Transcript DNA-->RNA-->Proteins notes

DNARNAProteins
Honors Biology
REVIEW! What is DNA?
 Deoxyribonucleic Acid (DNA)
 Monomers made up of nucleotides:
 Nucleotides consist of:
A five carbon sugar, deoxyribose
o Four in it’s ring, one extending above the ring
o Missing one oxygen when compared to ribose
 Phosphate group
o Is the source of the “acid” in nucleic acid
 Nitrogenous base (Adenine, Guanine, Cytosine, Thymine)
o A ring consisting of nitrogen and carbon atoms with various functional groups
attached
o Double ring= purines (A and G)
o Single ring= pyrimidines (T and C)
 Double helix consists of:
 Sugar-phosphate backbone held by covalent bonds
 Nitrogen bases are hydrogen bonded together; A pairs with T and C pairs with G

REVIEW! Nucleotides
Protein synthesis: overview
 DNA inherited by an organism specifies traits by dictating
the synthesis of proteins.
 However, a gene does not build a protein directly; it
dispatches instruction in the form of RNA, which in turn
programs protein synthesis.
 Message from DNA in the nucleus of the cell is sent on RNA
to protein synthesis in the cytoplasm.
 Two main stages:
 Transcription
 Translation
Protein Synthesis: Overview
 Two main stages:
 Transcription
 The transfer of genetic information from DNA into an RNA molecule
 Occurs in the eukaryotic cell nucleus
 RNA is transcribed from a template DNA strand
 Translation
 Transfer of the information in RNA into a protein.
Transcription
 Details:
 1. Initiation Promoter is the nucleotide sequence on DNA that marks where
transcription of a gene begins and ends; “start” signal
 Promoter serves as a specific binding site for RNA polymerase and
determines which of the two strands of the DNA double helix is used as the
template.
 Specific nucleotide sequence at promoter is TATAAA
 Called the “TATA box”; located 25-35 base pairs before the transcription
start site of a gene
 TATA box is able to define the direction of transcription and also indicates
the DNA strand to be read
 Proteins called transcription factors can bind to the TATA box and recruit
RNA polymerase; it has a regulatory function
 Note:TATA box is found upstream of start site and thus is NOT transcribed by RNA
polymerase
Transcription
 Elongation RNA elongates
 As RNA synthesis continues, the RNA strand peels away from its DNA
template, allowing the two separated DNA strands to come back together
in the region already transcribed.
Transcription
 3. Termination RNA polymerase reaches a sequence of bases in the DNA template called
a terminator.
 Signals the end of the gene; at that point, the polymerase molecule
detaches from the RNA molecule and the gene.
 mRNA (messenger RNA) or “transcript” exits the nucleus via the nuclear
pores and enter the cytoplasm
Transcription animation
 http://www-
class.unl.edu/biochem/gp2/m_biology/animation/gene/ge
ne_a2.html
RNA processing
 Before mRNA leaves the nucleus, it is modified or processed.
 1. addition of extra nucleotides to the ends of the transcript
 Include addition of a small cap (a single G nucleotide) at one end and
a long tail (a chain of 50 to 250 A’s) at the other end
 Cap and tail facilitate the export of the mRNA from the nucleus,
protecting the transcript from attack by cellular enzymes, and help
ribosomes bind to the mRNA
 Cap and tail are NOT translated into protein.
http://vcell.ndsu.edu/animations/mrnaprocessing/movie.htm
RNA processing
 2. RNA splicing
 Cutting-and-pasting process catalyzed by a complex of proteins
and small RNA molecules, but sometime the RNA transcript
itself catalyzes the process.
 Introns
 “intervening sequences”; internal noncoding regions
 Get removed from transcript before it leaves nucleus
 Exons
 Coding regions; parts of a gene that are expressed as amino acids
 Joined to produce an mRNA molecule with a continuous coding sequence
 Cap and tail are considered parts of the first and last exons, although are not
translated into proteins.
 http://student.ccbcmd.edu/biotutorials/protsyn/exon.html
RNA processing
More animations
 http://www.pbs.org/wgbh/aso/tryit/dna/protein.html
 http://www.wisc-
online.com/objects/index_tj.asp?objID=AP1302
Translation
 A typical gene consists or hundreds or thousands of
nucleotides in a specific sequence, which get transcribed onto
mRNA.
 Translation is the conversion of nucleic acid language into
polypeptide language
 There are 20 different amino acids.
 A cell has a supply of amino acids in cytoplasm, either obtained
by food or made from other chemicals.
 Flow of information from gene to protein is based on a
triplet code: genetic instructions for the a.a. sequence of a
polypeptide chain are written in DNA and mRNA as a series
of three-base pairs, or codons.
Translation- tRNA
 To convert the codons of nucleic acids on mRNA to the
amino acids of proteins, a cell employs a molecular
interpreter, called transfer RNA (tRNA)
 tRNA molecules are responsible for matching amino acids to
the appropriate codons to form the new polypeptide.
 tRNA’s unique structure enables it to be able to:
 1. pick up the appropriate amino acids
 2. recognize the appropriate codons in the mRNA
Translation- tRNA
 tRNA is made of a single strand of RNA consisting of about
80 nucleotides
 By twisting and folding upon itself, it forms several doublestranded regions in which short stretches of RNA base-pair
with other stretches.
 at one end of the folded molecule contains a special triplet of
bases called an anticodon.
 Complementary to a codon triplet on mRNA
 Anticodon recognizes a particular codon triplet on mRNA
 At the other end of the tRNA molecule is a site where an
amino acid can attach.
Translation- tRNA
Translation- tRNA
 Each amino acid is joined to the correct tRNA by a specific
enzyme.
 Each enzyme specifically binds one type of amino acid to all
tRNA molecules that code for that amino acid, using a
molecule of ATP as energy to drive the reaction.
 The resulting amino acid-tRNA complex can furnish its
amino acid to a growing polypeptide chain.
Translation- rRNA
 Ribosomal RNA (rRNA)
 Organelle in the cytoplasm that coordinates the functioning of
mRNA and tRNA and actually makes polypeptides.
 Consists of two subunits: large and small
 Each ribosome has a binding site for mRNA, and three binding sites
for tRNA.
 E site
Removes tRNA from ribosome
 P site
 Holds the growing polypeptide
 A site
 Obtains new amino-acid-tRNA

