Cell Structure and Function Final

genetic code

relationship between the DNA base sequence and the linear order of amino acids in the proteins

How many DNA bases are there

4

How many amino acids are there

20

doublet code = - bases specify a single amino acid

2

doublet code is - because only 16 possible combinations

inadequate

the triplet code is where there are combinations of - bases to specify amino acids

3

the triplet code has - possible combinations and is enough for all - amino acids

64, 20

Doublet code example

triplet code example

Codon

sequence of 3 nucleic acids coding for 1 amino acid (triplet code)

All 64 codons are used in the -

translation of mRNA

61 codons specify -

the addition of specific amino acids to a growing polypeptide chain

AUG is the -

start codon

UAA, UAG, and UGA are - which -

stop codons, terminate polypeptide synthesis

genetic code is - for all organisms

universal

Every codon has - meaning

one

The - is unambiguous

genetic code

The genetic code is degenerate;

many of the amino acids are specified by more than one codon

Most mutations to the genetic code cause -

codon changes and a changed amino acid

central dogma

DNA makes RNA makes protein

Sometimes - is the final product in the flow of genetic information

RNA

RNA is converted to DNA through a process called -

reverse transcription

Reverse transcription is catalyzed by the - called -

enzyme, reverse transcriptase

Viruses that carry out reverse transcription are called -

retroviruses

Example of a retrovirus

HIV, which causes AIDs, other retroviruses cause cancer in animals

transcription

RNA synthesis using DNA as a template

Messenger RNA (mRNA) =

RNA that is transcribed into protein

Ribosomal RNA (rRNA) =

an integral component of the ribosome

Transfer RNA (tRNA) =

molecules serve as intermediaries, bringing amino acids to the ribosome

Translation

synthesis of protein using the information in the RNA

Mutations that alter sequences near
the 5′ end of mRNA result in alterations
near the corresponding protein’s N-
terminal end, whereas mutations that
alter the 3′ sequences of mRNA result in
alterations in the protein’s C-terminal
end. What do these findings imply?

The order of nucleotides from 5′ to 3′ in mRNA
determines the order of amino acids from N- to
C-termini.

RNA - chemically similar to DNA

is

RNA contains -, DNA contains -

ribose, deoxyribose

RNA has the base - instead of -

Uracil, thymine

RNA is - stranded and -

single, highly flexible

RNA can form various structures by -

complementary base pairing within single strands.

RNA’s are synthesized from a - template

DNA

In mRNA synthesis 1 - strand is copied

DNA

In mRNA synthesis the strand being copied is called the -

template strand

The strand not being copied in mRNA synthesis is called the - because it is similar to the mRNA sequence.

coding strand

Direction of RNA synthesis

5’ to 3’ direction

Several DNA sequences code for -

tRNA, rRNA

Only a subset of the DNA in any organism codes for a -

protein

In eukaryotes regulatory RNA molecules are encoded such as -

siRNA, miRNA, and Non-coding RNA

Non-coding regions

Much of the human genome does not code for anything meaningful, and is not transcribed.

Much of the RNA from the human genome - translate to or code for proteins.

does not

Tandemly Repeated DNA

the multiple repeated copies are arranged next to each other in a row.

Interspersed repeated DNA

unique sequences that are found individually, but in multiple places in the genome (ex. LINEs and SINEs)

Transposable elements

most interspersed repeated DNA consists of families of transposable elements which can move around the genome and leave copies of themselves behind.

Roughly half of the human genome consist of

mobile DNA elements

LINEs

most abundant form in the genome, contain genes required for their own mobilization

SINEs

rely on enzymes from other elements for their movement.

Most common SINE in humans =

Alu sequences

10% of human genome

Which DNA sequences are to be transcribed must be -

regulated

Transcription Unit

The DNA components that give rise to one RNA molecule

RNA polymerase

an enzyme to use DNA as a template to add new ribonucleic acids on a growing strand of RNA

Promoter

A sequence of DNA that can decide where RNA polymerase can bind

TSS (Transcription Start Site)

a sequence of DNA that can decide where transcription starts

Start Codon

A coding sequence to start the first amino acid

Start codon in DNA =

ATG

Stop codon

a coding sequence to stop the addition of the first amino acid.

