DNA, RNA, Translation, and Transcription

Nucleic Acid

a macromolecule essential for living organisms (DNA and RNA)

Nucleotide

monomer of DNA and RNA

Components of a Nucleotide

1. Phosphate Group

2. Five-Carbon Sugar

3. Nitrogenous Base

Purines

nitrogenous base; Adenine and Guanine

How many rings are Purines?

2

How many rings are pyrimidines?

1

Pyrimidines

nitrogenous base; Cytosine, Uracil, Thymine

Where is Uracil found?

only in RNA

Where is Thymine found?

only in DNA

Deoxyribonucleotides

monomers of DNA; has H instead at 2’ carbon

Deoxyribose

sugar

Phosphodiester Linkage

bond between two nucleotides to form a nucleic acid

How do nucleic acids polymerize?

dehydration (condensation) reactions

What direction is the backbone of DNA and RNA strands?

5’ —> 3’

One end has unlinked 5’ __ group

phosphate

One end has unlinked 3’ __ group

hydroxyl 

What kind of helix do DNA strands form?

Antiparallel Double Helix

Backbone is __ and __ linked together via phosphodiester bond

sugar and phosphate

What holds the 2 strands together in a double helix?

Hydrogen bonds between pyrimidines and purines

Watson-Crick Pairing

Complementary base pairing: A and T, C and G

X-Ray Crystallography

measures distances between atoms in DNA; predicted helical structure

Chargaff’s Rules

in any organism the amount of A=T and amount of G=C

Does the sugar-phosphate backbone face exterior or interior?

Exterior

Does the nitrogenous base pair face exterior or interior?

Interior 

What structure of DNA is a double helix?

Secondary

Tertiary Structure of DNA

DNA forms compact 3-D structures in cells

Histones

DNA wraps around DNA-binding proteins

How long is DNA in each cell approximately?

6 feet

Chromatin

loose, uncondensed DNA and protein

Chromosome

condense, super coiled DNA

How many strands is RNA vs DNA?

RNA is one strand and DNA is double helix

What sugar does DNA vs RNA have?

DNA- deoxyribose

RNA- ribose

What base pairings does DNA have?

A, G, C, T

What base pairings does RNA have?

A, G, C, U

DNA Replication

duplication of a DNA molecule

What type of bond connects each nucleotide along a single strand?

a strong covalent bond

What type of bond connects the complementary strands by holding the base pairs together?

a weak hydrogen bond

What occurs right before a cell enters mitosis?

DNA replication

Semiconservative Model

Each new DNA double helix contains one old (template) and one new strand

Where does replication start?

replication bubbles forms when DNA is being synthesized

How many replication bubbles does bacteria have?

One

How many replication cells do eukaryotic cells have?

Many

How many replication forks does a replication bubble have?

2

Why do replication bubbles grow in 2 directions?

synthesis is bidirectional

How is the helix opened and stabilized?

Proteins

DNA Helicase

a protein that breaks hydrogen bonds b/w DNA strands to separate them

Single-Strand DNA-Binding Proteins

attaches to separated strands to prevent them from closing

Topoisomerase

cuts and rejoins DNA to relieve the tension that unwinding the DNA helix creates

DNA Polymerase

uses each strand as a template to construct a new strand 

What limits DNA Polymerase?

the antiparallel nature of DNA

What direction can DNA Polymerase synthesize?

5’ —> 3’

Can DNA polymerase start from scratch on a template strand?

No; it needs a guide (Primer-A short DNA fragment)

What is the purpose of ribosomes in translation?

helps translate the info that mRNA contains from the language of mRNA (bases) to the language of proteins (amino acids)

Where is mRNA transported after transcription?

from the nucleus to ribosomes in the cytoplasm

How many nucleotide bases are there compared to amino acids?

4 bases to 20 amino acids

Codon

mRNA information in sets of 3 bases read by ribosomes 

What are the 4 bases of mRNA?

A, C, G, U

Unambiguous

Each codon specifies only one amino acid

Redundant

Several different codons call for the same amino acid

What are ribosomes made of?

rRNA

What are the 3 types of RNA in gene expression?

Messenger, Ribosomal, Transfer

mRNA

Messenger: specifies the order of amino acids in a protein using a series of 3 base codons

rRNA

Ribosomal: assists in making the covalent bonds that link amino acids together to make a protein

What are the two subunits of ribosomes?

1) The small subunit holds the mRNA in place

2) The large subunit is where peptide bonds form

tRNA

Transfer: delivers specific amino acids to ribosomes as codons that are complemenary to the mRNA

What are at the ends of tRNA?

One end has an anticodon that binds the correct codon on the mRNA and at the other end the specific amino acid attaches

What end are amino acids always added to?

the carboxyl end of the polypeptide

Initiation

Begins when mRNA binds to a ribosome

P Site

holds the tRNA that carries the growing polypeptide chain

A Site

holds the tRNA that carries the next amino acid to be added to the chain

E Site

exit site where discharged tRNAs leave the ribosome

Elongation

amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain

Termination

Occurs when a stop codon in the mRNA reaches the A site of the ribosome

Where is the release factor protein accepted?

A Site

Release Factor

causes the addition of a water molecule instead of an amino acid to the polypeptide chain; the reaction releases the polypeptide and translation assembly comes apart

Mutation

any permanent change in an organism’s DNA- modification in info archive, change in genotype, new alleles

Point Mutation

result from one or a small number of base changes

Chromosome-level Mutation

larger in scale

Beneficial Mutations

increase fitness

What does fitness mean?

ability to survive and reproduce

Neutral Mutations

do no affect fitness

Deleterious Mutations

decrease fitness

Silent Mutation (Point Mutation)

does not change amino acid sequence due to redundancy in the code

Missense Mutations (Point Mutation)

change an amino acid in protein

Nonsense Mutation (Point Mutation)

change codon that specified an amino acid into stop codon

Frameshift Mutation (Point Mutation)

Shift reading frame, altering meaning of all subsequent codons

Where do genes have information content?

the sequence of nucleotides along stretches of DNA

Transcription is

DNA to mRNA

Translation is

mRNA to proteins

Initiation

attachment of RNA polymerase to the promoter- start RNA synthesis

Elongation

RNA grows longer

Termination

RNA polymerase reaches a terminator in DNA template that signals the end of transcription

Promoter

series of base pairs where RNA polymerase attaches

Transcription Factors

proteins that turn genes on and off by allowing or blocking the binding of RNA polymerase to promoter 

What direction can RNA polymerase add nucleotides?

5’—> 3’

As RNA polymerase moves along the DNA, how many bases at a time does it untwist the double helix?

10-20 bases

Can a gene be transcribed simultaneously?

Yes; using several molecules of RNA polymerase

Post-Transcriptional Modifications

Before genetic messages are dispatched to cytoplasm, enzymes modify pre-mRNA in eukaryotic nucleus 

What 2 things happen in RNA processing?

1) Alterations of both ends of RNA molecule

2) Removal of certain sections of RNA molecule

In eukaryotic RNA, what end has a guanylated cap added?

5’