Nucleic Acids and

Protein Synthesis

THE FUNCTIONS OF DNA

DNA has three roles/purposes/functions: 1. Storing information – genes are

segments of DNA that carry messages to make proteins.

2. Copying information – so that when cells divide, all cells get a complete copy of the genetic material.

3. Transmitting information – DNA is passed from parents to offspring.

THE STRUCTURE OF DNA

Nucleotides are the building blocks of DNA.

Each nucleotide contains a phosphate group, a five carbon sugar, and a nitrogen base. ◦ The five carbon sugar is

called deoxyribose. ◦ Covalent bonds hold the

sugar of one nucleotide to the phosphate group of another nucleotide to form chains.

THE STRUCTURE OF DNA

The full name of DNA is deoxyribonucleic acid.

Every nucleotide has the same sugar molecule and phosphate group, but each nucleotide contains one of four nitrogen bases. ◦ The four nitrogen bases that

make up DNA are adenine, thymine, guanine, and cytosine.

THE STRUCTURE OF DNA

Adenine and Guanine are called

purines. Purines have 2 rings of

carbon and nitrogen atoms.

Thymine and Cytosine are called

pyrimidines. Pyrimidines have a

single ring of carbon and nitrogen

atoms.

CHARGAFF’S RULE

1949-Erwin Chargaff showed that in DNA, the number of adenines equal the number of thymines, AND the number of cytosines equal the number of guanines. However, the amount of each nucleotide was not the same among different organisms.

Base-pairing / Chargaff’s rule:

◦ Adenine will always pair with Thymine; A and T are complimentary.

◦ Cytosine will always pair with Guanine; C and G are complimentary.

THE DNA MOLECULE IS A

DOUBLE HELIX

Rosalind Franklin and Maurice Wilkins used X

ray diffraction to take first picture of DNA.

Determined a two dimensional picture of DNA’s

structure.

James Watson and Francis Crick – 3-D shape

of DNA being 2 strands of nucleotides that form

a spiral staircase or double helix.

THE DNA MOLECULE IS A

DOUBLE HELIX

DNA is a twisted ladder with alternating patterns of phosphates and sugars making the sides of the ladder. ◦ Each rung is a purine/pyrimidine pair held together by hydrogen bonds.

THE DNA MOLECULE IS A

DOUBLE HELIX The base pair rules tell us what the rungs

can be, A and T or G and C.

Each strand of the double helix is complementary to each other; the sequence of 1 strand determines the sequence of the other.

The two strands of DNA in the double-helix are antiparallel – they run in opposite directions.

HOW DNA IS COPIED

DNA is double stranded – base pairing allows for easy copying; one strand serves as a template for a new strand.

DNA replication – the process of making a new DNA strand. ◦ Occurs before cells divide.

◦ Ensures that when cells divide, each cell produced has an entire copy of the organism’s DNA.

DNA double helix is unzipped by an enzyme called a helicase. Helicase breaks hydrogen bonds linking the nitrogen bases. ◦ Occurs at the replication forks of the double helix.

At the replication fork; an enzyme called DNA

polymerase moves along the strands, reading

the nitrogen base of each nucleotide, and

adding the complementary nucleotide to the

new strand. ◦ Remember that A and T are complimentary; C and G

are also complimentary.

HOW DNA IS COPIED

Telomeres – tips of chromosomes where DNA is hard to replicate. ◦ Telomerase – enzyme that adds repeated DNA

sequences to the ends of the chromosomes to prevent loss of the telomere DNA during DNA replication.

HOW DNA IS COPIED

Replication in prokaryotes– single circular chromosome; replication begins and proceeds from ONE location on the chromosome.

Replication in eukaryotes – many linear chromosomes; replication begins and proceeds from hundreds of locations on each chromosome.

HOW DNA IS COPIED

Gene – segment of DNA that codes for a protein.

Cells transfer the information found within the genes on DNA into a set of working instructions for use in building proteins.

This working set of instructions of the gene is called ribonucleic acid or RNA. ◦ RNA is a nucleic acid made of chains of nucleotides, just like DNA.

THE PATH OF GENETIC

INFORMATION

THE PATH OF GENETIC

INFORMATION

RNA is a single strand of nucleotides; DNA is

double stranded.

The sugar in RNA is a 5 Carbon sugar called

ribose; DNA’s sugar is deoxyribose.

RNA does not contain Thymine, but has replaced

Thymine with the base Uracil.

DNA compared to RNA

DNA RNA

How many strands?

2 1

Nucleotide subunit

Deoxyribose sugar

Ribose sugar

Bases Thymine (T) Adenine (A) Guanine (G) Cytosine (C)

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

Phos-

phate Group

Deoxy-ribose Sugar

Nitro-gen Base Phos-

phate Group

Ribose Sugar

Nitro-gen Base

T – A G – C

U – A G – C

THE PATH OF GENETIC

INFORMATION

Three forms of RNA are messenger RNA (mRNA),

transfer RNA (tRNA), and ribosomal RNA (rRNA).

All 3 RNA’s are responsible for processing the

information in a gene into protein. The process of

transferring the information in genes to proteins is

called gene expression.

THREE TYPES OF RNA

mRNA – used as a blueprint or template for a

protein; carries DNA’s information from the nucleus

to site of translation (ribosomes in cytoplasm).

tRNA – decodes mRNA into amino acid

sequences.

rRNA – RNA part of a ribosome’s structure (the

other component of ribosomes is protein).

Gene expression occurs in 2 stages. ◦ The first, transcription is where DNA is transferred to

mRNA.

