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BCHM 3050 Week 1 Notes (1/11/16-1/15/16)

by: Savannah Gorisek

BCHM 3050 Week 1 Notes (1/11/16-1/15/16) 85034 - BCHM 3050 - 001

Marketplace > Clemson University > Biological Sciences > 85034 - BCHM 3050 - 001 > BCHM 3050 Week 1 Notes 1 11 16 1 15 16
Savannah Gorisek
GPA 3.88
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About this Document

These were the first two sets of notes from Chapter 3 and 5a that we covered in class.
Dr. Srikripa Chandrasekaran
Class Notes
biochemistry, Biology, Chemistry, Clemson




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This 10 page Class Notes was uploaded by Savannah Gorisek on Saturday January 16, 2016. The Class Notes belongs to 85034 - BCHM 3050 - 001 at Clemson University taught by Dr. Srikripa Chandrasekaran in Summer 2015. Since its upload, it has received 61 views. For similar materials see Biochemistry in Biological Sciences at Clemson University.

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Date Created: 01/16/16
BioChem 3050 Week 1 01/06/2016 ▯ Introduction to Water  70-80% of our bodies  Bonds o Different bonds based on electronegativity values o Ionic bonding= very different electronegativity values o Similar electronegativity values=  Metallic bonding  Covalent bonding  Very close values = nonpolar  Different = polar covalent  Ex. Water ▯ ▯ Properties of Water  Hydrogen Bonding o An electron-deficient hydrogen of one water is attracted to unshared electrons of water forming a H bond o Has electrostatic (opposite charges) and covalent (electron sharing) characteristics o 1 water molecule can make 4 H-bonds o Water is the ideal  Cohesion o Ability of water to stay together because of H bonds  Adhesion o Ability of water to interact with other surfaces o Ex. Meniscus of water o Property that allows water to move upward  Surface Tension o Elastic layer of H bonds ▯ ▯ Boiling point- amount of energy needed to break H bonds  Water has a high boiling point  Addition of solutes to water increases the boiling point o Fresh water would boil faster than salt water  Addition of solutes to water lowers the freezing point of water ▯ ▯ Osmotic Pressure- pressure required to stop the net flow of water across the membrane  Measured with an osmometer or calculated by (pi=iMRT)  Isotonic solution (a)- preferred  Hypotonic solution (b)- solute concentration is lesser than inside the cell o water moves from the environment and goes into the cell o cell will swell and may burst  Hypertonic solution (c) - solute concentration is greater than inside the cell o water moves from inside of cell to the environment ▯ ▯ Osmotic Pressure formula  Pi= osmotic pressure in atm  i= van’t Hoff factor of the solute (1 because no ionize)  M= molar concentration in mol/L o Find molecular weight o Molarity= (wt (g)/molecular wt) x (1000/volume (mL))  R= universal gas constant= 0.08206  T= absolute temperature in K (273.15 + degrees Celsius) ▯ ▯ pH, acids and Buffers  pH- human measure of how many protons are given off o more protons= lower pH o less protons= higher pH (more basic) o pH= (-log H+) *must know* o p(OH)= (-log OH-) *must know* o pH + pOH =14 o H+= 10^-pH  Ionization of Water o Kw= [H+][OH-]  Acid = proton donor o Strong acid- 100% ionization  HCl o Weak acid- does NOT completely dissociate in water  Phosphoric acid  Conjugate base loses an electron (H)  pKa- used to express the strength of a weak acid  lower pKa = stronger acid  pka= -log(Ka)  Ka= the acid dissociation constant  Base = proton acceptor o Ammonia, anything with OH o Cleaning solutions  Buffers o Regulate pH o Universal and essential for all living things o Certain diseases can cause changes in pH that can be disastrous  Acidosis and alkalosis o Maintain a relatively constant hydrogen ion concentration o Establishes an equilibrium between buffer’s components  commonly composed of a weak acid and its conjugate base ▯ ▯ Henderson-Hasselbalch Equation  Establishes the relationship between pH and pKa for selecting a buffer  Buffers are most effective when they are composed of equal parts weak acid and conjugate base  Best buffering occurs 1pH unit above and below the pKa  pH=pKa + log ([A-]/[HA]) must know o when [A-]= [HA], pH=pKa IDEAL BUFFER  weak acids can have multiple ionizable groups o each ionizable group can have its own pKa o protons are released in a stepwise fashion ▯ ▯ ▯ Amino acids- building blocks of peptides & proteins  DNA is the director of the show, and amino acids are the actors (do the work) ▯ ▯ Central Dogma- information flow from DNA to Protein Structure  “Central Dogma”- explains the storage, retrieval & expression of genetic information  Replication- duplication of DNA