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Nucleotides

Nucleotides

The building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and one to three phosphate groups.

Sugar Phosphate backbone

Forms the structural framework of nucleic acids, consisting of sugar and phosphate groups.

Nitrogenous base

Includes purines (adenine and guanine) and pyrimidines (cytosine, thymine, and uracil in RNA).

Chargaff’s rule

(1) the base composition of DNA varies between species

• In any species the percentages of A and T bases are equal and the percentages of G and C bases are equal

Watson and Crick

were the first to determine the structure of DNA

• Based on crystallogrphic images, were able to deduce that DNA was helical

• Watson built a model in which the backbones were antiparallel (their subunits run in opposite directions)

• First to determine the double-helical structure of DNA.

• Based on crystallographic images, deduced DNA was helical.

• Watson built a model showing that the backbones were antiparallel (their subunits run in opposite directions).

Wilkings and Franklin

produced a picture of the DNA molecule using crystallography

• Used X-ray crystallography to produce a picture of the DNA molecule, aiding the structural discovery.

Antiparallel

their subunits run in opposite directions 

• Describes the orientation of DNA strands; their subunits run in opposite directions.

5’ and 3’

Refers to the orientation of carbon atoms in the sugar molecule in DNA and RNA strands.

 

Chromatin

a complex of DNA and protein, is found in the nucleus of eukaryotic cells

• Undergoes striking changes in the degree of packing during the course of the cell cycle

Histone

proteins that are responsible for the first level of DNA packing in chromatin

• can undergo chemical modifications that result in changes in chromatin organization

Heterochromatin

condensed chromatin is called ___

• Dense packing of the heterochromatin makes it largely inaccessible to the machinery responsible for transcribing genetic information

Euchromatin

 the more dispersed, less compacted chromatin is called __

Gene expression

The process by which DNA directs the synthesis of proteins.

Transcription

is the synthesis of RNA using information in DNA

• The first stage of gene expression 

• Three stages:

  • Initiation

  • Elongation

  • Termination

• All three stages require protein “factors” that aid in the translation process 

•  Energy is provided by hydrolysis of GTP

Messenger RNA

produced in transcription to carry genetic information to ribosomes.

Translation

Genetic information flows from mRNA to protein through the process of ___

• ___ is the synthesis of a polypeptide, using information in the mRNA

• In bacteria, translation of mRNA can begin before transcription has finished 

• In eukaryotes, the nuclear envelope separates transcription from translation 

• Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA

Triplet code

a series of nonoverlapping, threenucleotide words

• The flow of information from gene to protein is based on a ___

• The words of a gene are transcribed into complementary nonoverlapping three-nucleotide words of mRNA 

• These words are then translated into a chain of amino acids, forming a polypeptide

Codon

During translation, the mRNA base triplets, called ___, are read in the 5 to 3 direction 

•  Each one specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide • The term codon is also used for the DNA nucleotide triplets along the nontemplate strand • The nontemplate DNA strand is also called the coding strand

Template Strand

 During transcription, one of the two DNA strands, called the ___, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript

• always the same strand for any given gene 

• However, elsewhere on the chromosome, the opposite strand may function as the template for a different gene

Reading frame

Codons must be read in the correct ____ (correct groupings) in order for the specified polypeptide to be produced

Promoter

The DNA sequence where RNA polymerase attaches is called the ___

• signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point

Terminator

 in bacteria, the sequence signaling the end of transcription is called the ___

Transcription factor

mediate the binding of RNA polymerase and the initiation of transcription

TATA box

A promoter DNA sequence called a ____ is crucial in forming the initiation complex in eukaryotesTranscription elongation

RNA polymerase

An enzyme called ___ pries the DNA strands apart and joins together the complementary RNA nucleotides

• assemble polynucleotides only in the 5 to 3 direction ¢ ¢ 

• Unlike DNA polymerases, ___ can start a chain without a primer

RNA processing

Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm

•  During ___, both ends of the primary transcript are altered 

• Also, usually some interior parts of the molecule are cut out and the other parts spliced together

5’ cap

a modified form of a guanine nucleotide added to the 5' end of a newly synthesized pre-mRNA molecule in eukaryotic cells during RNA processing. 

Poly-A tail

a stretch of adenine nucleotides (A) added to the 3' end of a pre-mRNA molecule during RNA processing in eukaryotic cells.

RNA splicing

in ___ large portions of the RNA molecule are removed and the remaining portions reconnected

Exon

The other regions are called ___ and are usually translated into amino acid sequences

Intron

The noncoding regions are called intervening sequences

Transfer RNA

A cell translates an mRNA message into protein with the help of ___

• transfer amino acids to the growing polypeptide in a ribosome

• Each tRNA enables the translation of a particular mRNA codon into a certain amino acid • The tRNA contains an amino acid at one end and at the other end has a nucleotide triplet that can base-pair with the complementary codon on mRNA

• A ___ molecule consists of a single RNA strand that is about 80 nucleotides long

Codon

Three-nucleotide sequences in mRNA that specify amino acids.

Anticodon

In three dimensions, tRNA is roughly L-shaped, where one end of the L contains the ___ that base-pairs with an mRNA codon

Aminoacyl-tRNA synthetases

Accurate translation requires two steps – First, a correct match between a tRNA and an amino acid, done by the ____

Wobble

 Flexible pairing at the third base of a codon is called ___ and allows some tRNA’s to bind to more than one codon 

Ribosomes

are the sites of translation

rRNA

The large and small ribosomal are made of proteins and ___

A-site

A ribosome has a binding site for mRNA and three binding sites for tRNA – 1. The __ holds the tRNA that carries the next amino acid to be added to the chain

P-site: The ___ holds the tRNA that carries the growing polypeptide chain

E-site: The ___ is the exit site, where discharged tRNA’s leave the ribosome

P-site

The ___ holds the tRNA that carries the growing polypeptide chain

E site

The ___ is the exit site, where discharged tRNA’s leave the ribosome

Polypeptide

chains are modified after translation or targeted to specific sites in the cell

Ribosome initiation

• During synthesis, a ___ spontaneously coils and folds into its three-dimensional shape

Polypeptide elongation

a stage in protein synthesis (translation) where amino acids are sequentially added to a growing polypeptide chain. This process occurs at the ribosome, guided by the sequence of codons in the messenger RNA (mRNA).

polypeptide termination

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

• The A site accepts a protein called a release factor

Protein folding

process through which a protein chain achieves its functional three-dimensional structure from a linear chain of amino acids.

Mutations

are changes in the genetic material of a cell

Point mutations

are chemical changes in just one nucleotide pair of a gene 

• The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein

• If a ___  occurs in a gamete, it may be transmitted to offspring

Nucleotide-pair substitution

replaces one nucleotide and its partner with another pair of nucleotides

silent mutation

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

Nonsense mutation

change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

missense mutation

change one amino acid to another

Insertion

 additions of nucleotide pairs in a gene

Deletion

 losses of nucleotide pairs in a gene

Frameshift mutation

Insertion or deletion of nucleotides may alter the reading frame of the genetic message, producing a ____

Mutagen

are physical or chemical agents that can cause mutations