BIOCHEMISTRY SEMI-FINALS
present in both DNA and RNA
A. NUCLEIC ACIDS AND PROTEIN
SYNTHESIS
Chromosome - which means “colored
body”
- structure in the cell nucleus thought
to be the carrier of genetic
information
- it is when chromatin becomes even
more compact and organizes itself
Chromatin - is a compact, orderly tangle
of DNA
Histones - are organizing proteins where
DNA strand is twisted
Gene - is portion of a chromosome that
controlled a specific inheritable trait
such as brown eyes or red hair.
COMPOSITION OF NUCLEIC ACIDS
 Proteins are polypeptides
 Carbohydrates are polysaccharides
 Nucleic acids are polynucleotides
Nitrogenous Base - a nitrogen-containing
cyclic compound
Nucleotide has 3 parts:
 a five-membered cyclic
monosaccharide
 a nitrogenous base, and
 a phosphate group
2 CLASSES OF NUCLEIC ACIDS
 RNA (ribonucleic acid) – single
strand
 DNA (deoxyribonucleic acid) –
double strand
Thymine – is present only in DNA
molecules (with rare exceptions).
Uracil – is present only in RNA
molecules.
Adenine, guanine, and cytosine – are
Sugar + Base = Nucleoside
Nucleoside + Phosphate = Nucleotide
BASE PAIRING IN DNA: THE
WATSON –CRICK MODEL
Double Helix - Two strands coiled around
each other in a screw-like fashion
Base Pairing - The pairing of bases
connected by hydrogen bonding (G-C and
A-T), as in the DNA double helix.
*Always 5’ to 3’ first
REPLICATION OF DNA
Replication - The process by which copies
of DNA are made when a cell divides.
Process of Replication
1. Topoisomerase travels and
alleviates DNA supercoils
2. Helicase separates the two DNA
strands
3. Single-Strand Binding (SSB)
proteins bind to the separated DNA
strands to keep them apart
4. RNA Primase are short RNA
strands start, or prime, DNA
synthesis
5. DNA Polymerase III extends the
RNA primers until the 3’ end of an
Okazaki fragment reaches the 5’
6. DNA Polymerase I degrades the
RNA primers and replaces it with
DNA
7. DNA Ligase joins the 5’ phosphate
of one DNA molecule
KINDS OF RNA
 Ribosomal RNA (rRNA) - The
RNA that is complexed with
proteins in ribosomes.
 Messenger RNA (mRNA) - The
RNA that carries code transcribed
 from DNA and directs protein
synthesis.
 Transfer RNA (tRNA) - The
RNA that transports amino acids
into position for protein synthesis.
 Heterogeneous nuclear RNA
(hnRNA) - is RNA formed directly
by DNA transcription. Post-
transcription processing converts
the heterogeneous nuclear RNA to
messenger RNA.
 Small nuclear RNA (snRNA) - is
RNA that facilitates the conversion
of Heterogeneous nuclear. RNA to
messenger RNA. It contains from
100 to 200 nucleotides.
TRANSCRIPTION: RNA SYNTHESIS
Template Strand - The DNA strand that
is transcribed
Informational Strand - The complement
of the template strand in the original helix
Codons - triplets of consecutive bases
Heterogeneous nuclear RNA (hnRNA)
- The initially synthesized mRNA
strand containing both introns and
exons.
Exons - A nucleotide sequence in a gene
that codes for part of a protein.
Intron - A nucleotide sequence in mRNA
that does not code for part of a protein;
removed before mRNA proceeds to
protein synthesis.
Genetic Code - The sequence of
nucleotides, coded in triplets (codons) in
mRNA, that determines the sequence of
amino acids in protein synthesis.
TRANSLATION: TRANSFER RNA
AND PROTEIN SYNTHESIS
Ribosome - The structure in the cell where
protein synthesis occurs; composed of
protein and rRNA.
Anticodon - A sequence of three
ribonucleotides on tRNA that recognizes
the complementary sequence (the codon)
on mRNA.
Initiation – begins with the small
ribosomal subunit and the first tRNA
arriving at the start codon of the mRNA
Elongation – begins as the tRNA with
amino acid 2 binds to its codon at the
second site within the ribosome
Termination – occurs after the elongation
steps have been repeated until the stop
codon is reached. The ribosomal units, the
mRNA, and the polypeptide separate
NUCLEIC ACID BIOTECHNOLOGY
TECHNIQUES
Gel electrophoresis - a method for
separating molecules on the basis of
charge-to-size ratio using a gel as a
support and sieving material.
Electrophoresis - is based on the motion
of charged particles in an electric field
Agarose – for larger fragments (thousands
of oligonucleotides)
Polyacrylamide - for smaller fragments
(hundreds of oligonucleotides)
Submarine gel - an agarose gel in a
horizontal position that is underneath the
buffer in the chamber
Polyacrylamide gel - run in a vertical
position
Autoradiography - the technique of
locating radioactively labeled substances
by allowing them to expose photographic
film
Autoradiograph - the resulting film
image
Luminescence - emission of light as a
result of a chemical reaction
(chemiluminescence) or re-emission of
absorbed light (fluorescence)
