SESSION 2

DNA, RNA, AND Rio Hermantara

PROTEIN STRUCTURES
GOOD
MORNING/AFTERNOON!
Don’t forget to
➢ Check-in ACIS
 SESSION LEARNING
OUTCOMES
Session Learning - Able to describe the biochemistry of DNA, RNA, and protein
Objectives - Able to differentiate the organization of DNA in prokaryotes and
eukaryotes

Describe the basic role of each cellular biology components and its
CLO2
synergy to function

Define primary molecular biology components: DNA, RNA and

CLO3
Protein.
PRE-WATSON-CRICK’S
MODEL (PRE-1953)
Chargaff’s law
1. Composition of DNA
(bases) varies among
species → nucleotides
do not repeat in the
same order (see later)
2. The amount of A = T
amount of C = G
 OTHER DNA MODELS
Tetranucleotide
model
Triple-helix model

Linus Pauling’s Triple-helix model

https://www.youtube.com/watch?v=pR0zwrLSai4
 DISCUSSION
ROOM
1. They describe what is wrong with
Pauling’s and Frasser’s model
2. Helical chains (while describe the
phosphate backbone)
3. Agreeing with Furberg’s model No. 1
(bases are in the inside of the helix).
4. Water content affects the
conformation of DNA structure
5. Purine & pyrimidine base pairing is
what holds the structure together =
Chargaff’s law
6. Hypothesized that there is a copying
mechanism
 THE Youtube video link:
STRUCTURE https://www.youtube.com/watch?v=o_-6JXLYS-k
OF DNA
 DISCUSSION ROOM

WHAT DID WE LEARN FROM THE

VIDEO?
❖ dsDNA = double helix
❖ Most common form of DNA = B-form DNA
❖ Polynucleotide > nucleotide > sugar + phosphate + base (A, T, G, C)
❖ Location of base and phosphate to deoxyribose pentose sugar (carbon
numbering)
❖ Orientation of strands
❖ Hydrogen bonds between bases (A-T ; G-C)
❖ Double helix structure
❖ Major and minor grooves
DEOXY-RIBONUCLEIC ACID AND
PHOSPHATE BACKBONE
Poly-nucleotide chain

C5
C4 C1
C3 C2
DNA BASE PAIRING
THE DOUBLE HELICAL STRUCTURE –
BASE STACKING
ALTERNATIVE
DNA
STRUCTURE
DNA SUPERCOILING
(CIRCULAR DNA)
5 MIN BREAK
RNA BUILDING BLOCKS:
RIBO-NUCLEIC ACIDS
 DISCUSSION ROOM

Watch-along video:
https://www.youtube.com/watch?v=w9VsBW6D
Q7o
RNA
STRUCTURES Knowing the RNA structure (and the similarities
of DNA), what chemical properties does an RNA
has?
 RNA SECONDARY STRUCTURES

Conventiona
l base Nonconvention
pairing al base pairing
KINETICS OF RNA FOLDING
 DISCUSSION ROOM

TYPES OF RNAs
EXAMPLE: RELATIONSHIP AMONG FIVE
MAJOR RNAs DURING GENE EXPRESSION
VARIOUS RNA FUNCTIONS
1. RNA can serve as a “scaffold.” An RNA molecule may act as a scaffold or
framework upon which proteins can be assembled.
2. RNA–protein enzymes = ribonucleoprotein (RNPs). Example: telomerase,
where the RNA serves as the template for the addition of
deoxynucleoside triphosphates (dNTPs) by the reverse transcriptase
protein. In contrast, in other catalytic RNPs, such as ribonuclease
(RNase) P and the ribosome, the RNA is catalytic, not the protein.
3. RNA molecules termed “ribozymes” can catalyze a number of the
chemical reactions that take place in living cells
4. Small RNAs can directly control gene expression (riboswitches, RNAi,
etc)
5. RNA can be the hereditary material (for viruses)
RIBOZYMES
 5 MIN
BREAK
AMINO ACIDS
 Watch-along:
Protein structure overview (3:38)
https://www.youtube.com/watch?v=qBRFIMcxZ
PROTEIN NM
STRUCTURE
What is a protein? (6:57)
https://www.youtube.com/watch?v=wvTv8TqW
C48
 DISCUSSION ROOM

WHAT DO POLYPEPTIDES DO?

Non-covalent bonds of amino acids → drives protein conformations

PROTEIN STRUCTURE
(CONFORMATION) DETERMINE ITS
CHEMISTRY
MOST COMMON FOLDING PATTERNS
OF PROTEINS
α-helix β-sheet
 PROTEIN DOMAINS – ASSOCIATES
WITH FUNCTION
“a substructure produced by any contiguous part of a polypeptide chain that can fold
independently of the rest of the protein into a compact, stable structure”

Ribbon model Space-fill model

CONSERVED PROTEIN DOMAINS
BETWEEN PROTEINS
COMPLEX LARGE PROTEIN: MULTIPLE
POLYPEPTIDE FIBROUS PROTEIN
STRUCTURE
Globular protein = Src protein previously discussed
Fibrous proteins
Membrane protein
 DISCUSSION ROOM

TERTIARY STRUCTURE
DISULFIDE BOND (A COVALENT
BOND TO STABILIZE PROTEINS)
 DISCUSSION ROOM

PROTEIN AS BUILDING BLOCKS TO

FORM QUATERNARY STRUCTURE
PROTEIN
ASSEMBLIES -
CAPSID ASSEMBLY
OF A VIRUS
 LEVELS OF
PROTEIN
STRUCTURE
• Primary structure: the amino
acid sequence
• Secondary structure: the
conformation due to rotations
around C-C and C-N single
bonds
• Tertiary structure: the folding of
the peptide chain into its
characteristic 3D-shape
• Quaternary structure: the
aggregation of several subunits
held together by other than
covalent bonds (not all peptides
have this feature)