Lecture 2 Flashcards
At the molecular level, DNA is a polymer of –
four different deoxynucleotides
All nucleotides have a similar structure – an organic base (adenine, guanine, thymine, cytosine, or uracil) is linked by an N-glycosidic bond to the 1’ carbon atom in a 5 carbon sugar which contains a phosphate group in – with the 5’ carbon
ester linkage
in DNA the sugar is – while in RNA the sugar is ribose
2’ deoxyribose
purines
adenine and guanine
2 fused C/N rings
purines
pyrimidines
thymine and cytosine and uracil
single C/N ring
pyrimidine
do not have any 5’ phosphate
nucleoside
In the polymer of DNA, the nucleotides are linked by a – between the 3’ C of one nucleotide and the 5’ C of the next
phosphodiester bond
a chain of DNA has a –
polarity
DNA 5’ end has a free phosphate or hydroxyl at the –
sugar’s 5’ carbon
DNA’s 3’ end has a –on the sugar’s 3’ carbon.
free hydroxyl
Polynucleotides are conventionally written and read in the –
5’ to 3’ direction
Native DNA is a double helix of –
anti-parallel strands (B-form).
The – is on the outside of the helix and the bases form stacks in the helix interior
sugar-phosphate backbone
DNA strands held together by –
H bonds b/t opposing bases
A – T
2 H bonds
C – G
3 H bonds
Two single strands of DNA are said to be – if their sequence of bases allows regular base-pairing between the two strands.
complementary
The twisting of the helix produces grooves of different sizes – the major and minor grooves. These grooves provide access to the – for proteins and other molecules
base-pairs
The – in DNA is the key to information replication and expression since one strand can serve as a template to make additional copies.
complementarity of base-pairs
Strand separation (often called denaturation or melting) occurs during –
DNA replication and transcription.
Re-pairing of the complementary strands is known as renaturation or –.
annealing
–is used to detect specific nucleotide sequences in a mixture of DNA with different sequences.
Hybridization
In order to fit the DNA in human chromosomes into a cell nucleus (with a diameter of micrometers) the DNA is specially packaged into a compact DNA and protein complex called
chromatin
The basic structural unit of chromatin is the –
nucleosome.
A nucleosome consists of –, which are small basic proteins
DNA wrapped around a protein core of histones
In a chromosome the nucleosomes are arranged as “–” with 15-55 bp of DNA linking each nucleosome to the next
beads on a string
Each histone core is –and contains 2 copies each of histones H2A, H2B, H3 and H4.
octameric
– binds to the linker region and helps pack the nucleosomes into a higher order solenoid.
Histone H1
the tighter order of nucleosome called – is also arranged into loops
solenoid
In cells that are not undergoing mitosis, the chromosomes consist of DNA organized in two ways: 1) as loops (–); and 2) as more tightly packed DNA (heterochromatin, transcriptionally inactive).
euchromatin, transcriptionally active
When cells go through mitosis, the entire chromosome is compressed into – to facilitate distribution to the daughter cells.
heterochromatin
A gene can be defined as the – necessary to make a functional polypeptide.
entire DNA sequence
In eukaryotic cells, a gene is transcribed into – that will ultimately serve as the messenger that is translated into protein
single-stranded RNA
before the RNA can be used in protein synthesis it must be processed (–) and exported from the nucleus to the cytoplasm.
5’end capped
3’ end polyadenylated, introns spliced
Eukaryotic genes: The –: this is the sequence of DNA that actually codes for the amino acids in the protein.
coding region
There are 20 amino acids but only 4 nucleotides, so a group of 3 nucleotides is used to specify a particular amino acid, that is, DNA contains a triplet nucleotide code (–) for amino acids
codon
3 – codons that signal the end of a protein
termination
Synthesis of all proteins in eukaryotic and prokaryotic cells begins with – so the triplet that encodes – (ATG) is called the initiation codon.
methionine
Because there are more codons than amino acids most amino acids are specified by –
more than one codon
The triplet code that specifies the linear order of amino acids in a protein is called the –
reading frame
Non-coding regions (–): These are regions that are present at the ends of mRNA transcripts but do not encode amino acids.
untranslated regions – UTR
That is they lie upstream of the – (5’ UTR) and downstream of the termination codon (3’UTR)
initiator codon
They play roles in controlling processing of the 3’ end, controlling translation, and controlling RNA localization in the cell.
UTRs
These are sequences in the DNA that are transcribed into RNA but are removed during formation of the mature mRNA
Introns (intervening sequences)
T/F: introns can interrupt the coding region as well as 5’ and 3’ non-coding regions
true
removal of introns
splicing
The regions in the DNA and initial transcript that ultimately are retained in the mRNA
exons
These are regions in the DNA that regulate the initiation of transcription. They are found at the 5’ end of a gene and in many cases in introns and/or 3’ to the gene as well.
