Download terminal end

Properties
of amino
acids
Primary structure:
Sequence of amino acids within the peptide chain.
Peptide bonds
Amino-terminal end
Carboxy-terminal end
The α-helix II
¾ The peptide bond
causes a dipole which
becomes stronger by the
regular arrangement
¾ Consequence:
Positively charged Nterminal end
Negatively charged Cterminal end
Atome: rot, Sauerstoff;
schwarz: Kohlenstoff;
blau: Stickstoff; weiß;
Wasserstoff.
Biochemie/Proteine_28
3
Carbohydrates
¾ The simplest compound with the gross fomula (CH2O)n is formaldehyde: n=1
¾ H2C=O has little in common with usual concept of sugars
¾ Smallest carbohydrates are the trioses
¾There are two trioses: Glyceraldehyde and dihydroxyacetone
¾ Represent major classes of monosaccharides
¾ Glyceraldehyde is an aldehyde: Aldoses
¾ Dihydroxyacetone is a keton: Ketoses
¾ Tautomer structures
¾ Can interconvert through an instable intermediate: Enediol
Mathews, van Holde & Ahern, 2000
Ring structures
Example: ribose, a pentose
¾ Can form either a five-membered furanose ring
¾ Or a six-membered pyranose ring
¾ Reaction: formation of hemiacetals from the acldehyde group
¾ In each case, two enantiomeric forms, α or ß are possible
Nucleophilic
attack
Mathews, van Holde & Ahern, 2000
Hexose rings
Pyranose ring conformations
¾ Chair (more stable)
¾ Boat (less stable)
Mathews, van Holde & Ahern, 2000
Same monomers, different polymers:
h Starch (α-1,4 bonds)
h Cellulose (ß-1,4 bonds)
h Glycogen (α-1,4 and α-1,6 bonds)
Starch (Stärke)
Cellulose
ß-1,4
-1,4
Cellobiose
Influence of binding form on secondary structure
Cellulose is the most abundant
biopolymer on earth
Glycogen
Branched polysaccharide: The linkages between
glucose residues are of two types, α-1,4 and α-1,6
Glycogen in
liver cells
Storage polymer
composed of
glucose in
animal liver
Murein: Poly-N-acetyl glucosamine – the
construction material for bacterial cell walls
Smooth and rough colonies of B. anthracis
Sugars and blood groups
The ABO blood group antigens
The O oligosaccharide does not elicit
antibodies in most humans
The A and B antigens are formed by
addition of GalNAc or Gal, respectively,
to the O oligosaccharide
Each of the A and B antigens can elicit a
specific antibody
In this figure, R can represent either a
protein molecule or a lipid molecule
Mathews, van Holde & Ahern, 2000
Phospholipids
Hydrophobic Bonds („hydrophobic interactions“)
¾ Non-polar molecules mixed with
water do not dissolve (e.g. oil slick on
water). Why?
¾ Water is held together by hydrogen
bonds. If nonpolar molecule is inserted
into water, would have to break the
ordered lattice of water molecules held
together by H bonds.
¾ But this would require energy – it
canott happen spontaneously. Instead,
nonpolar molecules (or parts of
molecules) will aggregate to avoid
water.
¾ A similar situation occurs in parts of
many proteins.
¾ The Hydrophobic Bond is very weak
(ca. 2,5 J Mol-1), rather a lower energy
state than would occur if these
molecules were dissolved in water.
Functions of membranes
Fluid mosaic model
Diagram of the structure of the cytoplasmic membrane; the inner surface (In) faces the cytoplasm and
the outer surface (Out) faces the environment.
¾ The matrix of the unit membrane is composed of phospholipids, with the hydrophobic groups directed inward
and the hydrophilic groups toward the outside, where they associate with water.
¾ Embedded in the matrix are proteins that have considerable hydrophobic character in the region that
traverses the fatty acid bilayer.
¾ Hydrophilic proteins and other charged substances, such as metal ions, may be attached to the hydrophilic
surfaces.
