BIOLOGY – PROTEINS AND NUCLEIC ACID

PROTEINS • ✹ Asparagine
• ✥Also known as polypeptides
• ✥ Polymers of amino acids ✹ Aspartic acid
• ✥ Most diverse type of biomolecule in the • ✹ Cysteine
body
AMINO ACIDS ✹ Glutamic acid
• ✥ A monomer
• ✹ Glutamine
• ✥ Building blocks of protein
• ✥ C,H,O,N
FUNCTIONS ✹ Glycine
❖ Metabolism – ENZYMES – BIOLOGICAL • ✹ Proline
CATALYSTS EG. LIPASE, AMYLASE,
pepsin ✹ Serine
❖ Messenger/Receptors – HORMONES EG. • ✹ Tyrosine
GABI, ADH, LTH, Oxytocin,
norepinephrine/epinephrine
❖ Defense - ANTIBODIES EG. IG
❖ Structural Support – KERATIN,
COLLAGEN, ELASTIN,
❖ Homeostasis - PH LEVEL, FLUID
BALANCE EG. ALBUMIN, GLOBULIN, Na -
K+ Pump
❖ Transport and Storage – CHANNEL
PROTEINS EG. Calcium channels,
HEMOGLOBIN, GLUT, LIPOPROTEINS,
FERRITIN STRUCTURE OF AMINO ACID
❖ Provides Energy
❖ Movement- Actin & Myosin, Cilia & Flagella
❖ Growth and Maintenance of Tissues-
HGH
bradykinin
fibrin & fibrinogen
ESSENTIAL AMINO ACIDS
• ✹ Histidine
THE PEPTIDE BOND
✹ Isoleucine
 CARBOXYL GROUP + AMINO
• ✹ Leucine GROUP FORM A STRONG
✹ Lysine COVALENT BOND RELEASING
• ✹ Methionine WATER IN THE PROCESS = A
✹ Phenylalanine CONDENSATION REACTION (THE
• ✹ Threonine REVERSE IS HYDROLYSIS)
✹ Tryptophan  AMINO ACIDS JOIN TOGETHER IN
A LONG CHAIN: N TERMINAL END
• ✹ Valine TO C TERMINAL END = A
NON- ESSENTIAL AMINO ACIDS POLYPEPTIDE.
• ✹ Alanine

✹ Arginine
BIOLOGY – PROTEINS AND NUCLEIC ACID

PARALLEL AND ANTIPARALLEL B

SHEETS
• MULTI -STRAND INTERACTIONS
ARE CALLED SHEETS.
• SHEETS ARE HELD TOGETHER BY
THE HYDROGEN BONDING OF
AMIDE AND CARBONYL GROUPS
OF THE PEPTIDE BOND FROM
OPPOSITE STRANDS.

SECONDARY STRUCTURE
◆ localized conformations of the polypeptide
TERTIARY STRUCTURE
backbone
the complete folding pattern of an entire
TWO REGULAR ARRANGEMENTS ARE:
polypeptide chain
• THE  HELIX
❖ Stabilized by numerous weak interaction
– STABILIZED BY
HYDROGEN BONDS between amino acid side chains
BETWEEN NEARBY  largely hydrophobic and polar
RESIDUES interactions
• THE  SHEET  can be stabilized by disulfide
– STABILIZED BY bonds
HYDROGEN BONDS Two major classes:
BETWEEN ADJACENT fibrous and globular (water or lipid) soluble
SEGMENTS THAT MAY NOT Globular proteins – soluble, irregular
BE NEARBY sequence
• IRREGULAR ARRANGEMENT OF Ex. Hemoglobin
THE POLYPEPTIDE CHAIN IS myoglobin
CALLED THE RANDOM COIL. albumin
enzymes
• Fibrous proteins –insoluble, repetitive
sequence
BIOLOGY – PROTEINS AND NUCLEIC ACID

Ex.
• Collagen
• Keratin
QUATERNARY STRUCTURE
• the way multiple polypeptide subunits
come together to form a larger protein
BIOLOGY – PROTEINS AND NUCLEIC ACID

