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OVERVIEW
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AMINO ACIDS CONTAIN AN AMINO GROUP, A CARBOXYL GROUP, - CARBON AND A UNIQUE R GROUP
Summary of 20 proteinaceous AA
Essential (unexpendable) organism is not able to synthesize these AA but accept from food. Nonessential (expendable) organism produced from essential AA by transamination.
Essential AA
Valin Leucin Isoleucine Threonine Lysin Methionin Phenylalanine Tryptophan Arginine
Histidine
Besides basic 20 proteinaceous AA more AA exist found only in some organisms. Essential AA are different for variety of animal species and plants are able to synthesize all 20 AA.
20 AMINO ACIDS
Glycine (G)
Alanine (A) Valine (V) Isoleucine (I) Leucine (L)
Proline (P)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
Asparagine (N)
Glutamine (Q)
Serine (S)
Threonine (T)
Tyrosine (Y)
Cysteine (C)
Lysine (K)
Arginine (R)
Histidine (H)
Amino acids- with non- polar side or hydrophobic- chain that not bind or give up off the protons or participate in hydrogen or ionic bonds. The side chains of these be thought of as oily or lipid like .Amino acids with uncharged polar side chains or hydrophilicThese amino acids have zero net charge at neutral pH, although the side chains of cysteine and tyrosine can lose a proton at alkaline Ph.
1. Disulfide bond: The side chain of cysteine contains a sulfhydryl group (-SH), which is an important component of the active site of many enzymes. In proteins the SH groups of two cysteines can become oxidized to form a dimer, cysteine, which contains a covalent cross-link called a disulfide bond formation.
2. Side chains as sites of attachment for other compounds: Serine, threonine, and, rarely, tyrosine contain a polar hydroxyl group that can participate or serve as a site of attachment, for example, for a phosphate group. (Note: The side chain of serine is an important component of the active site of many enzymes). In addition, the amide group of asparagine, as well as the hydroxyl group of serine of threonine, can serve as a site of attachment of oligosaccharide chains in glycoproteins.
The amino acid aspartic and glutamic acid are the proton donors. At neutral pH the side chain of these amino acids are fully ionized, containing a negative charged carboxylate group (-COO). They are therefore called aspartate or glutamate to emphasize that these amino acids are negatively charged at physiologic pH.
The side chains of the basic amino acids accept protons. At physiologic pH the side chains of lysine and arginine are fully ionized and positively charged. In contrast, histidine is weakly basic and the free amino acid is largely uncharged at physiologic pH. However, when histidine is incorporated into a protein, its side chain can be either positively charged or neutral, depending on the ionic environment provided by the polypeptide chains of the protein. (Note: this is an important property of histidine that contributes to the role it plays in the functioning of proteins such as myoglobin.
2. Most commonly occurring amino acids have priority: If more than one amino acid begins with a particular letter, the most common of these amino acids receives this letter as its symbols. For example, glycine is more common than glutamate, so G=glycine consist . Alanine = Ala = A Glycine = Gly = G Leucene = Leu = L Proline = P = P Threonine = Thr = T
3. Similar sounding names: Some one- letter symbols sound like the amino acid they represent for example,F= phenylalanine, or W= ( Twyptophan as Elmer Fudd would say.) Arginine = Arg = R ( aRginine) Asparagine = Asn = N ( contains N) Aspartate = Asp =D (asparDic) Glutamate = Glu =E (glutEmate) Glutamine = Gln =(Q- tamine)
Peptide Bonds join amino acids Its a condensation reaction (meaning that H20 is released when the bond is formed).
POLYPEPTIDES are formed from more than two amino acids bonded together
PRIMARY STRUCTURE IS
THE AMINO ACID SEQUENCE
THE AMINO ACID SEQUENCE IS CODED FOR BY DNA AND IS UNIQUE FOR
EACH KIND OF PROTEIN
C
TCT TCC TCA TCG CCT CCC CCA CCG ACT ACC ACA ACG GCT GCC GCA GCG
Second letter A
Ser TAT TAC TAA TAG CAT CAC CAA CAG AAT AAC AAA AAG GAT GAC GAA GAG Tyr Stop His Gln Asn Lys Asp Glu
G
TGT TGC TGA TGG CGT CGC CGA CGG AGT AGC AGA AGG GGT GGC GGA GGG Cys Stop Trp Arg T C A G T C A G T C A G T C A G
Third letter
Leu
Pro
First letter
Ser Arg
Thr
Ala
Gly
Secondary structure- polypeptide chains folded into regular repeating structural patterns.