 Ribosome holds tRNA and mRNA molecules close together, allowing
the amino acids carried by the tRNA molecules to be connected into
a polypeptide chain.
Translation- Steps
 Can be divided into same three phases: initiation, elongation,
and termination.
 1. Initiation
 Brings together the mRNA, a tRNA bearing the first amino acid,
and the two subunits of a ribosome.
 Role is to establish exactly where translation will begin, ensuring
the mRNA codons are translated into the correct sequence of
amino acids.
Translation
 1. Initiation (continued…)
 Two steps:
 1. an mRNA binds to a small ribosomal subunit. A special initiator tRNA
binds to the specific codon, called the start codon, where translation
begins on mRNA.
 Initiator tRNA carries the amino acid Methionine (Met); its anticodon
UAC binds to the start codon, AUG
 2.A large ribosomal subunit binds to the smaller one, creating a function
ribosome. The initiator tRNA fits into tRNA binding site (P site) on the
ribosome. A site is vacant and ready for the next amino-acid carrying
tRNA.
 2. Elongation
 Once initiation is complete, amino acids are added one by one to
the first amino acid. Each addition occurs in a three step process:
 1. codon recognition
The anticodon of an incoming tRNA carrying an amino acid, pairs with
the mRNA codon in the A site of the ribosome
 2. peptide bond formation
 Polypeptide separates from the tRNA to which it was bound (P site) and
attaches by a peptide bond to the amino acid carried by the tRNA in the A
site.
 The ribosome catalyzes formation of the bond.
 3. translocation
 P site tRNA, moves to the E site and leaves the ribosome.
 The ribosome then translocates (moves) the tRNA in the A site, with its
attached polypeptide, to the P site.
 Codon and anticodon remain bonded, and the mRNA and tRNA move as
a unit
 Movement brings into the A site the next mRNA codon to be translated,
and the process begins again at step 1.