PROTEIN • the  helix

Prōteios – stabilized by hydrogen bonds
“holding first place” between nearby residues
LEVELS OF PROTEIN ORGANIZATION • the  sheet
• primary structure – stabilized by hydrogen bonds
• secondary structure between adjacent segments that
• tertiary structure may not be nearby
• quaternary structure • Irregular arrangement of the polypeptide
FUNCTIONS chain is called the random coil.
• enzyme The  Helix
• receptors • Helical backbone is held together by
• hemoglobin hydrogen bonds between the backbone
• muscle and organ tissue amides of an n and n + 4 amino
AMINO ACIDS
acids.
• C, H, O, N
Primary Structure: The Peptide Bond • It is a right-handed helix with 3.6
 linear sequence of amino acids residues (5.4 Å) per turn.
 the sequence of amino acids in a protein, • Peptide bonds are aligned roughly
is like the order of letters in a long word parallel with the helical axis.
• Side chains point out and are roughly
perpendicular with the helical axis.
 Sheets
• The planarity of the peptide bond and
tetrahedral geometry of the  carbon
create a pleated sheet-like structure.
• Sheet-like arrangement of the backbone
is held together by hydrogen bonds
between the backbone amides in
different strands.
• Side chains protrude from the sheet,
alternating in an up-and-down direction.
Parallel and Antiparallel b Sheets
• Multi -strand interactions are called
sheets.
• Sheets are held together by the hydrogen
bonding of amide and carbonyl groups
of the peptide bond from opposite
strands.
• Two major orientations of  sheets are
determined by the directionality of the
strands within:
– Parallel sheets have strands that
are oriented in the same
direction.
– Antiparallel sheets have strands
Secondary Structures
that are oriented in opposite
• Secondary structure refers to a local
spatial arrangement of the polypeptide directions.
backbone. In parallel  sheets, the H-bonded strands run in
• Two regular arrangements are common: the same direction.
BIOLOGY – PROTEINS AND NUCLEIC ACID
• Hydrogen bonds between
strands are bent (weaker).
Quaternary Structure
Amino acids
Types of amino acids
In antiparallel  sheets, the H-bonded strands
run in opposite directions.
• Hydrogen bonds between
strands are linear (stronger).
Tertiary Structure
• Tertiary structure refers to the s overall
spatial arrangement of atoms in a
protein.
• Stabilized by numerous weak interaction
between amino acid side chains
• largely hydrophobic and polar
interactions
• can be stabilized by disulfide
bonds
• Two major classes:
• fibrous and globular (water or
lipid soluble)
A quaternary structure is formed by the
assembly of individual polypeptides into a
larger functional cluster.
amino group, carboxyl group, hydrogen
and a variable side group (residue) each
joined to a central carbon atom
Amino end and carboxyl end can be ionised
NH3+ and COO- to give acidic and basic
characteristics
• At pH 7 both groups are ionised
• The residues are side chains which give
the individual properties to the amino
acid (acidic, basic, neutral and
nonpolar).
• 20 different amino acids used in
protein synthesis though others do occur
in nature
The peptide bond
 Carboxyl group + amino group form a
strong covalent bond releasing water in
the process = a condensation reaction
(the reverse is hydrolysis)
 Amino acids join together in a long
chain: N terminal end to C terminal end
= a polypeptide.
BIOLOGY – PROTEINS AND NUCLEIC ACID

