UNIT 3 - DNA AND GENE EXPRESSION Flashcards
what is DNA?
-deoxyribonucleic acid
-genetic material
-short segments of DNA code for specific traits (genes)
where is DNA found in eukaryotic cells?
-in the nucleus mainly
-small amount in the mitochondria
what are the 2 forms of chromatin?
-euchromatin
-heterochromatin
what is euchromatin?
-open and loose
-usually transcriptionally active
-appears lighter under the microscope
what is heterochromatin?
-more compact
-not transcriptionally active
-appears darker under the microscope
what are nucelosomes?
-DNA rolled around a bunch of 8 histones
when does heterochromatin condense to a chromosome?
-when cells are dividing
what are the different stages of chromatin hierarchy?
-euchromatin
-nucleosomes
-heterochromatin
-chromosomes
what is the structure of DNA?
-double helix
-each strand has a series of nucleotides
what are DNA nucleotides made of?
-3 subunits
-phosphate
-pentose sugar (deoxyribose)
-nitrogen containing base
what are the 4 nitrogen containing bases in DNA?
-adenine
-guanine
-cytosine
-thymine
which of the 4 bases in DNA are purines? what makes them a purine?
-adenine
-guanine
-2 carbon rings
which of the 4 bases in DNA are pyrimidines? what makes them a pyrimidine?
-cytosine
-thymine
-1 carbon rings
how many hydrogen bonds pair the complementary bases together?
-A pairs with T using 2 H-bonds
-G pairs with C using 3 H-bonds
what is specific about how the DNA strands are joined together?
-they run antiparallel (opposite directions)
-because of the position of carbon molecules on the deoxyribose sugar
-5’ carbon at one end
-3’ carbon at the other end
When does DNA replication occur?
-during the S phase of interphase
what is special about DNA replication?
-semi- conservative
-each double helix has one original strand and one new strand
-original strand serves as a template
which direction is DNA replicated in?
-5’ to 3’
-new nucleotides are added on the 3’ end
what are the 3 stages of DNA replication?
-initiation
-elongation
-termination
what occurs during initiation of DNA replication?
-proteins bind to the origin
-helicase unwinds DNA
-2 replication forks are formed
what occurs during elongation of DNA replication?
-primase adds an RNA primer
-DNA polymerase adds DNA nucleotides to the 3’ end of each strand
what occurs during termination of DNA replication?
-RNA primers are removed and replaced with DNA nucleotides
-backbone + okazaki fragments are sealed by ligase
what is the leading strand?
-DNA strand that gets made continuously
-OG strand in the 3’ to 5’ direction
-new strand in the 5’ to 3’ direction
-follows the helicase enzyme
what is the lagging strand?
-DNA strand made in fragments called okazaki fragments
-OG strand in the 5’ to 3’ direction
-new strand in the 3’ to 5’ direction
-primers need to be placed multiple times
what is the role of topoisomerase?
-prepares DNA for helicase
-stops DNA from supercoiling
what is the role of helicase?
-unwinds DNA by breaking hydrogen bonds between bases
what is the role of DNA polymerase?
-adds new DNA nucleotides
what is the purpose of Single Strand Binding proteins (SSBs)?
-stabilize DNA strands (keep them seperate)
what is the role of primase?
-puts RNA primers on each strand to allow DNA polymerase to begin
-replaced at the end by DNA nucleotides
what is the role of DNA polymerase delta and flap endonuclease?
-remove RNA from the okazaki fragments
what is a mutation? how is this taken care of?
-error in replication
-sequence of bases in new strand is not identical to template strand
-repair enzymes usually fix it
what happens when repair enzymes cannot fix a mutation?
-genetic variability is introduced
-new allele that alters the phenotype
does only one origin exist in a DNA strand?
-No!
-more than 1 origin is necessary for efficiency
what is RNA?
-ribonucleic acid
-assists in processing genetic information
-gene regulation + producing proteins
what is the structure of RNA?
-single strand of nucleotides
what are RNA nucleotides made of?
-3 subunits
-phosphate
-pentose sugar (ribose sugar)
-nitrogen containing base
what are the 4 nitrogen containing bases in RNA?
-adenine
-uracil
-cytosine
-thymine
is uracil a pyrimidine or a purine?
-pyrimidine like thymine
what are the types of RNA?
-mRNA (messenger)
-rRNA (ribosomal)
-tRNA (transfer)
-small non coding RNAs
when and where is mRNA produced?
-during transcription
-in the nucleus
-DNA is used as a template
what is mRNA’s purpose?
-carry genetic info from DNA to ribosomes in the cytoplasm (for protein synthesis)
where and how is rRNA produced?
-in the nucleolus
-using a DNA template
what will rRNA eventually form? how is this done?
-ribosomal subunits
-4 sizes of rRNA join with proteins to form the large ribosomal subunit and the small ribosomal subunit
what happens after ribosomal subunits are formed?
-leave the nucleus
-attach to the endoplasmic reticulum or remain free in the cytoplasm
-will combine to form a ribosome during protein synthesis
where and how is tRNA produced?
-in the nucleus
-using DNA as a template
what is the purpose of tRNA?
-transfer amino acids to the ribosomes during protein synthesis
-each tRNA will carry a different amino acid
how many types of amino acids are there?
-20/21
what is the 3 base sequence that is present on tRNA?
-anticodon
what are the 4 classes of small non coding RNAs?
-small nuclear RNAs (snRNAs)
-small nucleolar RNAs (snoRNAs)
-microRNAs (miRNAs)
-small interfering RNAs (siRNAs)
what are small nuclear RNAs purpose?
-splicing mRNA before it leaves the nucleus
what are small nucleolar RNAs purpose?
-modify the ribosomal RNAs within the nucleolus
what are microRNAs purpose?