 Termination
 Elongation continues until a stop codon reaches the ribosome’s
A site.
 Stop codons- UAA, UAG, and UGA, do not code for amino
acids but instead act as signal to stop translation.
 The completed polypeptide is released from the last tRNA and
exits the ribosome, which then splits into its separate subunits.
Translation Animation
 http://www-
class.unl.edu/biochem/gp2/m_biology/animation/gene/ge
ne_a3.html
Polysome
Several ribosomes can translate an mRNA at the same time,
forming what is called a polysome.
Peptide Bond Formation
Free ribosomes vs. bound
ribosomes
 Free ribosomes
 Found in cytoplasm
 Synthesize proteins for use primarily within the cell
 Bound ribosomes
 Found on rough ER
 Synthesize proteins primarily for secretion or for lysosomes
Free ribosomes vs. bound
ribosomes
After protein synthesis…
 Each polypeptide coils and folds, assuming a 3-D shape, its
tertiary structure.
 Several polypeptides may come together, forming a protein
with quaternary structure.
 Overall significance:
 Process whereby genes control the structures and activities of
cells
 The way genotypes determine phenotypes; proteins made from
the original DNA nucleotides determine the appearance and
capabilities of the cell and organism!
Mutations
 Mutation is any change in the nucleotide sequence of DNA.
 Can involve large regions of a chromosome or just a single
nucleotide pair, as in sickle cell disease
 In one of the two kinds of polypeptides in the hemoglobin
protein, the sickle-cell individual has a single different amino
acid.
 This small difference is caused by a change of a single
nucleotide in the coding strand of DNA. Only ONE base pair!
Mutations on DNA
 Two general categories:
 Base substitution
 Also known as a point mutation
 Replacement of one nucleotide with another.
 Depending on how the base substitution is translated, it can result in no
change in the protein (due to redundancy of genetic code), an insignficant
change, or a change that significantly affects the individual.
 Occasionally, it leads to an improved protein that enhances the success
of the mutant organism and its descendants.
 More frequently, its harmful.
o May cause changes in protein that prevent it from functionally
normally.
o If stop codon is a result of mutation and protein is shortened, it may
not function at all.
Mutations on DNA
 Base insertions or deletions
 Also known as frameshift mutation
 Often has a disastrous effect
 Adding or subtracting nucleotides may result in an alteration of
the reading frame of the message
 all the nucleotides that are “downstream” of the insertion or deletion will
be regrouped into different codons.
 Result will most likely by a nonfunctional polypeptide
Mutations on DNA
 What causes mutations?
 Mutagenesis, or the production of mutations, can occur in a
number of ways.
 Errors that occur during DNA replication or recombination are
called spontaneous mutations.
 Mutagen, a physical or chemical agent that causes mutations
 Physical mutagen: high-energy radiation, such as X-rays and UV light
 Chemical mutagen: consists of chemicals that are similar to normal DNA
bases pair incorrectly.
Mutations on DNA
 Can also be helpful both in nature and in the laboratory.
 It is because of mutations that there is such a rich diversity of
genes in the living world, that make evolution by natural
selection possible.
 Also essential tools for geneticists.
 Whether naturally occurring or created in the laboratory,
mutations create the different alleles needed for genetic
research.
Mutations- Chromosome Number
 Nondisjunction
 Members of a chromosome fail to separate.
 Can lead to an abnormal chromosome number in any sexually
reproducing diploid organism.
 For example, if there is nondisjunction affecting human
chromosome 21 during meiosis I, half the resulting gametes will
carry an extra chromosome 21.
 Then, if one of these gametes unites with a normal gamete, trisomy 21
(Down Syndrome) will result.
Mutations- Chromosome Number
Mutations- Chromosome Structure
 Abnormalities in chromosome structure:
 Breakage of a chromosome can lead to a variety of rearrangements
affecting the genes of that chromosome:
 1. deletion: if a fragment of a chromosome is lost.


Usually cause serious physical and mental problems.
Deletion of chromosome 5 causes cri du chat syndrome: child is mentally
retarded, has a small head with unusual facial features, and has a cry that
sounds like the mewing of a distressed cats. Usually die in infancy or early
childhood.
Mutations- Chromosome Structure
 2.duplication: if a fragment from one chromosome joins to a sister
chromatid or homologous chromosome.
 3.inversion: if a fragment reattaches to the original chromosome but in the
reverse direction.
 Less likely than deletions or duplications to produce harmful effects,
because all genes are still present in normal number
 4. translocation: moves a segment from one chromosome to another
nonhomologous chromosome
 Crossing over between nonhomologous chromosomes!
Mutations- Chromosome Structure
Karyotype
 The term karyotype refers to the chromosome complement of a
cell or a whole organism.
 A karyotype is an ordered display of magnified images of an
individual’s chromosomes arranged in pairs, starting with the
longest.
 In particular, it shows the number, size, and shape of the
chromosomes as seen during metaphase of mitosis.
 Chromosome numbers vary considerably among organisms and
may differ between closely related species.
Karytype
 Karyotypes are prepared from the nuclei of cultured white
blood cells that are ‘frozen’ at the metaphase stage of mitosis.
 Shows the chromosomes condensed and doubled
 A photograph of the chromosomes is then cut up and the
chromosomes are rearranged on a grid so that the homologous
pairs are placed together.
 Homologous pairs are identified by their general shape, length,
and the pattern of banding produced by a special staining
technique.
Karyotype
 Male karyotype
 Has 44 autosomes, a single X chromosome, and a Y chromosome
(written as 44 + XY)
 Female karyotype
 Shows two X chromosomes (written as 44 + XX)
Karyotype- Normal
Karyotype- Abnormal