NUCLEIC POLYMER
NUCLEIC ACIDS Backbone
Information Storage sugar to PO4 bond
• Function: new base added to sugar of previous
store & transmit genetic information base
• Examples: polymer grows in one direction
RNA (ribonucleic acid) (rRNA, mRNA, tRNA) N bases hang off the sugar-phosphate
backbone
DNA (deoxyribonucleic acid)
DNA molecule
ATP (adenosine triphosphate)
Double helix
Supplies energy for synthetic reactions and for H bonds between bases join the 2 strands
other energy-requiring processes in cells Adenine:: Thymine
• Structure: (A-T)
monomers = nucleotides Cytosine:: Guanine
Polymers = polynucleotides (DNA, RNA) (C-G)
Nucleotides
3 parts RNA
nitrogen base (C-N ring) A-U (Uracil)
pentose sugar (5C) G-C
ribose in RNA INFORMATION POLYMER
Function
deoxyribose in DNA
series of bases encodes information like
phosphate (PO4) group
the letters of a book stored information is passed
RNA & DNA from parent to offspring need to copy accurately
RNA stored information = genes (genetic information)
• single nucleotide chain PROTEIN SYNTHESIS
DNA  The Making of Protein
• double nucleotide chain Quick Protein Review
• N bases bond in pairs
across chains  A chain of amino acids is a protein.
• spiraled in a double helix  Protein is a macromolecule or polymer.
 Proteins an organic molecule with
C,H,O,N.
 Monomer of protein is amino acid.
 There are 20 amino acids, found in food.
 Ribosomes make protein.
 Proteins make up structural and
functional
BIOLOGY – PROTEINS AND NUCLEIC ACID

components of the cell.

Protein structure is determined by the genetic
code in your DNA. The section of DNA that
codes for one protein is called a GENE
• A gene is a section of DNA that
determines the sequence of amino
acids in a protein.
• Therefore, the gene determines the
shape and therefore, the function of the
protein it codes for.

1. Transcription complete!
2. mRNA receives message
Step One: Transcription
(Trans = across, scription = to write)
The coded message of a gene on DNA has
specific instructions on how to make each
particular protein that our bodies need
The instructions from a gene are copied from
DNA to messenger RNA (mRNA) in the
nucleus
Then, the mRNA moves through the nuclear
pores and into the cytoplasm where the proteins
are made.
• The process of making mRNA is called
TRANSCRIPTION
Enzymes involved!
Step 1: Helicase unwinds the DNA (starting at
the promoter).
Step 2: Complementary RNA base pairs attach
to form the mRNA strand
Step 3: RNA polymerase forms the RNA sugar-
phosphate backbone and checks for mistakes
Step 4: The RNA detaches & leaves the
nucleus, & the DNA winds back up
BIOLOGY – PROTEINS AND NUCLEIC ACID

Why a Triplet Code?

It takes 3 nucleotides on the mRNA to code for
1 amino acid
Why?
We must code for 20 different amino acids and
there are only 4 letters (nucleotides) in the DNA
alphabet.
With a single nucleotide, there are only 4
possible codes (41).
For two nucleotides, there are only 16 possible
codes (42).
However, for three nucleotides there are 64
possible codes (43), and that is enough to code
for the 20 amino acids.
Step 2: Translation
Step Two: Translation
• The written code (codons) on mRNA is
· The mRNA code is made up of groups of three
‘translated’ into a specific amino acid
nucleotide bases known as codons. Each codon
sequence by ribosomes in the
codes for a specific amino acid. Use the
cytoplasm.
CODON Chart provided.
• This is carried out with the help of
relatively small transfer RNA (tRNA)
molecules.
A tRNA molecule is a small piece of RNA
that has a specific amino acid attached to
it.
BIOLOGY – PROTEINS AND NUCLEIC ACID

The tRNA also has a special sequence of 3

nucleotide bases known as an anticodon.
There is at least one type of tRNA for each of
the 20 amino acids.

As the correct amino acids are brought to the

ribosome by the tRNAs, they are joined together
by Peptide Bonds to form the protein that the
original DNA coded for.

4. TERMINATION: The last codon on any

mRNA molecule is called the ‘TERMINATOR’
codon, which is a message to STOP translation.
This codon will be either UAA, UAG, or UGA.

None of these have a matching tRNA anticodon,

so when no more tRNA’s attach, the ribosome,
protein, and mRNA detach from each other.

There are 2 types of MUTATION:

1. Chromosomal mutations: a mutation

of all or part of a chromosome.
This usually involves MANY GENES,
and therefore, MANY PROTEINS.
Example: Down’s syndrome.
2. Gene mutations: a mutation that occurs
within a gene at some point along a
chromosome. This mutation is only a
change of 1 or a few ‘letters’
(nitrogenous bases).
It usually only affects ONE GENE, and
therefore, ONE PROTEIN.
Example: Sickle cell anemia.