BIOCHEM C785 BIO notes latest 2022

BIOCHEM C785 BIO notes latest 2022 FORM = FUNCTION ATOMS An element is a substance that cannot be broken down 92 elements Water compound of H20 = elements hydrogen (H) and oxygen (O) A compound has characteristics different from those of its elements essential elements that an organism needs to live but cannot make on own. An atom is the smallest unit of matter that still retains the properties of an element. SUBATOMIC PARTICLE- smaller parts of atom = Protons and neutrons in nucleus while electrons float in outer cloud/ring. Atoms are mostly empty space with tiny nucleus, nucleus’s of two never come close to react, only the electrons react in chemical reaction. Each proton has one unit of positive charge each electron has one unit of negative charge. A neutron is neutral. MASS= DALTON. Neutrons and protons have masses close to 1 dalton. Electron mass is ignored cuz tiny. Energy is defined as the capacity to cause change. Potential energy is the energy that matter possesses because of its location or structure(ball on hill). the more distant an electron is from the nucleus, the greater its potential energy. Inner shell holds 2, next 2 shells hold 8 electrons the chemical behavior of an atom depends mostly on the number of electrons in its outermostshell. We call those outer electrons valence electrons and the outermost electron shell the valence shell. Atoms with the same number of electrons in their valence shells exhibit similar chemical behavior. An atom with a completed valence shell is unreactive; that is, it will not interact readily with other atoms. It is called inert. This is only helium, neon, and argon. AMINO ACIDS / PROTEINS Ionic bond- between positive and negation ions when attracted to each other. Covalent bond - bonds occur when atoms share electrons Hydrogen bond- portion of a polar molecule that is partially positive interacts with a portion of a polar molecule that is partially negative. Broken by ph and salt. Van der Waals cond- interactions occur due to random, weak, transient movements of electrons ** amino acids form polypeptides with fold to make functional proteins. **bond between amino acids is called a peptide bond, so a polymer of amino acids is called a polypeptide. **Protein = one or more polypeptide each folded and coiled into a specific three- dimensional structure AMINO ACIDS – . 20 different amino acids in your body used to make proteins. ONLY ACTIVE PROTEIN WHEN IT FOLDS. Can be roughly spherical (globular proteins) or long fibers (fibrous proteins) 1. Hydrophilic (polar)= oxygen or nitrogen, or both. Can be positive (basic) or negative(acidic) End in o-h, n-h, or sh. Have hydrogen bond, can be broken by ph or salt. SH endings are disulfide bonds broken by reducing agent. 2. Hydrophobic (nonpolar)- end in CH, disrupted by heat. Weakest interaction. AMINO ACID STRUCTURE 1. alpha Carbon 2. Amino group – nitrogen with a hydrogen 3. Carboxyl group- carbon with 2x oxygen 4. Variable group- side chain (not apart of backbone Amino acid structures- 1. Primary • Linear chain of amino acids or sequence. Peptide bonds made through dehydration synthesis. • Starts with amino end, ends with carboxyl end. 2. Secondary • Regions stabilized by hydrogen bonds between atoms of polypeptide backbone. • Segments of polypeptide chain is coiled or folded into pattern that gives protein its shape. • Basically a double of primary structure. • Hydrogen bonds between polypeptide backbone are what from secondary structure. • Hydrogen is partially positive, oxygen is partially negative so bonds form. Repeated makes them stronger. • Contains alpha helix, a coil held together by hydrogen bond between every 4th amino acid. • Contains beta pleated sheet, the “core” which holds together the beta strands (segments of polypeptide chains laying side by side held together by hydrogen bonds) 3. Tertiary • 3D shape stabilized by interactions between side chains. • Shape results from interactions between r groups of various amino acids • Has **hydrophobic interactions(heat denatures) (nonpolar)- hydrophobic side chains cluster to center of protein to avoid water. Leads to van der waals • Has covalent / disulfide bonds – (s-s) two cysteine monomers with sulfhydryl groups come close together during folding. (not broken down by heat denaturing) • Has hydrogen bonds, disulfide bonds, ionic bonds, hydrophobic interactions, and van der waals interactions 4. Quaternary – more than one polypeptide chain that globs. Like hemoglobin. If the pH, salt concentration, temperature, or other aspects of its environment are altered, the weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shape, a change called denaturation IN HEAT- hydrogen bonds and hydrophobic interactions break. This denatures and unravels a protein. However disulfide bonds do not break in heat. Hydrogen bonds – broken by salt or pH change Disulfide bonds – broken by reducing agent Hydrophibic interaction – broken by heat (ex; fever)