Introduction: Biochemistry Flashcards
What is entropy?
Going from order to disorder.
Entropy of Energy
Focus - Dispersed
Entropy of Information
High - Low
Entropy of Organisation
Complex - Simple
General Entropy
Life - Death
Four main classes of biological molecule
Proteins Lipids Carbohydrates DNA (water)
Percentage of Biological Molecule Proteins
15-20%
Percentage of Biological Molecule Lipids
10 -15%
Percentage of Biological Molecule Carbohydrates
2%
Percentage of Biological Molecule DNA / RNA
1%
Percentage of Biological Molecule Water
50-65%
Metabolism What is Catabolism?
Breakdown
Metabolism What is Anabolism?
Synthesis (combination of separate elements to form a coherent whole - creating)
Metabolism must be tightly regulated by
Health Efficiency
Metabolism is context dependent.
i.e. greater caloric intake for someone in the arctic to someone in the UK.
Proteins General
Large biomolecules Mr > 10,000 Da Most abundant organic compounds in healthy humans Formed of amino acids
Proteins General Roles
Cell structure Transport Catalysis Metabolic Regulation
Amino Acids General
Amino acids are monomers, “building blocks” that bond to form peptide / protein polymers. 20 principal amino acids Same fundamental structure differentiated by side chains: asymmetric, “left handed” Essential / Non-essential
alpha-Amino acid structure
Chain of carboyx group. Alpha carbon with hydrogen and amino group. Side chain (residue; “R”) connected to alpha-carbon.
Amino acids
Nonpolar
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Methionine (Met)
Tryptophan (Trp)
Phenylalanine (Phe)
Proline (Pro)
Amino acids
Polar
Serine (Ser)
Theronine (Thr)
Cysteine (Cys)
Tyrosine (Tyr)
Asparagine (Asn)
Glutamine (Gln)
Amino Acids
Electrically Charged
Acidic
Aspartic Acid (Glu)
Glutamic Acid (Asp)
Amino Acids
Electrically Charged
Basic
Lysine (Lys)
Arginine (Arg)
Histidine (His)
Features of Amino Acids
Cysteine
Able to form Disulfide (S-S)
Features of Amino Acids
Proline
Imide rather than Amide
Features of Amino Acids
Buffering capabilities
Weak acid groups (COOH)
Base groups (NH2)
Amino Acids
Peptide
Amino acids linked by peptide bonds
Amino Acids
Polypeptide
>50 amino acids linked by peptide bonds
Amino Acids
Proteins
Formed by one or more polypeptide chains
Residue meaning
Table
Generic other atoms
Non-polar meaning
Electromag the same
No significant +/- charge
Hydrophobic
Polar meaning
Active groups
Strong +/- charge
Repel lipids
Acidic meaning
Releasing hydrogens
Basic
Accepting hydrogens
Primary structure
Amino Acids
Protein
Peptide bonds: link the alpha-amino group to the carbonyl group of thenext.
Trans-arrangement: side chains of bonded as in opposite directions (except prolin, wich can be cis- or trans-)
By convention, start at N-terminus and end at C-terminus
No rotation around peptide bonds
Enzymes
General function
Change shape to cause chemical reactions.
Secondary Structure
Local organisation polypeptide chains causedby folding.
Primary structure determines how proteins fold.
Folding assisted by chaperone proteins.
Maintained by hydrogen bonds formed between amide and carboyl elements of peptide bonds.
Alpha helix
Structure
3.6 a.a. residues per helix turn, 0.54nm pitch.
Densely-packed, side chains on outside
Beta-pleated sheet
Parallel or anti-parallel rows of AAs linked by H-bonds.
Pleated structure
Tertiary Structure
Geometric arrangement of a singly polypetide chain
Contains multiple secondary structures
Maintained by hydrophobic interactions, ionic bonds, disulfide bonds and hydrogen bonds,
Quaternary Structure
What are oligomers?
