IPS1-Introduction to Nucleic Acids p1

RNA

[RNA / DNA]

Nitrogenous bases: A, G, C, U (Adenine, Guanine, Cytosine, Uracil)

DNA

[RNA / DNA]

Nitrogenous bases: A, G, C, T (Adenine, Guanine, Cytosine, Thymine)

RNA

[RNA / DNA]

Sugar: Ribose

DNA

[RNA / DNA]

Sugar: Deoxyribose

[RNA

[RNA / DNA]

Structure: Single helix

DNA

[RNA / DNA]

Structure: Double helix

RNA

[RNA / DNA]

Example sequence: UGCAUGGCAUUU GAC UCG GCU

DNA

[RNA / DNA]

Example sequence: ACGTACCGTAAA CTG AGC CGA

2 hydrogen bonds

[Complementary Base Pairing]

Adenine (A) pairs with Thymine (T) in DNA via _____ hydrogen bonds

3 hydrogen bonds

[Complementary Base Pairing]

Guanine (G) pairs with Cytosine (C) via _____ hydrogen bonds

Uracil (U)

[Complementary Base Pairing]

In RNA,____ replaces Thymine (T)

Nucleic acids

_____- are unbranched polymers made up of repeating units called nucleotides.

nucleotides

Nucleic acids are unbranched polymers made up of repeating units called____

• DNA (Deoxyribonucleic Acid)

• RNA (Ribonucleic Acid)

Two main types of nucleic acids such as ____

DNA

[RNA / DNA]

____- 

• Stores the genetic information of an organism.

• Transmits that information from one generation to the next.

RNA

[RNA / DNA]

____- 

• Tanslates the genetic code from DNA.

• Helps produce proteins necessary for all cellular functions.

two polynucleotide chains

DNA is made up of ____ chains

nucleotides

Each polynucleotide chain of DNA contains____

nucleotides

____- are the monomer units of DNA and other related nucleic acids.

• Nitrogenous base

• Monosaccharide

• Phosphate group

Each Nucleotide Consists of Three Parts such as ___ 

Adenine 

[Identify the Purine Base Structure]

Guanine 

[Identify the Purine Base Structure]

Cytosine

[Identify the Pyrimidine Base Structure]

Uracil

[Identify the Pyrimidine Base Structure]

Thymine 

[Identify the Pyrimidine Base Structure]

Thymine (T)

[Pyrimidine]
In DNA, ____ pairs with Adenine (A).

Uracil (U)

[Pyrimidine]

In RNA,_____ replaces Thymine and pairs with Adenine (A) instead.

• D-2-deoxyribose

• Aldopentose

In DNA

• The monosaccharide (sugar) is____ [2]? 

aldopentose

____- is a a five-carbon sugar with an aldehyde group

True

[T/F]

Both DNA and RNA contain a five-carbon sugar (aldopentose).

• D-ribose

• D-2-deoxyribose (which lacks one oxygen atom (hence “deoxy”).

Both DNA and RNA contain a five-carbon sugar (aldopentose).

• In RNA, the sugar is ____.

• In DNA, the sugar is  _____

Nucleotide

_____- are different from nucleosides , which consist of nitrogenous base and sugar

Nucleoside

_____- is formed by joining the 1’ carbon of the monosaccharide with an N atom of the base

UNDERSTAND ONLY

Naming Nucleosides Derived from Pyrimidine Bases

Use the suffix “-idine  

Example: 

• Thymine → Thymidine (Nucleoside)

• Uracil → Uridine (Nucleoside)

• Cytosine → Cytidine (Nucleoside)

UNDERSTAND ONLY

Naming Nucleosides Derived from Purine Bases

Use the suffix “-osine”

Example: 

• Guanine → Guanosine (Nucleoside)

• Adenine → Adenosine (Nucleoside)

UNDERSTAND ONLY

For Deoxyribonucleosides

Add the prefix “deoxy”

Example:

• Deoxyadenosine

• Deoxycytidine

Phosphate group

Nucleotides are formed by adding a _____ group to the 5-OH of a nucleoside

Nucleotides

____- are formed by adding a phosphate group to the 5-OH of a nucleoside

polymer

Nucleic acids (DNA and RNA)  are _____ [polymer / monomer]

Nucleic acids (DNA and RNA) 

_______- are polymers of nucleotides joined by phosphodiester linkages.

phosphodiester linkages

Nucleic acids (DNA and RNA)  are polymers of nucleotides joined by_____ linkages

[Nucleic Acid]

_____ [type of bond] join the 3′- carbon of one sugar to the 5′-carbon of the next sugar.

• two polynucleotide chains

• hydrogen bonds

Each DNA molecule is composed of _____ polynucleotide chains joined by _____ between the bases

thymine

[DNA DOUBLE HELIX]

Adenine on one chain forms a base pair with______ on the other chain.

cytosine

[DNA DOUBLE HELIX]

Guanine base pairs with ____

• Watson and Crick

• Maurice Wilkins

• Rosalind Franklin

People Respnsible for the Discovery of DNA

Watson and Crick

_____- known for proposing the model of the DNA double helix, which explained the structure of DNA and how genetic information is stored and replicated.

