N-linked oligosaccharides

Glycoproteins- one or several oligosaccharides of

varying complexity joined covalently to protein
-Found on outer face of plasma membrane, in
extracellular matrix and in blood
-Inside the cells they are found in specific organelles
such as golgi complexes, secretory granules and
lysosomes
N-linkage: Begins in ER and complete in Golgi
O-linkage: In Golgi
All N-linked oligosaccharides have a
common pentasaccharide core of 2 N-
Acetyl glucosamine and 3 mannose
residue but nature of side chain differs
In high mannose type of N linked
oligosaccharide, typically 2-6
additional mannose residues are
joined to pentasaccharide core .
In complex type, of N-linked
oligosaccharide contain 2-5 outer
branches attached to mannose of
pentasaccharide core; these branches
contain different combination; GlcNac,
Gal, Sialic acid, mannose and fucose
Nucleic acid protein
interaction

DNA protein interactions

When a protein binds a
DNA

It regulates function of
DNA, usually expression
of gene

Among proteins that bind to

DNA are transcription factors
that activate or repress gene
expression by binding to DNA
MOTIFS
There are several types of
proteins found in a cell.

But only those proteins

interact with DNA, which
have the DNA binding
domains.
CHROMATIN = long dsDNA and nearly equal mass of
small basic proteins( HISTONES) as well as non histone
proteins (enzymes for DNA replication) and small quantity
of RNA

Nucleosome = DNA
wound around histone
proteins

Purpose of histones is to
condense DNA
Histones are basic
proteins H1 (Linker
histone) is least
tightly bound to
chromatin and can
CORE nucleosome be easily seperated
has 4 classes of with salt solution
histones- H2A,
H2B, H3,H4 H2A AND H2B-
LYSINE RICH
H3 AND H4-
ARGININE RICH
Specific
Interactions
Transcription
Have 2 domains
factors

DNA
ACTIVATION
BINDING
DOMAIN
DOMAIN

Recognize Responsible for

specific DNA bringing
sequence to transcriptional
bind activation
Each DNA binding domain---------- has at least
one motif---------------- which is a conserved
amino acid sequence of this protein---------------
which can potentially recognize a double stranded
or a single stranded DNA.

These DNA binding domains

possess an affinity to bind to
either double stranded or
single stranded DNA.
 Many Transcription
factors operate as
dimers

HOMODIMERS
(IDENTICAL
SUBUNITS)
HETERODIMERS
(DISSIMILAR SUBUNITS
HELD TOGETHER BY
DIMERIZATION
DOMAINS)
 Was originally discovered in
transcription factors involved in
early Drosophila development

These proteins contain 60 amino

acid DNA binding region calledd
HOMEODOMAIN or
HOMEOBOX
-20 AMINO ACID MOTIF
8 amino acids form alpha helix
followed by a right “turn” consisting of
3 amino acids followed by another
alpha helix of 9 amino acids
 Zinc finger
Two types of Zn fingers have
been reported

C2H2 FINGER-loop of 12 amino

acids with 2 cysteine and 2
histidines at the base of the
loop that coordinate
tetrahedrally with zinc ion eg.
RNA polymerase III
Transcription factor A has 9 zinc
fingers C4 FINGER

4 cysteines coordinate
with zinc ion eg steroid
hormone receptor
protein
Leucine zipper

Leucine zipper domains are made

up of two motifs:

a basic region that recognizes a

specific DNA sequence and

a series of leucines spaced 7

residues apart along an α-helix
(leucine zipper) that mediate
dimerization.

Forms a continuous α-helix that can dimerize through

formation of a coiled-coil structure involving paired
contacts between hydrophobic leucine zipper domains

Also act as DIMERIZATION DOMAINS

It contains leucine residues at
every seventh position in the
C-terminal end of the DNA-
binding domains
 Helix loop helix

Dimerization domain distinct

from Helix turn helix motif

2 alpha helices seperated by

non helical loop

C terminal of alpha helix has

hydrophobic amino acids
Helix-loop-helix motif consists of
2 alpha helices seperated by a
loop of amino acids
 ACTIVATION DOMAINS

Acidic Proline rich

activation Glutamine domains
domains rich
domains