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Biochemistry: Structural Aspects

(CHM 63400 001)

Lecture 2
Central Dogma (Part-II)

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Our genetic information consists of

genes
➢Defined by the sequence of the 4 bases:

➢Promoter: Binding site for RNA

polymerase
➢Accessory proteins often required:
transcription factors
➢Messenger RNAs are the template for
protein synthesis RNA DNA
➢Some RNA molecules have functions of
their own

One strand of the DNA serves as a template for

RNA synthesis

The terminator leads to release

of the transcription machinery

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Transcription

In eukaryotes, mRNAs are processed and

exported from the nucleus
➢Chemical “cap” on
5’ end

➢Long tail of
consecutive “A”
nucleotides on 3’ end

➢Introns removed

➢Transcription occurs
in the nucleus

➢Translation in the
cytoplasm

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Chapter 1: Structure and Bonding I

O
C coenzyme A
3x
H3C S eukaryotes, archaea

O O
O P O P O
O O
O
C O bacteria isopentenyl diphosphate
H 3C C
O
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pyruvate
+

O OH isoprenoid compounds
O P O H
O
O
glyceraldehyde phosphate

1.3B: Biopolymer basics

DNA, RNA and Proteins are All Polymers
Carbohydrates, proteins, and nucleic acids are the most important polymers in the living
world. To understand what a polymer is, simply picture a long chain made by connecting
lots of individual beads, each of which is equipped with two hooks. In chemical
terminology, each bead is a monomer, the hooks are linking groups, and the whole
chain is a polymer. H O
O OH H2NH O
O OH HN O
H3N
O O OH
H2N H2N
OH OH
monomer HN
H O
H O -O O
Amino Acids -O O
Amino Acids
polymer
fig 59 OH
O O
H
H3N N
1.3C: Carbohydrates N O
H H-O-H
O
The term 'carbohydrate', which literally means 'hydrated carbons', broadly refers to H-O-H
monosaccharides, disaccharides, oligosaccharides (shorter polymers) and polysaccharides
-O O
Organic Chemistry With a Biological Emphasis (2016 ed.)
Tim Soderberg
39 Peptide

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The twenty amino acids

Protein chains are made of amino acids

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How do we translate RNA “language” into

protein “language?”
➢Four bases in RNA
➢20 amino acids in proteins
➢How many bases do we need to encode each
amino acid uniquely?

tRNA
Ribosome:

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The genetic code convert nucleotide sequence into amino

acid sequence

One or more 3-letter

codons are used for
each amino acid

AUG is always used

as a start codon

There are three stop

codons.

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A special class of RNA molecule is needed to convert

RNA codons into amino acids

➢tRNAs (transfer RNAs)

➢There is a unique tRNA molecule for each codon
➢Anti-codon site is complementary to codon and can
bind to the codon in an RNA molecule
➢One end of tRNA is linked to an amino acid
molecule

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Aminoacyl-tRNA synthetases link

tRNAs to the correct amino acid

➢AARSs create the

physical link between
each codon & correct
amino acid

➢Each recognizes a
single tRNA and a
single amino acid

➢We refer to tRNAs

carrying amino acids
as “charged”

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The ribosome is a large enzyme complex that

synthesizes proteins from an mRNA template

➢Primarily an RNA enzyme!

➢ Proteins play mostly structural and
regulatory roles
➢Bind to mRNAs and recognize the
translation initiation site
➢Allow tRNAs to bind to their specific
codons
➢Covalently link amino acids carried by
consecutive tRNAs to create a growing
polypeptide (protein) chain

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How does a ribosome assemble a protein from an

mRNA sequence?

Initiation

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Elongation

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Termination

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 Chapter 1: Structure and Bonding I
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The possibilities for carbohydrate structures are vast, depending on which monomers are
used (there are many monosaccharides in addition to glucose and fructose), which
carbons are linked, and other geometric factors which we will learn about later. Multiple
linking (branching) is also common, so many carbohydrates are not simply linear chains.
In addition, carbohydrate chains are often attached to proteins and/or lipids, especially on
the surface of cells. All in all, carbohydrates are an immensely rich and diverse subfield
of biological chemistry.

