Human Genetics
Translation of RNA into Protein
Central Dogma
Replication
DNA
Transcription
RNA
Nucleus
Translation
Protein
Cytoplasm
Human Genome
3.2 million DNA base pairs
1.5% encode proteins 98.5% not protein encoding
~ 31,000 genes encoding 100,000 - 200,000 proteins
How are 100,000 to 200,000 proteins produced from
31,000 genes?
What is the 98.5% of the human genome that does not
encode proteins?
Noncoding portion of the human
genome
Type of sequence Function or characteristic
Noncoding RNAs Translation (tRNA,rRNA)
Pseudogenes
RNA processing
Introns Removed with RNA processing
Promoters and other Determine when and where
regulatory regions transcription occurs
Repeats:
Transposons DNA that moves around genome
Telomeres Chromosome tips
Centromeres Important for attachment to spindle
Duplications Unknown
Simple short repeats unknown
Two types of nucleic acids
RNA DNA
Usually single-stranded Usually double-stranded
Has uracil as a base Has thymine as a base
Ribose as the sugar Deoxyribose as the sugar
Carries protein-encoding Carries RNA-encoding
information information
Can be catalytic Not catalytic
# of strands
kind of sugar
bases used
RNA Structure Depends on
Sequence
A can pair with U and the C with G via
hydrogen bonding just as with DNA.
Secondary RNA structure is critical in
how it performs its function.
RNA Structure and RNA Sequence
enable an RNA to interact specifically
with proteins.
RNA Processing
mRNA transcripts are modified before use as a
template for translation:
- Addition of capping nucleotide at the 5’ end
- Addition of polyA tail to 3’ end
Important for moving transcript out of nucleus
And for regulating when translation occurs
Splicing - the removing internal sequences
- introns are sequences removed
- exons are sequences remaining
RNA Processing
Protein Structure was solved
before DNA was known to be
genetic material
Linus Pauling and Alpha Helix led
to model building by Watson and
Crick
Proteins
most abundant type of molecules in cells
responsible for most biological functions
muscle contraction - myosin and actin
oxygen transport - hemoglobin
immune system -antibodies
connective tissue - cartilage
hair/skin - keratin
metabolism - enzymes
Gene Expression changes in
Proteins during Development
Protein Basics
Proteins are polymers assembled from amino
acids
20 different amino acids are used
Bond between amino acids is called the "Peptide
Bond".
Peptide Bond is formed between the carboxyl
group of one amino acid and the Alpha amino
group of another amino acid.
mRNAs have a 5' end and a 3' end - they have
Polarity.
Proteins also have polarity.
Protein Folding is Critical
How is protein folding directed within
cells?
This is still an active area of research, but
to a large degree, protein sequence
determines protein folding.
Misfolding of Protein Impairs
Function
Protein Polarity
The Amino acid at one end of a protein chain
has a free Alpha amino group.
Called "Amino-Terminus" or "N-terminus" of the
protein.
Amino acid at other end has a free Alpha
carboxyl group.
Called "Carboxy-Terminus" or "C-terminus" of
the protein.
Direction of Protein Synthesis is from N-
terminus to C-terminus.
The Genetic Code
There is a 3 to 1 correspondence
between RNA nucleotides and amino
acids.
The three nucleotides used to encode
one amino acid are called a codon.
The genetic code refers to which codons
encode which amino acids.
How do we know it is a 3 letter code?
How Do the mRNA Nucleotides Direct
Formation of the Amino Acids in a Protein?
Proteins are formed from 20 amino acids in humans.
Codons of one nucleotide: Codons of two nucleotides:
A AA GA CA UA
G AG GG CG UG
C AC GC CC UC
U AU GU CU UU
Can only encode Can only encode
4 amino acids 16 amino acids
Codons of three nucleotides:
AAA AGA ACA AUA AAG AGG ACG AUG
AAC AGC ACC AUC AAU AGU ACU AUU
GAA GGA GCA GUA GAG GGG GCG GUG
GAC GGC GCC GUC GAU GGU GCU GUU
CAA CGA CCA CUA CAG CGG CCG CUG
CAC CGC CCC CUC CAU CGU CCU CUU
UAA UGA UCA UUA UAG UGG UCG UUG
UAC UGC UCC UUC UAU UGU UCU UUU
Allows for 64 potential codons => sufficient!
Theoretical Codes
The Genetic Code
Three Conceivable Kinds of Genetic Codes
Translation
The process of reading the RNA sequence of an
mRNA and creating the amino acid sequence of a
protein is called translation.
DNA DNA
template
T T C A G T C A G
Transcription strand
A A G U C A G U C Messenger
RNA
mRNA
Codon Codon Codon
Translation
Polypeptide
Protein Lysine Serine Valine (amino acid
sequence)
How do we know a 3 nucleotide
codon determines amino acid choice?
Prediction of Amino Acid Sequence
from Synthetic RNA molecules
The genetic code is non-
overlapping
Universal Code?
In some organisms, a few of the 64 possible
"words" of the genetic code are different.
Do a few different words mean that the code is
not universal?
Perhaps: if you're willing to say that the US and
Britain don't share a common language
because elevators in the UK are called "lifts"
and they spell the word "color" with a "u.“
The Genetic Code Is
Linear: uses mRNA which is
complementary to DNA sequence.
Triplet: the unit of information is the
codon, a series of three ribonucleotides.
Unambiguous: each codon specifies
only one amino acid (AA).
Degenerate: more than one codon exists
for most amino acids.