Proteins made up of multiple polypetide subunits
Quaternary Structure
homomers
All the same subunit
Quaternary Structure
Heteromers
Different subunits
Quaternary Structure
Subunits
Subunits helf together by non-covalent forces.
Can undergo rapid conformational changes.
These conformational changes enabe to facilitate protein functions.
Non-amino acid Protein Elements
How are they further modified?
Attachment ofcarbohydrate, lipid, RNA groups.
Atachment of small inorganic and organic molecules: metal ions, vitamins, methyl groups, phosphorylation, etc.
Non-amino acid Protein Elements
How are they further modified?
Cofactors
Usually metal ions or small organic molecules necessaru for protein activity
Summary of Protein Structure
Amino acids
Peptide Bonds
Summary of Protein Structure
Secondary structure
a-helix and B-pleated sheet
Summary of Protein Structure
Tertiary Structure
Folded arrangement of polypeptide chain
Summary of Protein Structure
Quaternary Structure
Subunit arrangement in oligomers
Types of Protein
Globular Proteins
Fibrous Proteins
Membrane Proteins
Types of Protein
Globular proteins
Fold into roughly spherical shape.
Usually water soluble.
Enzymes, messengers, transporters.
Usually insoluble.
Types of Protein
Membrane Proteins
Embedded in the cell membrane, transmembrane or integral monotopic.
Globular Proteins
Blood Proteins
Albumins
>50% of blood protein.
Transports steriods, hormones, fatty acids, stabilises blood value.
Types of Protein
Blood proteins
Globulins
Various functions (e.g. inhibitors, immune system, etc.)
Globular proteins
Haemoglobin
General
4 subunits (“tetramer”) in roughtly tetrahedral arrangement.
Each subunit comprises multiple a-helices binding a heme group.
Heme groups bind O2 / CO2
O2 bound in one heme induces conformation change to enhance binding at others.
Fibrous proteins
Collagen
General
Most abundant mammalian protein; >20 types
Trimer - 3 subunits wrapped in a helix, rich in glycine and proline.
High strength - connective tissues (ligaments, tendons, skin), also bone, muscle, etc.
Brittle bone disease is a mutation in collagen Type 1.
Fibrous Proteins
Elastin
General
Flexible - common in tissues requiring tension, stretching or deformation (lungs, arteries, bladder, skin, connective tissue)
Covalently crosslinked polypeptides that are coiled at rest, but can stretch out
Rich in non-polar aas, especially glycine, ananine, valine, proline.
Smoking promotes elastin breakdown: emphysema, wrinkles.
Muscle proteins
Actin & Myosin
Actin
Globular monomers (G-actin) polymerise to fibrous, thin filament (F-actin)
Muscle proteins
Actin & Myosin
Myosin
Thick filament with globular “head”
Conformational change when ATP is hydrolysed to ADP, pulling the actin filament.
Transmembrane Proteins
Transmembrane portion rich in hydrophoic alpha-helices.
Often function by undergoing conformational changes
Regulateactivity between extra- and intracellular
Ion channels, transporters, receptors, enzymes.
Membrane proteins
Ion channels
Proteins form pores that allow movement of ions and small molecules across the membrane.
Gated ion channels undergo conformational changes to open or close the pore.
Pentameric ion channel.
Cystic fibrosis transport conductance regulator
Gated channel
Allows movement of Cl-
Mutations prevent of impair Cl- movement leading to build-up of mucus
Membrane Proteins
Cell adhesion Molecules
e.g. Integrins, Cadherins
Bind cells to surroundings - other cells and extracellular matrix. Often linked to cystoskeleton.
Summary - Protein Function
Structure
Globular - Spherical, usually soluble and free-floating
Fibrous (usually involved in structural tissues)
Membrane
Summary - Protein Function
Function
Structural, Enzymes, Cell Transport, Carriers, Cell Signaling, Metabolic regulation