¾ Although there are some chemical differences, the overall structure of the cytoplasmic membrane shown is
similar in both prokaryotes and eukaryotes
Brock, 10th ed.
Pyrimidine bases
Sugar binding sites
Purine bases
Sugar binding sites
Structure of the bases of D N A and RNA. The letters, C, T, U, A and G are used
to designate the individual bases. In attaching the base to the 1‘ carbon of the
sugar phosphate, pyrimidine bases are bonded through N-1 of the ring and
purine bases through N-9 of the ring
Structural formulas of nucleic acid sugars.
The name „deoxy“
comes because here
an O is lacking
¾ The formulas can be represented in two alternate ways, open chain and ring.
¾ The open chain is easier to visualize, but the ring form is the commonly used
structure.
¾ Note the numbering system on the ring.
This is a nucleoside
This is a nucleotide
5‘ end
3‘ end
5‘ end
3‘ end
Primary structure of nucleic
acids: base sequence
G-C: 3 hydrogen bonds
Secondary structure of
nucleic acids: Base pairs
2 hydrogen bonds
The tertiary structure of nucleic acids
Franklin's X-ray diagram of the B form
of sodium thymonucleate (DNA) fibres,
published in Nature on 25 April 1953,
shows "in striking manner the features
characteristic of helical structures"5.
„Her photographs are among the most
beautiful X-ray photographs of any
substance every taken." — J. D. Bernal,
1958.
From the Nobel prize winning publication in Nature
Quarternary structure
of DNA: supercoiling
Relaxed and supercoiled DNA
Melting and denaturizing of DNA
¾ A=T pairs are more easily
separated than G≡C pairs
¾ Therefore, denaturation starts
with A=T pairs
¾ High G≡C proportion: higher
melting point
RNA: ribonucleic acid – single stranded
•Backbone:
Ribose,
Phosphoric acid
•Bases: A,G,C,U
• single stranded
•80-85% of
bacterial RNA is in
ribosomes
• Ribosomes:
Protein synthesis
• Information
encoded on DNA
is translated into
protein via RNA
during protein
synthesis
Three major types of RNA
• messenger RNA (mRNA)
• transfer RNA (tRNA)
• ribosomal RNA (rRNA)
→ Two types of function
• genetic
- carries genetic information of DNA (mRNA)
• structural
e.g. -structural role in ribosome (rRNA),
- amino acid transfer (tRNA),
- catalytic (enzymatic) activity (ribozymes)
PD Dr. Bettina Siebers
The UV damage to DNA
Ultraviolet (UV) photons harm the DNA molecules of living organisms in different
ways. In one common damage event, adjacent bases bond with each other,
instead of across the “ladder.”
This makes a bulge, and the distorted DNA molecule does not function properly.
(Illustration by David Herring)
http://web.indstate.edu/thcme/micro/bactGen/thy_dmr.gif
ATP
Components of the important nucleotide, adenosine triphosphate (ATP)
The energy of hydrolysis of a phosphoanhydride bond (shown as squiggles) is greater
than that of a phosphate ester and will have significance in Chapter 5 (Section 5.8)
[Brock, 10th ed.]
NAD+/NADH
Coenzyme
Required for redox reactions
Example: Reduction of pyruvate
Although not used in the electron transport chain, Coenzyme A is a major cofactor which is used
to transfer a two carbon unit commonly referred to as the acetyl group. The structure has many
common features with NAD+ and FAD in that it has the diphosphate, ribose, and adenine. In
addition it has a vitamin called pantothenic acid, and finally terminated by a thiol group. The thiol
(-SH) is the sulfur analog of an alcohol (-OH).
The acetyl group (CH3C=O) is attached to the sulfur of the CoA through a thiol ester type bond.
Acetyl CoA is important in the breakdown of fatty acids and is a starting point in the citric acid
cycle
www.elmhurst.edu/~chm/vchembook/images/594CoA.gif