to make an identical copy  Transcription- reading of a gene and its transcription into RNA  Translation- translation of RNA sequence into the corresponding sequence of amino acids to form a protein ▯ ▯ Proteins vs. Traits  Proteins are the first biological step towards the outward display of phenotypic traits  They exhibit a great variety of shapes, structures, and functions o Enzymes o Structural o Hormones o Regulatory o Toxins o Storage ▯ ▯ General Structure of the “Standard” Amino Acids  20 standard amino acids  each has an amino group & carboxyl group joined via a CH- group (the alpha carbon)  the R group is the unique feature for each amino acid ▯ ▯ Classification of Amino Acids  Based primarily on “R” group properties: o Potential interactions with water o Presence/absence of dissociable groups  Four main groups of amino acids: o Neutral non-polar (no charge, hydrophobic)  Contain hydrocarbon groups with no charge o Neutral polar (no charge, hydrophilic)  Have functional groups that can easily interact with water through hydrogen bonding  Contain a hydroxyl group or an amide group o Acidic (extra carboxyl; can be “-“ charged)  R group has carboxylate group that ionizes at physiological pH o Basic (extra amino; can be “+” charged)  Bear a positive charge at physiological pH  At physiological pH, lysine and its conjugate acid (-NH3+), arginine is permanently protonated, and histidine is a weak base, because it is only partly ionized o Charge occurs in the R group ▯ ▯ ▯ ▯ Characteristics of Amino Acids  Amphoteric- can act as acid or base (depending on pH) o Because has amino and carboxyl group  Both –COOH & -NH3 + groups have dissociable protons o pK of –COOH = 1.8-2.8; pK of –NH3+ = 8.8-10.8  Amino acids are “zwitterions”- carry both + and – charges on the same molecule o Normally in equal numbers (thus have no net charge) o pH when there is no net charge (isoelectric point = pI)  The alpha- carbon is “asymmetric”- all four attached groups are different ▯ ▯ Titration of Alanine & Illustration of the Isoelectric Point  pI= pH of which 100% of amino acid exists as a charge of zero  pI= average of two pK values  Acidic & Basic Amino Acids Have Three PKa’s o Acids  +1  0  -1  -2  pI= pk1+pk2/2 o Bases  +2  +1  0  -1  pI= pk2+pk3/2 ▯ ▯ Essential vs. Non-essential Amino Acids  Essential o Must be obtained in the diet (from foods)  Isoleucine  Leucine  Lysine  Methionine  Phenylalanine  Threonine  Tryptophan  Valine o (ILL Men “Phail” To Try Valine)  Non-Essential o Can be made by the human body ▯ ▯ Peptide Bond formation  R groups do NOT participate in peptide bond formation  Carboxyl group binds to the amino group of another amino acid o Lose a molecule of water o Form peptide linkage  Less structurally complex than larger proteins, peptides still have important functions o Glutathione- tripeptide found in most all organisms and is involved in protein and DNA synthesis, toxic substance metabolism, and amino acid transport (Glu-Cys-Gly) o Vasopressin- an antidiuretic hormone that regulates water balance, appetite, and body temperature o Oxytocin- peptide that aids in uterine contraction and lactation ▯ ▯ Oxidation Reactions  Cysteine oxidation leads to a reversible disulfide bond  A disulfide bridge forms when two cysteine residues form this bond o Helps stabilize polypeptides and proteins ▯ ▯ Schiff’s base (Maillard reaction)  Schiff’s bases, aldimines, are intermediates formed by the reaction of an amino group (in proteins) with an aldehyde group (in sugars) o Browning of sugar ▯ ▯ Non-Standard Amino Acids  300 “non-standard” amino acids  Neurotransmitters: o GABA- inhibitory NT of the brain, involved in muscle relaxation, sleep, diminished emotional reaction and sedation o Serotonin- NT of the brain; modulates mood, appetite, sexual activity, aggression, body temperature, body temperature, sleep, smooth muscle constriction  Hormones: o Melatonin- secreted by the pineal gland during darkness; linked to circadian rhythms and sleep-wake cycles o Thryoxine- secreted by thyroid; increases rates of chemical reactions and metabolism in almost all cells of the body o Indole-3-Acetic Acid- (IAA)- major plant hormone, stimulates cell growth & elongation, rooting; inhibits axillary bud development  FOUND IN PROTEINS (must know) o Carboxyglutamate- found in proteins that bind Ca2+ ions, including pro-thrombin for blood clotting & Osteocalcin in bone o 4- Hydroxyproline- found in plant cell walls and collagen of connective tissues o 5- Hydroxylysine- also found in collagen of connective tissues o o-Phosphoserine- phosphorylated derivative of –OH containing AA’s; involved I signaling & gene expression ▯ ▯ ▯ ▯ ▯ ▯


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