Stop codon in DNA =

TAA, TAG, TGA

Stop codon in RNA =

UAA,UAG, UGA

Stop codon - stop transcription

does not

Transcription stages

Binding

Initiation

Elongation

Termination

Binding promoter

• RNA polymerase recognizes and binds to a promoter sequence on DNA.

• This causes local unwinding of the double helix, forming a transcription bubble

Initiation of RNA synthesis

RNA polymerase begins synthesizing RNA using one DNA strand (template strand).

Elongation – RNA polymerase moves along DNA

• RNA polymerase travels down the DNA.

• As it moves, it continues unwinding DNA ahead and elongating the RNA chain by adding nucleotides.

Termination – (RNA polymerase releases RNA) is when

• Eventually, RNA polymerase reaches a termination signal.

• It dissociates from the DNA, and the new RNA molecule is released.

Many bacterial promoters contain - associated with particular strong promoters.

Upstream elements (UP)

Transcription start site is almost always a - and usually an -

purine, adenine

At 10 bp upstream of the start site is the sequence - called the -

TATAAT, -10 sequence or the Pribnow box

At or near the - is the sequence - which is recognized by RNA polymerase subunits to start transcription

-35, TTGACA

Bacterial Cells have a - that synthesizes all major classes of RNA

single kind of RNA polymerase

RNA polymerase is a large protein consisting of -

two a subunits, two b subunits, and a dissociable subunit called the sigma factor

The core enzyme lacks the - and can carry out RNA synthesis

sigma subunit

The holoenzyme contains - subunits and is required to ensure transcription initiation within the DNA molecule

all

RNA chain elongation continues as -

RNA polymerase moves along the DNA molecule

RNA is elongated in the 5’ to 3’ direction and each new nucleotide is added to the - end

3’

As polymerase moves along the DNA strand, the double helix is - and DNA behind it is - into a double helix

unwound, rewound

RNA backtracking

the polymerase backs up slightly to replace an incorrect nucleotide with a correct one

Occasional errors in RNA molecules - as critical as errors in DNA replication

are not

Elongation of the RNA chain proceeds until the RNA polymerase copies a sequenced called the -

termination signal.

Many termination sequences contain a - sequence followed by several -

GC-rich, U’s

The GC region in the RNA forms a - pulling the RNA molecule away from the DNA.

hairpin loop

When the bonds between the U’s and A’s break during termination of RNA synthesis,

the RNA is released

A DNA sequence might be the promoter that drives expression of a dynein motor gene. You make a mutation that removes the sequence TATATAT from the −25 region of this putative promoter. If the original sequence serves as a promoter, what should happen to transcription of the dynein motor gene in the mutant?

Transcription should decrease.

Transcription in Eukaryotic cells has additional - compared to prokaryotes

complexity

RNA polymerases in eukaryotes require additional proteins called -

Transcription factors

-Different RNA polymerases transcribe one or more different classes of RNA

3

Eukaryotic promoters are more varied than - ones, some even located downstream of the gene

bacterial

RNA cleavage/processing is more important than - in determining the 3’ of the mRNA transcript.

termination of transcription

Pre-mRNA contains - and - splicing result in mRNA maturation

coding (exons), noncoding regions (introns)

RNA processing

done on newly formed RNA molecules, chemical modification during and after transcription.

A - is always required for RNA polymerase binding to promoters

general transcription factor

Transcription factors bind - elements first and recruits - to the promoters on DNA to initiate transcription.

DNA, RNA polymerase

Protein-protein interactions

play a prominent role in eukaryotic transcription

Transcription factors

bind the promoter in a defined order, starting with TFIID

preinitiation complex

a large complex of proteins on the promoter

TFIID is essential for

beginning the process of transcription