Bio 161 W2 - Nucleic Acids

What is a nucleic acid?

a macromolecule that stores and transmits genetic information (DNA & RNA)

• a string of nucleotides

DNA & RNA make up

the human genetic material for life

• DNA & RNA can be found in nucleus

What are the two main nucleic acids found in humans?

DNA & RNA

What is the function of DNA

long term storage of genetic information

What is the function of RNA

involved in gene expression

What is a karyotype?

organized display of chromosomes

• we have 23 pairs of chromosomes

What is the utility of a karyotype?

Detect genetic disorders, determine sex, identify chromosomal abnormalities

Nucleic acids can

un-spool chromosomes

What is a nucleotide?

base subunit of nucleic acids

What are the three components of a nucleotide?

• Phosphate group

• 5 carbon sugar (ribose or doexyribose)

• Nitrogenous base

What is a nitrogenous base?

the base component (A, T, C, U, G)

What is a nucleoside?

nitrogenous base + 1’ carbon sugar (ribose/deoxyribose)

What is a nucleotide?

nitrogenous base + sugar + phosphate group(s)

What attaches to the 1’ carbon?

nitrogenous base

What attaches to the 5’ carbon?

phosphate group

What is special about the 3’ carbon?

has -OH group used in polymerization

difference in ribose & deoxyribose?

Ribose (in RNA) has OH at 2′; deoxyribose (in DNA) has H at 2′

ribose has

(in RNA) an OH at the 2’ carbon

deoxyribose

(in DNA) an H at the 2’ carbon

What is a purine?

• Double ring nitrogenous bases

• Adenine (A) & Guanine (G)

• Pure As Gold

What is a pyrimidine?

• Single ring nitrogenous bases

• Cytosine (C), Uracil (U), Thymine (T)

Which bases are in DNA?

Adenine (A), Guanine (G), Cytosine (C), & Thymine (T)

Which bases are in RNA

Adenine (A), Guanine (G), Cytosine (C), Uracil (U)

What is a nucleobase

• nitrogenous base alone

• Adenine, Guanine, Thymine, Cytosine, Uracil

What is the naming pattern from nucleobase —> nucleoside —> nucelotide

base alone —> base + sugar —> base + sugar + phosphate group(s)

How are purine nucleosides named?

end in -osine (adenosine, guanosine)

How are pyrimidine nucleosides named?

end in -idine (cytidine, thymidine, uridine)

What is adenine (nucleobase) called when it becomes a nucleoside? (based linked to 1’ sugar)

Adenosine

What is guanine (nucleobase) called when it becomes a nucleoside? (based linked to 1’ sugar)

guanosine

What is cytosine (nucleobase) called when it becomes a nucleoside? (based linked to 1’ sugar)

cytidine

What is thymine (nucleobase) called when it becomes a nucleoside? (based linked to 1’ sugar)

thymidine

What is uracil (nucleobase) called when it becomes a nucleoside? (based linked to 1’ sugar)

uridine

What does AMP stand for?

Adenosine monophosphate (nucleotide)

What does ADP stand for?

Adenosine diphosphate (nucleotide)

What does ATP stand for?

Adenosine triphosphate (nucleotide)

How are DNA nucleotides distinguished in naming?

Include “deoxy” (e.g., deoxyadenosine)

What does dATP stand for?

Deoxyadenosine triphosphate

What is the difference between ATP and dATP?

ATP has ribose (RNA, -OH 2’C); dATP has deoxyribose (DNA, -H 2’C)

If you see “adenosine,” what components are present?

Adenine + ribose (no phosphate)

If you see “adenosine triphosphate,” what components are present?

Adenine + ribose + three phosphates

What are the 5 nucleoside? (nucleobase linked to 1’ C sugar)

Adenosine, Guanosine, Cytidine, Thymidine, Uridine

What bond links nucleotides?

Phosphodiester bond/linkage

• through condensation reaction (water released)

Between which carbons does a phosphodiester bond/linkage form?

3′ OH and 5′ phosphate

What is the direction of nucleic acid synthesis?

5′ → 3′

• polymerization is directional only on 3’ end (adding to this end)

polymerization

small molecules, called monomers, react and link together to form long, chain-like, or network molecules known as polymers

Nucleic acids have an overall…

• NEGATIVE charge

• polar, can dissolve in water

What makes up the backbone of nucleic acids?

Sugar-phosphate backbone

Does this polymerization of nucleotides linked to form polynucleotide chain lead to an increase or decrease in entropy?

