CA641-Biometrics

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Nov 29, 2013 (3 years and 7 months ago)

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CA641
-
Biometrics

Basic definitions

Central Dogma


DNA
-
> RNA
-
> Protein


DNA



2 strands of
nucleotides (bases
) joined
together by hydrogen bonds to form a
helix


Nucleotides
: ACGT.
Complementarity
: A
-
T, C
-
G


DNA is present in the nucleus ‘packed’ in
chromosomes :
in humans, 23 pairs


Locus:
specific position on a chromosome (where
a base pair is present)


Genetic map:
ordered

set of
loci

plus the
information they contain




Genome:

all genetic material


Gene
: substring of DNA that encodes for a
specific protein, length measured in
base
-
pairs


Alleles:
some nucleotides may differ in different
individuals


A gene contains
introns

(non
-
coding) and
exons

(coding)


Example: 18bp


TACAagTACAaattGATT



ATGTtcATGTttaaCTAA




From DNA to RNA (
transcription
)


RNA


(usually) single stranded sequence of
nucleotides : A , C, G,
U.
A
-
U, C
-
G


Obtained from DNA sequence


Example:

Step1: Nuclear RNA


TACAagTACAaattGATT

-
>
AUGUucAUGUuuaaCUAA

Step2:
mRNA

(
transcript
)
-

discard
introns

-
>
AUGUAUGUCUAA


Some other types of RNA exist, that do not code
for proteins, but have other roles (
sRNA
,
microRNA
)

From mRNA to proteins

(translation)


Protein
: substance in charge of a specific
function, composed of building blocks named
aminoacids

(AA)


20
possible
aminoacids


AAs are obtained by ‘reading’ the mRNA, using
the
genetic code:
every 3 nucleotides (
codon
) in
RNA encode for one
aminoacid



E.g. UUG
-
> L (
Leucine
)


Stop
codons
: UAA, UAG, UGA


Start
codon
: AUG

From mRNA to proteins
(translation)


Example:


mRNA
:
AUG|
UAU
|
GUC
|UAA


=> aminoacids:

START
(M
-
Methionine),
Y
(Tyrosine),
V

(Valine),
STOP


Note:
a change from UAU to UAA would
transform Y into STOP, yielding the wrong
protein (SNPs

single nucleotide
polymorphism, alleles)

Genetic code

Misc.


DNA sequence => mRNA sequence => protein AA
sequence
=>

protein 3D structure
=>
function
(
algorithms to determine structure...)


E.g.


2TRX :
MSDKIIHLTDDSFD

TDVLKADGAILVDFWA EWC

GPCKMIAPILDEIAD

EYQGKLTVAKLNDQNPGT

APK
YGIRGIPTLL
LFKNGE

VAAT KVGALSKGQLK EFL

DANLA

Misc.


Sequence matching/alignment
is a way to
arrange the sequences of DNA, RNA or
protein, s.t. regions of similarity can be
identified.


Gaps

may be opened to improve alignment


Expression levels


mRNA


microarrays, RNA
-
seq


Protein
-

qPCR