- Formed by a H-bond between every 4th peptide bond C=O to N-H - Usually in proteins that span a membrane - The helix can either coil to the right or the left - Can also coil around each other coiled-coil shape a framework for structural proteins such as nails and skin
Sheets
Core of many proteins is the sheet Form rigid structures with the H-bond Can be of 2 types
Anti-parallel run in an opposite direction of its neighbor (A) Parallel run in the same direction with longer looping sections between them (B)
TERTIARY STRUCTURE DEPENDS ON THE INTERACTIONS AMONG THE R GROUP SIDE CHAINS
TYPES OF INTERACTIONS
Hydrophobic interactions: amino acids with nonpolar side chains cluster in the core of the protein, out of contact with water
= charged
= hydrophobic
TYPES OF INTERACTIONS
TYPES OF INTERACTIONS
TYPES OF INTERACTIONS
Disulfide bridge (strong covalent bonds) between sulfur atoms in the amino acid cysteine
Link to video
Link to video
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PROTEINS.
If there is a job to be done in the molecular world of our cells, usually that job is done by a protein.
A protein hormone which helps to regulate your blood sugar levels
CATALASE
An enzyme which removes Hydrogen peroxide from your body so it does not become toxic
Examples of proteins include hormones acting as messengers; enzymes speeding up reactions; cell receptors acting as antennae; antibodies fighting foreign invaders; membrane channels allowing specific molecules to enter or leave a cell; they make up the muscles for moving; let you grow hair, ligaments and fingernails; and let you see (the lens of your eye is pure crystalised protein).
Source: http://courses.washington.edu/conj/protein/insulin2.gif http://www.biochem.ucl.ac.uk/bsm/pdbsum/1gwf/main.html
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1. -Keratins
Fibrous Proteins
Found in: mammals, provide strength Hair, wool, nails, claws, quills, horns, hooves, skin
Fibrous Proteins
-Keratins
Permanent waving of hair 1. Reduce disulfide bonds 2. Moist heat breaks H-bonds and causes uncoiling of helix 3. Remove reducing agent, add oxidizing agent, new S-S bonds
Fibrous Proteins
2. Collagen
helices, left-handed helix with 3 amino acids per turn 35% Gly, 11% Ala, 21% Pro/4-Hyp (Gly-X-Y) repeat with X as Pro and Y as 4-Hyp Coiled-coil, three separate polypeptides called chains are supertwisted Provide strength (stronger than ??) Connective tissue (tendons, cartilage, organic matrix of bone, cornea)
Fibrous Proteins
Collagen
Rigid and brittle bones caused by: Crosslinks in collagen fibrils over time Gly-X-Y repeat important - single change results in disease Osteogenesis imperfecta - abnormal bone formation in babies Ehlers-Danlos syndrome - loose joints Both diseases involve: mutation of Gly to a different amino acid
Fibrous Proteins
Silk
Fibrous protein of silk = Fibroin Secondary structure present: sheets Forces involved: H-bonds between different sheets Made by: insects and spiders Silk does not stretch because it is already highly extended
Disulfide bond
Actin and myosin contract to create the cleavage furrow and to move muscles Contractile proteins move cilia and flagella
GLOBULAR PROTEINS HAVE THEIR CHAINS FOLDED INTO COMPACT, ROUNDED SHAPES
Ovalbumin is the protein in egg whites Casein is the protein in milk, source of amino acids for baby mammals
Hemoglobin, the iron containing protein in blood, transport oxygen from lungs to other parts of the body (C3032H4816O872N780S9Fe4)
Membrane transport proteins such as channels for potassium and water
Hormone proteins function as cellular messenger molecules that help maintain homeostasis
Insulin: sends message allow sugar into cells (when blood glucose levels are high, cells will transport glucose into the cells for use or storage) Glucagon: sends message we need more sugar in the blood (when blood glucose is too low, cells will release glucose)
Growth factor receptors initiate the signal transduction pathway when a growth hormone attaches
Cholesterol receptors on the cell membrane allow LDL to be endocytosed into the cell
Amylase and other digestive enzymes hydrolyze polymers in food Catalase converts hydrogen peroxide H2O2 into water and oxygen gas during cellular respiration
PROTEINS
Chains
of amino acids
AA AA
Many
AA AA
Enzymes
AA
ENZYMES AS CATALYSTS
Catalyst
- Speeds up chemical reactions in living organisms by decreasing the energy needed to start the Energy reaction (activation energy)
Without a catalyst
With a catalyst
Time
DEFINITIONS
Substrate-
monomers that bind to the active site of an enzyme Active site- area on enzyme where substrate binds Product- what the enzyme produces
Chemical reaction!!!
Enzyme