• DECREASES’

• many individual free floating molecules bonded together & lose ability to move independently, polymer more ordered & overall change in entropy is negative

What provides energy for nucleotide polymerization?

Nucleoside triphosphates (ATP, GTP, etc.)

Why are phosphates important?

• Their removal releases energy to drive reactions

Triphosphates have..

Triphosphates have increased Potential Energy!

Entropy of Polymerization: Does the process of linking nucleotides into DNA/RNA chain represent increase or decrease in entropy?

• decrease in entropy

• free-floating independent molecules move to single/organized rigid chain —> reduces disorder

Entropy of Polymerization: In context of nucleotide triphosphates, what represents clamped spring & why?

• the three phosphate groups

• all negatively charged, repel each other strongly

• holding them together stores high chemical potential energy —> released when bond is broken

What did Chargaff discover?

A = T and G = C

What did Franklin & Wilkins discover?

DNA is helical with specific dimensions

Who proposed the double helix model?

Watson and Crick

What does antiparallel mean?

Strands run in opposite directions (5′→3′ and 3′→5′)

Why is antiparallel important?

Allows proper base pairing and stability

What are base-pairing rules?

1) Directional 5’—>3’

2) A–T (2 H-bonds), G–C (3 H-bonds)

3) Antiparallel

What is the primary structure of nucleic acids?

The linear sequence of nucleotides connected by phosphodiester bonds

What specifically is included in the primary structure of nucleic acids?

The order of bases (A, T/U, G, C) along the 5′ → 3′ backbone

Why is primary structure of nucleic acids important?

It stores genetic information and determines higher-level structures

What type of bonds stabilize primary structure of nucleic acids?

Covalent phosphodiester bonds

What does 5′ → 3′ directionality refer to in primary structure?

The orientation of the sugar-phosphate backbone from 5′ phosphate to 3′ OH

What is the secondary structure of DNA?

A double helix formed by two antiparallel strands with complementary base pairing

What interactions stabilize DNA secondary structure?

Hydrogen bonds between bases and base stacking interactions

What is complementary base pairing?

Specific pairing: A–T (or A–U in RNA), G–C

What does antiparallel mean in DNA?

The two strands run in opposite directions (5′→3′ and 3′→5′)

Why is antiparallel orientation necessary?

It allows proper hydrogen bonding and stable helix formation

What is the secondary structure of RNA?

• Single stranded, folding with itself: stem-loop

• Intramolecular base pairing forming structures like hairpins and stem-loops

Why can RNA form secondary structures within a single strand?

Because complementary bases can pair within the same molecule

What is the tertiary structure of DNA?

The 3D folding and supercoiling of the double helix into compact forms

How is DNA packaged in cells (tertiary structure)?

DNA wraps around histone proteins = nucleosomes → chromatin → chromosomes

Tertiary Structure: Chromosomes

• composed of condensed chromatin, a complex of DNA,RNA & proteins

• DNA is wrapped around histones (protein) in a ‘bead- on-a-string’ format, yielding multiple nucleosomes

What is a nucleosome?

DNA wrapped around histone proteins

what is chromatin

a complex of DNA,RNA & proteins

How is RNA different from DNA structurally?

Single-stranded, ribose sugar, uracil instead of thymine

Why is RNA less stable than DNA?

Has OH group at 2′ carbon

RNA: Tertiary Structures

Increase uses for nucleotides: —> Information Catalysis (ribozymes) Regulation

What does mRNA do?

Carries genetic code to ribosome (protein)

What does tRNA do?

Brings amino acids to ribosome (protein)

What does rRNA do?

Forms ribosome and catalyzes peptide bonds

What is a ribozyme?

RNA molecule that acts as an enzyme

How do RNA enzymes differ from protein enzymes?

• RNA uses base pairing

• proteins use diverse side chains and are more efficient

How does nucleic acid tertiary structure compare to protein tertiary structure?

Both involve 3D folding, but DNA is more uniform while proteins have diverse shapes based on amino acid interactions

Which level of structure of nucleic acids directly determines genetic information?

Primary structure

Which level of structure of nucleic acids involves base pairing?

Secondary structure

Which level of structure involves overall 3D folding and packaging of nucleic acids?

Tertiary structure

Why is DNA more structurally stable than RNA?

Double-stranded structure and lack of 2′ OH group

Why is RNA more versatile structurally?

Single-stranded → can fold into many shapes (functional diversity)