• 5′ TO 3′

• 3′ TO 5′

Antiparallel strands of DNA [2]

True

[DNA DOUBLE HELIX]

[T/F]

Molecule is twisted to form a helix with major and minor grooves

spiral staircase

[DNA DOUBLE HELIX]

[T/F]

Two strands are stacked like  a _____  in the interior of the  molecule

outside

[DNA DOUBLE HELIX]

The phosphate group are on the _____ [outside / inside] of the double helix

phosphodiester bonds

[DNA DOUBLE HELIX] 

Two acidic groups of each phosphate are involved in ____

negative charge

[DNA DOUBLE HELIX] 

• Two acidic groups of each phosphate are involved in phosphodiester

The third group is free and dissociates its proton at physiologic pH, giving the molecule a ____[positive / negative] charge

B form

[Form of DNA]

The ______ form of DNA, first described by Watson and Crick, is right-handed and contains 10 base pairs per turn, with each base pair separated by 3.4 A

A form

[Form of DNA]

______- is similar to the B form but more compact

Z form

[Form of DNA]

______- 

• Is lefthanded

• Has its bases positioned more toward the periphery of the helix.

• A form

• B form

Common form of DNA [2]

Z form

Less common form of DNA

Denaturation

Alkali or heat causes the strands of DNA to separate but does not break phosphodiester bonds.

A.) Denaturation

B.) Renaturation

C.) Hybridization

B.) Renaturation

If strands of DNA are separated by the heat and then the temperature is slowly decreased under the appropriate conditions, base pairs re-form and complementary strands of DNA come back together.

A.) Denaturation

B.) Renaturation

C.) Hybridization

C.) Hybridization

A single strand of DNA pairs with complementary base sequences on another strand of DNA or RNA

A.) Denaturation

B.) Renaturation

C.) Hybridization

chromatin

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

In eukaryotic cells, _____ is made of DNA wrapped around proteins called histones in structures called nucleosomes.

histones

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

In eukaryotic cells, chromatin is made of DNA wrapped around proteins called _____in structures called nucleosomes.

nucleosomes

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

In eukaryotic cells, chromatin is made of DNA wrapped around proteins called histones in structures called _______

Histones

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

______- are small, basic proteins rich in arginine and lysine.

True

[T/F]

• Prokaryotes don’t have histones

octamer

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

Eight histone proteins form a group called an_____

140 DNA bases

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

Eight histone proteins form a group called an octamer, and about ____ DNA bases wrap around it to make the nucleosome core.

nucleosome core

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

Eight histone proteins form a group called an octamer, and about 140 DNA bases wrap around it to make the______core

H1

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

The DNA connecting one nucleosome to the next is wrapped with another histone called _____

solenoid structures (helical, tubular coils)

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

The “beads on a string” nucleosomal structure of chromatin is further compacted to form______

solenoid structures

[PACKING OF DNA IN THE NUCLEUS OF EUKARYOTIC CELLS]

____structure have helical, tubular coils that help organize and tightly pack the DNA within the nucleus.

• ribose

• uracil

[STRUCTURE OF RNA]

The polynucleotide structure of RNA is similar to DNA except that RNA contains sugar ______ rather than deoxyribose and ______ rather than thymine.

• single-stranded

• double-stranded

[STRUCTURE OF RNA]

In addition,

• RNA is generally  ____ [single-stranded / double-stranded] 

• DNA is generally   ____ [single-stranded / double-stranded] 

True 

[T/F]

• RNA, like proteins, can have enzymatic activity

• Messenger RNA (mRNA)

• Transfer RNA (tRNA)

• Ribosomal RNA (rRNA)

Types of RNA [3]

Ribozymes

____- are usually precursors of rRNA

Ribozymes

____- can remove internal segments of their own sequence and splice the ends together.

Example – CAU CCU ACC GCU GGG GCC

ribonucleases

RNAs also act as____ cleaving (cutting of) other RNA molecules

 Example: RNase P cleaves tRNA precursors

Peptidyl transferase 

____- is an enzyme involved in protein synthesis, is made up of RNA rather than protein.

• Cap structure 

• Poly (A) Tail 

Eukaryotic mRNA contains ___  and a ____, and is synthesized in the NUCLEUS 

Nucleus

Eukaryotic mRNA contains cap structure and a  Poly(A) Tail , and is synthesized in the____

cap

___- is a special modified guanine (with a methyl group) attached to the start (5′ end) of the mRNA

poly(A) tail

____- is a string of up to 200 adenine (A) bases added to the end (3′ end) of the mRNA.

True

[T/F] 

rRNA contains many loops and extensive base-pairing

Svedberg units (S)

rRNA molecules have different sizes, measured in ____, and combine with proteins to make ribosomes.

Bacterial ribosomes

[Type of Ribosome]

____- are called 70S, made of a 50S large and 30S small part

Eukaryotic ribosomes

[Type of Ribosome]

____- are 80S, made of a 60S large and 40S small part

Prokaryotes

[Eukaryotes / Prokaryotes]
____- have three types of rRNA: 16S, 23S, and 5S, plus 55 proteins.

Eukaryotes

[Eukaryotes / Prokaryotes]

_____- have four types of rRNA: 18S, 28S, 5S, and 5.8S, plus 83 proteins

80 nucleotides 

[tRNA / mRNA]

____-structure are relatively small ,containing about ____ nucleotides 

tRNA

[tRNA / mRNA]

Adapter molecules that act in protein synthesis

tRNA

[tRNA / mRNA]

Read the information encoded in the mRNA

tRNA

[tRNA / mRNA]

Transfer the appropriate amino acid to a growing polypeptide chain during protein synthesis

True

[T/F]

In eukaryotic cells, many parts of tRNA are changed

• pseudouridine (ψ)

• dihydrouridine (d)

• ribothymidine (t)

Most tRNAs have special modified parts called ___ [3]

True

[T/F]

All tRNA molecules share the same overall cloverleaf structure, even though their base sequences differ

D loop 

[tRNA Molecule]

The first loop is called ___ 

dihydrouridine

[tRNA Molecule]

The first loop (called the D loop) has _____

anticodon

[tRNA Molecule]

The middle loop has the ____ , which matches with the mRNA codon