-attach to mRNAs in the cytoplasm
-prevents unnecessary translation
-when the cell is down regulating the production of specific proteins
what are small interfering RNAs purpose?
-attach to mRNAs
-prepare them for degradation
what is the basic overview of gene expression?
-transcription (1st step)
-copies DNA to RNA (mRNA)
-translation (2nd step)
-makes a protein from the mRNA (mRNA > amino acids)
what can be said about each different cells genetic template?
-they are all the same
-express different RNAs which lead to cell specific proteins
what is the importance of cell specific proteins?
-basis of cell differentiation
-basis of cell function
what are proteins composed of? how do proteins differ?
-subunits called amino acids
-differ b/c of the number and order of amino acids
what type of structure is the sequence of amino acids? what type of structure does this lead to?
-sequence is primary structure
-leads to tertiary structure (proteins particular shape)
what is a codon? what does it represent?
-three base sequence in mRNA
-different amino acids
how many possible codons are there?
-64
how many codons correspond to a specific amino acid? what are the remaining codons?
-61
-remaining 3 are stop codons
what is the purpose of stop codons?
-polypeptide termination
which codon/amino acid acts as the start codon?
-methionine (AUG)
what differs in the transcription of different RNA molecules?
-the RNA polymerase involved
-RNA poly 1 (rRNA)
-RNA poly 2 (mRNA)
-RNA poly 3 (tRNA)
what is RNA polymerase?
-large complex that adds RNA nucleotides using base pairing rules
-always add on the 3’ end
what is the only coding mRNA?
-mRNA
what does it mean to be a coding RNA?
-leading to/coding for a protein
how is mRNA first processed before it leaves the nucleus?
-process primary mRNA into mature mRNA
-primary mRNA contains introns and exons
-introns are removed leaving only exons in the mature mRNA
what are introns?
-segments of DNA that do not code for any part of a protein
what are exons?
-segments of DNA that will potentially be translated to produce a protein
how are the introns removed from primary mRNA?
-mRNA is spliced
-completed by a complex called a spliceosome
what is a spliceosome composed of?
-RNA protein complexes (small nuclear ribonucleic proteins)
-other various proteins
what is alternative mRNA splicing? what does this result in?
-cells only will use certain exons (some exons are removed as well as introns)
-different proteins from a single gene
what occurs during the final processing of mRNA?
-5’ end is capped by an altered guanine nucleotide
-3’ end is given a tail (addition of multiple adenosine nucleotides)
what is the 3’ ends tail often referred to as? what is the purpose for this tail?
-polyA tail
-increases stability
does every mature mRNA molecule that leaves the nucleus result in a protein?
-NO
-a portion go to the cytoplasm and are decayed
what is the translation complex? how does it work?
-small and large ribosomal subunit joined together (ribosome)
-reads the mRNA and elongates the protein by adding amino acids
what are the 3 sites of the ribosome involved in translation?
-A site (enters)
-P site (elongated)
-E site (exits)
what are the 3 stages of translation?
-initiation
-elongation
-termination
what occurs during the initiation stage of translation?
-mRNA binds to the small ribosomal subunit (initiates translation complex)
-tRNA binds with AUG codon (methionine)
-sets the open reading frame
-large ribosomal subunit completes the complex (ribosome)
what is a reading frame?
-way to divide DNA or RNA into a set of consecutive non-overlapping triplets (codons)
how many possible reading frames does each nucleic acid have?
-DNA (6)
-RNA (3)
what occurs during the elongation stage of translation?
-the polypeptide lengthens
-tRNA arrives at the A site
-ribosome “moves down” the mRNA strand one codon at a time
-P site now is filled by a tRNA peptide complex
-tRNA moves to the E site and exits the ribosome
can more that one tRNA occupy the ribosomes different sites?
-YES
-one tRNA can be in the P site and another can be in the A site
-the polypeptide chain gets passed from the tRNA at the P site to the arriving tRNA at the A site
what occurs during the termination stage of translation?
-protein synthesis is terminated once a stop codon has entered the A site
-a protein called a “release factor” is required for termination
-ribosomal subunits dissociate
what does the release factor do?
-binds to the stop codon and cleaves the polypeptide from the last tRNA
what is a polyribosome? what does this allow for?
-multiple ribosomes that can move along one mRNA at the same time
-allows for several polypeptides of the same type to be synthesized using 1 mRNA molecule
what are the different levels of control of gene expression?
-pre-transcriptional
-transcriptional
-post-transcriptional
-translational
-post-translational
what is the pre-transcriptional mechanism of control?
-occurs in the nucleus
-accessibility of DNA
-DNA must uncoil to give access for transcription
-proteins + chemical modifications that protect the DNA must be removed
-euchromatin (open) vs heterochromatin (compact)
what is the transcriptional mechanism of control?
-several mechanisms
-regulate which genes are transcribed and the rate of transcription
-called transcription factors
what are transcription factors?
-DNA-binding proteins
-once binded to DNA, recruit RNA polymerase
what controls which genes are active on a cell?
-the specialization of a cell
what is the post-transcriptional mechanism of control?
-occurs in the nucleus
-splicing + RNA degradation
what is the translational mechanism of control?
-occurs in the cytoplasm
-microRNAs bind to mRNAs to inhibit translation
-small interfering RNAs mark the mRNA for destruction by nucleases
what is the post-translational mechanism of control?
-occurs in the cytoplasm
-phosphorylations of proteins
-folding modifications
-glycosylations
what is epigenetics?
-study of heritable and stable changes in gene expression
-occurring through alterations of the chromosome rather than DNA sequence
-modify DNA bases and change chromosome superstructure
what are examples of epigenetic mechanism?
-DNA methylation
-histones modifications
-non-coding RNAs