Control regions
Regulation of – is a major way the cell controls which gene (therefore which protein) is expressed in which cell type, at what time in development, and at what amounts.
transcriptional initiation
Synthesis of RNA is carried out by –
RNA polymerase
The polymerase uses a DNA template and synthesizes a new strand in the –
5’ to 3’ direction, copying the template in the 3’ to 5’ direction
RNAP substrates
NTPs (nucleoside triphosphates)
The basis for accurate copying of the template strand is that the proper NTP base-pairs with the template base and then RNA polymerase catalyzes formation of the –
phosphodiester bond
In RNA, – (U) nucleotide is used instead of the thymidylate nucleotide in DNA. Like T, U base-pairs with A.
uridylate
Unlike DNA replication, only – of DNA is copied during transcription.
one strand
The DNA strand that is copied is called the –
template strand.
the RNA has the same sequence of nucleotides as the non-template (also called the –) strand of DNA
coding
RNA that encodes proteins
mRNA
used in translation of mRNA into protein
tRNA
components of ribosomes
rRNA
some small structural RNAs such as those used in splicing and microRNAs and –, newly appreciated non-coding RNAs involved in gene regulation.
long non-coding RNA (lncRNA)
RNA pol that synthesizes rRNA
Pol I
RNA pol that synthesizes mRNA and some small structural RNAs, microRNA and lncRNA
Pol II
RNA pol that synthesizes tRNA and 5S rRNA
Pol III
Each polymerase is a complex, –
multisubunit enzyme
To transcribe a gene, the RNA polymerase must recognize where to start and which strand to transcribe (template strand). And it must do this only in – in the genome that need to be expressed in a particular cell at a particular time.
the fraction of genes
specific DNA sequences in the 5’ ends of genes that serve as signals to position RNA polymerase at the proper site to begin transcription
promoter
since the sequences of the promoter are located on the same DNA as the gene they are referred to as–
cis-acting elements
In many eukaryotic genes a key cis-acting element is the – located 18-34bp before the start site of transcription
sequence TATAAA (TATA box)
The TATA box serves as a binding site for a –that positions RNA polymerase at the 5’ end of the gene.
general transcription factor
T/F: Other sequences near the TATA box also bind other general transcription factors.
true
There are also other DNA sequences that are necessary for optimal transcription. Some are located near to the TATA box.
promoter proximal elements
promoter proximal elements are sometimes – meaning they aid transcriptional initiation of a gene in some cells but not others
cell-type specific
Other sequences can be located very far (thousands of base-pairs) from the promoter, either upstream or downstream of the gene
enhancers (usually cell type specific)
Both promoter-proximal elements and enhancers are bound by other transcription factors called – that increase the rate of transcriptional initiation
activators
Some DNA sequences are recognized by proteins that decrease the rate of transcription. The DNA elements are called –and the proteins are generally called repressors.
silencers
Most genes have – that finely regulate the level of transcription and determine tissue-specific expression
multiple control elements
For any given gene in a particular cell type, the level of expression is determined by which control elements are present in the gene, and which –(activators and repressors) are active in the cell.
transcription factors
General transcription factors such as – are required at most promoters for transcription initiation by Pol II.
TFIIB, TFIID (each is a multiprotein complex)
TFIID contains –which directly binds to the TATA box, plus associated proteins called TAFs.
TATA-binding protein (TBP)
Pol II and TFs can carry out –levels of transcriptional initiation
low (basal)
– bind to promoter-proximal and enhancer elements and increase the rate of transcriptional initiation. They act synergistically (more than additive) to increase transcription by increasing the binding of RNA pol II to the promoter.
Transcriptional activators
one domain of activators is a DNA binding domain that binds to the base-pairs in the –
promoter-proximal element or enhancer
one domain of activators an – that is responsible for transcriptional activation.
activation domain
Many activation domains do not interact directly with RNA PolII but instead interact with an intermediary complex (also known as a co-activator) called the –.
Mediator complex
Mediator complex bridges – with RNA Pol II
activators
If there are multiple activators then there are multiple interactions with Mediator which increases the binding of mediator at the promoter leading to –
increased binding of RNA Pol II.
Activators are generally classified by –
their DNA binding domains
Most DNA binding domains contain an – that fits into the major groove of the DNA and makes specific hydrogen bonds with the basepairs.
alpha helix
Repressors bind silencer sequences in DNA and lower transcription by – the binding of an activator to DNA or by preventing binding of activators to Mediator or by modifying chromatin structure.
preventing
Transcription is also regulated by –structure.
chromatin
Packing of chromatin into condensed structures can prevent transcription factors from gaining–to the DNA.
access
there is much interest in enzymes that acetylate or deacetylate –residues in the N-terminal regions (“tails) of histones
lysine
Some activators function by binding histone –
acetylases
Some repressors function by binding histone –.
deacetylases
Histones can also be modified by lysine or arginine –(and other modifications).
methylation
Chromatin (and DNA) modifications that are passed on to daughter cells are referred to as –because they alter the gene structure without changing the DNA sequence
epigenetic