Fluorescence - a sensitive method for
detection and identification of substances
that absorb and re-emit light
Ethidium bromide solution - used as a
stain for DNA in a gel
Ethidium bromide is a strong carcinogen
Nucleases - catalyze the hydrolysis of the
phosphodiester backbones of nucleic acids
- enzymes that hydrolyze nucleic
acids; specific for DNA or RNA
Exonucleases - cleavage ends of the
molecule
Endonucleases - cleavage in the middle of
the chain
Restriction endonucleases - enzymes
that
hydrolyze double-stranded DNA at
specific spots on opposite strands
Bacteriophages (phages) - viruses that
infect bacteria;
- are frequently used in molecular
biology to transfer DNA between
cell
Palindrome - a message that reads the
same backward or forward
EcoRI - A typical restriction endonuclease
Methylation of endogenous DNA -
protects it from cleavage by its own
restriction endonucleases
Sticky ends - short, single-stranded
stretches at the ends of double-stranded
DNA
- they can provide sites to which
other DNA molecules with sticky
ends can be linked
Star (*) activity - can often be seen if the
enzyme concentration is too high or the
enzyme is incubated with the DNA too
long.
Recombinant DNA (Chimeric DNA) -
DNA molecules containing covalently
linked segments derived from two or more
DNA sources
DNA ligases - enzymes that link separate
stretches of DNA
Plasmid - a small circular DNA molecule
that is not part of the main circular DNA
chromosome of the bacterium.
Cloning - the process of making identical
copies of DNA is called.
- the introduction of a section of
DNA into a genome in which it can
be reproduced many times
Clone - a genetically identical population
of organisms, cells, viruses, or DNA
molecules
Vector - a carrier molecule for transfer of
genes in DNA recombination
The gene of interest is called many things:
- “foreign DNA,”
- the “insert,”
- “geneX,”
- “YFG,”for “your favorite gene.”
Selection - a process that allows bacteria
that have been transformed to be identified
and isolated
Multiple cloning site (MCS) or a
polylinker - regions that had many
different restriction sites in a small space.
Multiple cloning site (MCS) - a region of
a mRNA
bacterial plasmid with many restriction
sites
Polylinker - a region of a bacterial
plasmid with many restriction sites
Blue/white screening - a method for
determining whether bacterial cells have
incorporated a plasmid that includes a
gene of interest
Genetic engineering - the process of
manipulating the genome of an organism
to achieve a desired en
Gene therapy - a method for treating a
genetic disease by introducing a good copy
of a defective gene
Genetic Engineering in Agriculture
1. Disease Resistance
2. Nitrogen Fixation
3. Frost-free plants
4. Tomatoes with a long shelf-life
5. Good predator attraction
Intron - an intervening sequence in DNA
that does not appear in the final sequence
of mRNA
Exons - DNA sequences that are
expressed in sequences of mRNA
Expression vector - a plasmid that has
the machinery to direct the synthesis of a
desired protein
DNA library - a collection of clones that
include the total genome of an organism
Fusion proteins - proteins made via
recombinant DNA techniques that include
the desired protein sequence as well as a
leader sequence that will aid in quick
separation and purification of the protein
cDNA library - a library constructed from
complementary DNA obtained from
rather than from genomic DNA
Polymerase chain reaction (PCR) - a
method for amplifying a small amount
of DNA based on the reaction of isolated
enzymes rather than on cloning
Quantitative PCR (qPCR) - a
polymerase chain reaction technique that is
used to determine the amount of a target
DNA initially present
Southern blot - a technique used for
transferring DNA from an agarose gel
after electrophoresis onto a membrane,
such as one made of nitrocellulose
Alleles - corresponding genes on paired
chromosomes
Homozygous - exhibits no differences
between a given gene on one chromosome
and the corresponding gene on the paired
chromosome
Heterozygous - exhibits differences in a
given gene on one chromosome and the
corresponding gene on the paired
chromosome

Restriction-fragment length
polymorphisms (RFLPs) - differences in
the lengths of DNA fragments from
different sources when digested with
restriction enzymes; a forensic technique
using DNA to identify biological samples

Proteome - the total protein content of the

cell

Proteomics - study of interactions among

all the proteins of the cell

DNA microarray (DNA chip or gene

chip) - a microarray of DNA samples on a
single computer chip, on which many
samples can be examined simultaneously

Transcriptome - a group of genes that are

being transcribed at a given time