss of water Primary linear sequence of amino acids linked by peptide bonds Secondary folding of protein into alpha helixes or beta sheets Tertiary secondary structures loops and turns in one polypeptide chain Quaternary protein is made of more than one polypeptide Function of Protein Regulation ways we can turn cells on and off Can control whether cells should work or not Structure Ex Make up cytoskeleton Movement Actin and Myosin move muscles Or looking at the movement of organelles proteins in the cell Catalysis enzymes proteins that make or break covalent bonds Transport how ions are pumped and other molecules are moved in and out of cells Signaling how cell responds to its external environment and how it decides what it s supposed to do 3 1 Structure of Proteins Primary structure sequence of amino acids Should know the characteristics of each amino acid and what makes each one different from the others Should know the basic function of each amino acid Hydrophobic Amino Acids Alanine Valine Isoleucine Leucine Methionine Phenylalanine Tyrosine Tryptophan Polar Amino Acids Serine Threonine Asparagine Glutamine Basic Amino Acids Lysine Arginine Histidine have charge Acidic Amino Acids Aspartate Glutamate have charge Serine Threonine and Tyrosine have a hydroxyl group OH in their R group o Means that these AA can be phosphorylated Glycine is the smallest amino acid H as R group so it can fit in very tight spaces other AA cannot don t need to be able to write out the amino acids but should be familiar with them Secondary structure sequence of amino acids starts to form a 3 dimensional shape Is stable spatial arrangement of polypeptide chain R groups do NOT play a role at this level Structure held together by ionic bonds in the backbone Most often in these two forms 1 Alpha Helix spiral structure where carbonyl oxygen s hydrogen binds to amine hydrogen 4 AA s away o Holds the backbone straight and the side chains stick out 2 Beta Sheet hydrogen bonds between backbone atoms in separate but adjacent beta strands Cell Bio Chapter 3 Protein Structure and Function Tertiary structure overall 3D shape confirmation of the protein R groups come into play help stabilize the protein through interactions bonds between R groups o These can be polar ionic hydrophobic bonds 3D structure tends to be flexible and has movement because these bonds aren t permanent Have disulfide bridges that can lock things together but not as major in role Domains Motifs specialized structure forms 1 Structural Motifs particular combinations of secondary and tertiary structure o Use same basic amino acids together to perform a function no matter what protein it is a part of A Leucine Zippers or Coiled Coils used for transcription factor dimerization o Transcription factor protein that binds to DNA and helps transcribe DNA into RNA o Dimerization 2 proteins that interact together like 2 TF s coming together to help each other transcribe DNA o Leucine zipper made of 2 alpha helicases 1 from protein A 1 from protein B and made of hydrophobic amino acids so they bind together very tightly o Have an incredibly stable interaction 2 proteins can essentially bind together and stay together to work in thousands of different proteins B EF Hand Alpha helix loop alpha helix o In the loop there is a polar or negatively charged AA that s function is to bind to calcium which stabilizes the structure of the EF hand C Zinc Finger Alpha helix adjacent to a loop o Found mostly in transcription factors o Allows transcription factor to fit into the major groove of the DNA o Coordination of zinc that helps stabilize the alpha helix so that it stays in the groove for as long as it needs to 2 Domains distinct regions of tertiary structures tend to be larger than a motif and are a building block of protein o o Has a particular look has a certain size and performs a certain function these things do not change no matter what the domain is used to build Ex Made comparison of domain to a red lego block no matter what you build with the red block it is always still a red block A Functional Domain something characteristic of a particular function B Topological Domain transmembrane extra cellular domains cytosolic domain o In a particular location in the cell Exs Dbl homology domain binds to GTP SH3 domain binds to proline SH2 domain binds to phosphorylated tyrosine 3 3 Protein binding and enzyme catalysis The functions of many proteins are based on their ability to bind to a ligand Specificity protein prefers to bind to one substance vs another Affinity how tight that binding is or the strength of that bond Based on inverse of the binding reaction typically the smaller the number the higher the affinity Active Site amino acids involved in binding and catalyzing the reaction often controls the specificity Cell Bio Chapter 3 Protein Structure and Function Maximum Velocity Vmax indicator of how fast how much product an enzyme is made in that reaction per unit of time Proportional to the amount of enzyme Km Michaelis constant measure of affinity how tight binding is between substrate and enzyme Want to look at the substrates concentration at half of the maximum velocity If affinity is low Km high then it means the substrate doesn t bind well to the enzyme and it takes longer for the product to form and produces a lower curve on the graph As Km decreases the affinity increases Km Vmax Refer to slide 9 to look at graphs with the Vmax Km values To find Vmax find where Km is labeled and draw a dotted line UP to where it meets the curve Then draw a horizontal dotted line from that point to the left until it reaches the Rate of Reaction y axis The value where this horizontal line is draw is equal to the Vmax 3 4 Regulating Protein Function 1 Can increase decrease level or concentration of protein by altering rate of synthesis degradation 2 Can change the location of concentration of the substrate or cofactor 3 Can regulate the intrinsic activity the affinity of substrate binding Altering Protein Degradation Life span of proteins most proteins are designed to last a certain amount of time and then they are degraded and new proteins are made Some can only last for