1.3D Amino acids and proteins

Proteins are polymers of amino acids linked through amide
bonds
Proteins are polymers of amino acids, linked by amide peptide
groups known asbonds
peptide bonds.
An amino acid can be thought of as having two components: a 'backbone', or 'main Chapter 1: Structure and Bonding I
chain', composed of an ammonium group, an ' -carbon', and a carboxylate, and a variable
'side chain' (in green below) bonded to the -carbon.
glutamate (E)
a-carbon
a carbon cysteine (C) O O green: side chain
HO HS blue: main chain
H CH3 peptide bonds circled
H R H H O H O
C O C O N-terminus H H
C O N N
H 3N C H 3N C H 3N HC3N N O
O O O H C-terminus
O H O H
a generalized alanine serine
amino acid NH S
H3C
fig 63 N methionine (M)
There are twenty different side chains in naturally occurring amino acids (see Table 5 in
histidine (H)
the tables section at the back of this book), and it is the identity of the side chain that
determines the identity of the amino acid: for example, if the side chain is a -CH3 group,
CHEM peptide
the amino acid is alanine, and if the side chain is a -CH2OH group, the amino acid is
fig 64 group (the side chain of serine,
serine. Many amino acid side chains contain a functional
When an
for example, contains a primary alcohol), while others, likeamino acid
alanine, is aincorporated
lack functional into a protein it loses a molecule of water and what
group, and contain only a simple alkane. remains is called a residue of the original amino acid. Thus we might refer to the
'glutamate residue' at position 3 of the CHEM peptide above.
19 on an amino acid monomer are the amine and carboxylate groups.
The two 'hooks'
Proteins (polymers of ~50 amino acids or more) Once a protein
and peptides polymer
(shorter is constructed,
polymers) are it in many cases folds up very specifically into a
formed when the amino group of one amino acidthree-dimensional
monomer reacts with structure, which often includes one or more 'binding pockets' in which
the carboxylate
other molecules
carbon of another amino acid to form an amide linkage, can be terminology
which in protein bound. It is this
is a shape of this folded structure, and the precise
peptide bond. Which amino acids are linked, and in what order
arrangement of -the
thefunctional
protein sequence
groups-within the structure (especially in the area of the
is what distinguishes one protein from another, and is coded
binding for bythat
pocket) an determines
organism's DNA.the function of the protein.
Protein sequences are written in the amino terminal (N-terminal) to carboxylate terminal
(C-terminal) direction, with either three-letter or Enzymes
single-letter abbreviations for
are proteins which catalyzethe aminobiochemical reactions. One or more reacting
acids (see table 5). Below is a four amino acid peptide
moleculeswith -the sequence
often called"cysteine
substrates - - become bound in the active site pocket of an
histidine - glutamate - methionine". Using the single-letter
enzyme, where code,the the actual
sequence is
reaction takes place. Receptors are proteins that bind
abbreviated CHEM. specifically to one or more molecules - referred to as ligands - to initiate a biochemical
process. For example, we saw in the introduction to this chapter that the TrpVI receptor
in mammalian tissues binds capsaicin (from hot chili peppers) in its binding pocket and
initiates
Organic Chemistry With a Biological Emphasis a heat/pain
(2016 ed.) signal which is sent
41 to the brain.
Tim Soderberg

Shown below is an image of the glycolytic enzyme fructose-1,6-bisphosphate aldolase

(in grey), with the substrate molecule bound inside the active site pocket.

42 Organic Chemistry With a Biological Emphasis (2016 ed.)

Tim Soderberg

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Amino Acid Properties: Polar vs Nonpolar

O R
NH 2
N
H
O
blocked amino
acid

mimics amino
acid residue

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The Twenty Amino Acids

Most Hydrophobic Most Polar

R
O-
+H
3N

O
Phenylalanine Leucine Tryptophan Glycine Tyrosine Glutamine Lysine
NH 3
H NH 2

O
OH
N
H
Methionine Valine Alanine Serine Histidine Asparagine Aspartate
NH 2 O-
S
CH 3 CH 3 OH
O O
N
NH
Isoleucine Cysteine Threonine Proline Glutamate Arginine
NH 2
O-
CH 3
SH N CO2- N NH 2
H2 O H
OH

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