◦ The second stage; translation, is when the information in

mRNA is used to make protein.

THE PATH OF GENETIC

INFORMATION

TRANSCRIPTION: MAKING RNA

Transcription takes place inside the nucleus.

Transcription begins when RNA polymerase binds to the beginning of a gene on a region of DNA.

TRANSCRIPTION: MAKING RNA

The region of DNA to which RNA polymerase

binds is called a promoter. Promoters are

sequences of DNA that act as a start signal.

The RNA polymerase begins to unzip and

separate the double helix.

The polymerase uses only one of the DNA

strands as a template for mRNA – The non-coding

or complimentary strand is the template for

mRNA synthesis.

TRANSCRIPTION: MAKING RNA

Follows the same base pairing rules as replication

except Uracil is used in place of Thymine.

RNA nucleotides are added one at a time in the

active site of the RNA polymerase.

DNA reforms the double helix following the RNA

Polymerase.

Transcription occurs at about 60 nucleotides per

second.

Terminator - the stop signal in the sequence of

DNA – RNA Polymerase detaches here.

TRANSCRIPTION: MAKING RNA

Coding DNA: CTC TTG ATC ATG

Non-coding/complimentary DNA:

GAG AAC TAG TAC

RNA: CUC UUG AUC AUG

http://207.207.4.198/pub/flash/26/transmenu_s.swf

Post –transcriptional mRNA processing

RNA editing - mRNA must be processed, or

prepared for the next phase of gene expression,

translation. ◦ Introns – non-coding gene regions that are cut out of the

RNA molecule in the nucleus.

◦ Exons – expressed sequences of the RNA molecule;

codes for a protein.

◦ The introns are cut out and the exons are spliced together to make a final mRNA.

Post –transcriptional mRNA processing

A protective cap and tail are then added before the mRNA leaves the nucleus through one of the pores and heads to the cytoplasm where translation will occur on ribosomes.

THE GENETIC CODE

Instructions on mRNA are written as a series of

three nucleotide sequences called a codon.

Each codon (set of three nucleotides) corresponds

to a certain amino acid or a stop signal. ◦ 64 possible codon combinations.

◦ Genetic code – collection of codons of mRNA, each of

which directs the incorporation of a particular amino acid

during protein synthesis.

Codon Table

START AND STOP CODONS

Start codon or initiator codon – AUG; cues the

start of translation by inserting a methionine. ◦ Thus, all proteins begin with the amino acid methionine.

Translation proceeds until a stop codon is

reached. ◦ Stop codon – triggers the end of translation.

TRANSLATION: MAKING PROTEINS

Translation – when ribosomes in the cytoplasm

use the sequence of codons in mRNA to assemble

amino acids into polypeptide chains.

tRNA is a single stranded RNA folded into a

compact shape with three loops. ◦ One loop has a three nucleotide sequence (called an

anticodon) that is complementary to one of the 64

codons.

◦ Each tRNA carries one amino acid.

TRANSLATION: MAKING PROTEINS

TRANSLATION: MAKING PROTEINS

tRNA bonds with mRNA at the codon/anticodon

site by hydrogen bonds. ◦ Every tRNA carries a particular amino acid that

corresponds to the particular codon.

Once the amino acid has been added to the

growing polypeptide chain, the tRNA is released.

Many amino acids link to form peptides – once a

peptide is folded into its proper shape it is

considered a protein.

Central Dogma

Central dogma of molecular biology –

information is transferred from DNA to RNA to

protein. ◦ This allows gene expression, or DNA, RNA, and proteins

working together to put the genetic information contained

in cells into action.

Regulation of gene expression -

Prokaryotes

Prokaryotic gene expression is regulated by DNA

binding proteins. ◦ These regulatory proteins help switch genes on and off.

◦ Operon – group of prokaryotic genes regulated together.

Promoter – DNA sequence where RNA polymerase binds to

begin transcription.

Operator – DNA sequence where regulatory proteins can

bind to repress transcription.

Regulation of gene expression -

Eukaryotes

Eukaryotic gene expression is also regulated by

DNA binding proteins, however, eukaryotes

typically regulate individual genes, not groups of

them. ◦ TATA box – short sequence of DNA that marks the

beginning of a gene; used to help position RNA

polymerase.

Regulation of gene expression -

Eukaryotes

Transcription factors – proteins

that help regulate gene

expression by binding DNA

promoter/enhancer sequences

and blocking or activating

transcription.

◦ Promoter/enhancer –

sequences of DNA with binding

sites for multiple transcription

factors.

Regulation of gene expression -

Eukaryotes Not all genes are expressed in all eukaryotic cells.

◦ Cell specialization – all cells in multicellular organisms

contain all of the organism’s DNA, yet they only

transcribe and translate part of it.

Ex. Liver cells only transcribe and translate liver specific

genes while skin cells only transcribe and translate skin

specific genes.

◦ RNA interference (RNAi) – used to regulate gene

expression in eukaryotes.

During RNAi, microRNAs (miRNAs) bind to transcribed

mRNA to block it from being translated into protein.

Regulation of gene expression -

Eukaryotes

Differentiation – when gene regulation allows eukaryotic cells to become specialized in structure and function. ◦ Occurs during embryonic development.

◦ Homeotic genes aka master control genes – specific group of genes that controls the identity of body parts in embryos. Homeobox genes – code for transcription factors that

activate other genes important for development and differentiation. ◦ In flies, these are called Hox genes.

The environment also plays a role in the regulation of prokaryotic and eukaryotic gene expression.