Download Amino acids

Proteins
- Amino acids
- Structure
- Protein domains
- Physicochemical properties
- Folding and chaperones
- Connective tissue proteins
AMINO ACIDS
Amino acids: general structure
Nonpolar alifatic
Aromatic
Polar uncharged
Positively charged
Negatively charged
Proteins consist of amino
acids and have carboxyland amino-terminal ends
STRUCTURE OF PROTEINS
Primary structure: sequence of amino
acids
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLS
FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAV
AHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLL
VTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
Amino acid alignment of same
proteins from different organisms
Protein globule is the functional
structure (tertiary structure)
Secondary structure: alfa-helix
Secondary structure: beta-sheet
Tertiary structure: position of all
protein atoms in space
Quaternary structure: association of
two or more molecules
Quaternary structure: association of
two or more molecules
hemoglobin
DOMAINS: DISTINCT COMPACT
PARTS IN PROTEIN STRUCTURE
Domains of pyruvate kinase
Domain 1
Domain 2 (catalytic)
Domain 3 (regulatory)
FOLDING AND CHAPERONES
There is no universal way for protein
folding (each protein follows its own
folding pathway)
But there is one general rule:
- Hydrophobic amino acids form
hydrophobic core inside protein
globule
Forces that fold protein
Folding: example of stages
Chaperones
Chaperones are the proteins that help other proteins
to fold properly.
Functions of chaperones:
1. To prevent aggregation of newly synthesized
proteins.
2. To assist in folding of unfolded proteins (due to
changes of temperature, pH)
Prions: “infective” proteins
CONNECTIVE TISSUE PROTEINS
Keratin
Keratin of hairs
Keratin of hairs
Hydrophobic interactions stabilises
supercoiled alfa-helix in keratin
Disulfide bonds
FIBRILLAR PROTEINS:
- COLLAGEN
Collagen
Collagen triple helix:
Gli – Х – Pro
Vitamin C is necessary for hydroxylation of
proline in collagen
Lysine and hydroxy-lysine make cross-bridges in
collagen to hold helices together
Conjugated proteins
- Classification
- Functions
HEMOPROTEINS: HEMOGLOBIN AND
MYOGLOBIN
Heme = protoporphyrin + Fe2+
Physiological functions
• Myoglobin stores
oxygen in muscles. It
releases oxygen only
when oxygen
concentration is very
low (hypoxia)
• Hemoglobin transfers
oxygen from lungs to
tissues. It releases
oxygen when oxygen
concentration is in
physiological range.
Complex between ligand and protein
О2 is bound to heme group
Oxygen saturation curves for myoglobin (hyperbolic) and
hemoglobin (sigmoidal): different ability to transfer oxygen
Lungs: both proteins are
saturated with oxygen.
Tissues:
- myoglobin is 90% saturated
(gives back only 10%)
- hemoglobin is 50%
saturated (gives back 50%)
COOPERATIVITY OF OXYGEN
BINDING
Myoglobin consists of single polypeptide chain,
while functional hemoglobin molecule contains
four polypeptide chains (which are very similar to
myoglobin ones)
Myoglobin (single chain)
Hemoglobin (one
subunit)
Hemoglobin (four subunits)
Oxygen binding leads to structural (conformational)
changes in binding site, which are transmitted to
neighboring subunits through contacts between subunits
Binding of oxygen molecule by the first
subunit enhances oxygen binding to other
subunits
This feature is called cooperativity
2,3-BISPHOSPHOGLYCERATE AND
COOPERATIVITY
2,3-BPG is produced from one of the glycolysis
intermediates
The presence of 2,3BPG indicates sites of
high energy
production and,
therefore, oxygen
demand
2,3-BPG binds to the central cavity of
hemoglobin molecule
Effects of 2,3-BPG:
• 2,3-BPG weakens oxygen binding.
Therefore:
• High 2,3-BPG in tissue → weak oxygen binding →
better oxygen supply
This plays role in adaptation to highlands and
intensive work
HEMOGLOBIN ISOFORMS:
- ADULT
- FETAL
Protein isoforms
Synthesis of different isoforms during embryonic
development
Fetal vs. adult hemoglobin
PHYSIOLOGICAL REGULATION OF OXYGEN
BINDING: EFFECTS OF PH AND CO2
Effects of pH and CO2
Tissues with high
energy demand
(high glycolysis):
- high CO2
-low pH
Nucleic acids
- Nitrogen bases
- Nucleotides
- DNA and RNA
DNA and RNA contain nitrogen bases
Nucleotides vs. nucleosides
How is this
nucleoside /
nucleotide
called?
There are some other nitrogen bases
• Alkaloids
• Products of nitrogen bases breakdown
Some bases are not included in nucleic acids
structure: alkaloids
H
caffeine
H
theophilline
theobromine
Nitrogen bases which are formed during
metabolism from adenine and guanine
hypoxanthine
xanthine
Uric acid
Elevation of uric acid causes gout
• Uric acid forms
insoluble salts
• Causes: increased
production OR
decreased
excretion
DNA contains minor (modified) bases: regulation of
gene expression by methylation
RNA contains minor bases:
recognition, stability, regulation
mRNA
tRNA
FUNCTIONS
ATP as energy carrier
high energy bond (macroergic
bond, high energy phosphate)
= good leaving group,
high transfer potential
(correct meaning)
Nucleotide moieties of coenzymes: coenzyme A
Nucleotide moieties of coenzymes: NAD
Nucleotide moieties of
coenzymes: FAD
Regulatory functions of cyclic nucleotides
cAMP has positive effect on
energy-production pathways
(glycolysis). One of the
mechanisms of caffeine
action is inhibition of cAMP
breakdown. This leads to
prolongation of cAMP
stimulatory action.
cGMP mediates muscle
relaxation caused by NO. Effect
of nitroglycerin on heart muscle
relaxation is mediated by cGMP
formation.
Summary
• Nucleotides consist of nitrogen base
(A,T,G,C,U) + (deoxy)ribose + phosphate
• Nucleotides are the building blocks of
nucleic acids (DNA, RNA)
• Nucleotides perform signaling functions
(cAMP, cGMP)
• Nucleotides play role in catalysis (parts of
coenzymes).
• Nucleotides are energy carriers (ATP, GTP)
NUCLEIC ACIDS: DNA
Nucleotides (in DNA or RNA) are
joined by phosphodiester bonds
Conventional order of
sequence description is from
5`- to 3`- end:
5` ATG 3`
DNA is a double helix
DNA STRUCTURE AND DRUGS
Intercalation – insertion between planar bases of
double helix
Intercalating drugs: bacteriostatics
proflavin
Intercalating drugs for cancer
cisplatin
Mechanism of intercalation
NUCLEIC ACIDS: RNA
Differences between RNA and DNA: pentose
Lack of OH-group makes DNA more chemically
stable: DNA is more suitable for storing genetic
information
RNA functions in protein synthesis:
ribosomal RNA perform catalytic functions
RNA is the major structural component of ribosomal subunits
30S
rRNA (brown)
+ proteins
(blue):
rRNA:
50S
RNA functions in protein synthesis:
transfer RNA (tRNA)
Real conformation in 3D
RNA functions in protein synthesis: messenger
RNA (mRNA)
Other functions of RNA:
• Catalysis (ribozymes): ribosome, RNAse P,
hammerhead ribozyme.
• Regulation of gene expression (RNA
interference): small interfering RNAs
RNA as catalyst: ribozymes
RNase P plays role in:
- tRNA processing
- regulation of
transcription