The Genetic Code Is:
Punctuated: there are codons that indicate
“start” and “stop.”
Commaless: there is no punctuation within a
mRNA sequence.
Nonoverlapping: any one ribonucleotide is
part of only one codon (some exceptions exist).
Universal: the same code is used by viruses,
bacteria, archaea, and eukaryotes.
Point Mutations
Single Base Change can alter protein
product.
Misssense: results in one amino acid
change.
Nonsense: results in stop codon.
Frame-shift: change "reading-frame" of
genetic message.
Silent mutations: point mutations that
DON’T alter the protein product because of
the degenerate nature of the genetic code.
Frame Shift
Within a gene, small deletions or insertions of a
number of bases not divisible by 3 will result in
a frame shift. For example, given the coding
sequence:
AGA UCG ACG UUA AGC
corresponding to the protein
arginine - serine - threonine - leucine - serine
Frame Shift
The insertion of a C-G base pair between
bases 6 and 7 would result in the following
new code, which would result in a non-
functional protein. Every amino acid after the
insertion will be wrong.
AGA UCG CAC GUU AAG C
Corresponding to the protein:
arginine - serine - histidine - valine – lysine
The frame shift could generate a stop codon
which would prematurely end the protein.
How to Recognize Protein
Information in DNA
Don't assume that a dsDNA molecule will be
read from left to right on the top strand.
Every dsDNA sequence has six possible
translations:
top / bottom strand each with a 1st / 2nd / 3rd
reading frame
Not every AUG or "stop" sequence is a start or
stop codon.
ORF is the Open Reading Frame- It has an
ATG in frame with a Stop codon. It could
encode a protein.
Comma free and non-
overlapping are correct.
The living cell does decodes the messenger
RNAs by a kind of dead-reckoning.
Ribosomes march along the messenger RNA
in strides of three bases, translating as they go.
Except for signals that mark where the
ribosome is supposed to start, there is nothing
in the code itself to enforce the correct reading
frame.
Three codons serve as stop signs: UAA, UAG
or UGA
What reading frame should be
used?
In any mRNA sequence, there are three
ways triplet codons can be read.
Each way to read the codons is called a
"Reading Frame".
It is very important for ribosome to find
correct reading frame.
If the wrong reading frame is used,
translation generates a protein with the
wrong amino acid sequence which is not
functional.
At what codon in the mRNA does
the ribosome begin translation?
Recall there is a 5’ untranslated region of
the messenger RNA.
The solution is that the ribosome begins
translation at a specific AUG codon within
the mRNA template termed the "Start
Codon".
This is a methionine codon, so the first
amino acid in proteins is almost always
methionine.
Translation has Three Steps
Initiation - translation begins at start codon
(AUG=methionine)
Elongation - the ribosome uses the tRNA
anticodon to match codons to amino acids and
adds those amino acids to the growing peptide
chain
Termination - translation ends at the stop codon
UAA, UAG or UGA
Translation Initiation
Translation Initiation
Leader Small ribosomal subunit
sequence
5’ 3’
mRNA mRNA
U U C G U C A U G G G A U G U A A G C G A A
U A C
Assembling to
begin translation Initiator tRNA
Met
Translation Initiation
Ribosome
5’ 3’
mRNA
A U G G G A U G U A A G C G A
U A C C C U
tRNA
Amino acid Met Gly
Large ribosomal subunit
Translation Elongation
5’ 3’
mRNA
A U G G G A U G U A A G C G A
U A C C C U
Met Gly
Translation Elongation
5’ 3’
mRNA
A U G G G A U G U A A G C G A
C C U A C A
Gly Cys
Translation Elongation
5’ 3’
mRNA
A U G G G A U G U A A G C G A
C C U A C A
Gly Cys
Translation Elongation
5’ 3’
mRNA
A U G G G A U G U A A G C G A
A C A U U C
Cys Lys
Lengthening
polypeptide
(amino acid chain)
Translation Elongation
5’ 3’
mRNA
A U G G G A U G U A A G C G A
A C A U U C
Cys Lys
Translation Elongation
5’ 3’
mRNA
A U G G G A U G U A A G C G A
A C A U U C
Cys Lys
Translation Termination
Stop codon
5’
mRNA
A U G G G A U G U A A G C G A U A A
U U C
Lys
Release
factor
Translation Termination
Stop codon
Ribosome reaches stop codon
5’
mRNA
A U G G G A U G U A A G C G A U A A
Release
factor
Translation Termination
Once stop codon is reached,
elements disassemble.
Release
factor
Translation In the Cell
Multiple copies of a protein are
made simultaneously
5'- G T A A T C C T C -3' DNA sense (partner)
strand
3’- C A T T A G G A G -5’ DNA template (antisense)
strand
5'- G U A A U C C U C -3' mRNA
N - val - ile - leu - C protein
By convention, amino acid sequences are
written and numbered left-to-right from N-
terminus to C-terminus.
tRNA is a connection between anticodon
and amino acid
5'-AUG-3' codon in mRNA
|||
3'-UAC-5'anticodon in tRNA
5'-CAU-3'if anticodon is written 5’->3'
RNA Splicing Depends on
Sequence and Structure
http://bcs.whfreeman.com/thelifewire/content/chp14/1402001.html
Alternative
splicing of
exons forms
distinct
proteins:
one gene, many
proteins
Alternative splicing of exons
forms distinct proteins:
one gene, many proteins
Exon shuffling forms distinct
proteins: