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78 Cards in this Set
- Front
- Back
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What is genetics?
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is the science of heredity
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What does the study of genetics include?
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- the study of what genes are
- the study of how the genes carry information - the study of how genes are replicated and passed to future generations of cells or passed between organisms - the study of how the expression of the genetic information within an organism determines the particular characteristics of that organism |
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What is a gene and what does it code for?
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a segment of DNA that codes for a functional product, usually a protein (or rRNA).
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What does it mean that the two strands of the DNA are complementary?
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the sequence of the constituent molecules on one strand of the double stranded structure chemically matches the sequence on the other strand.
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Know the general characteristics of DNA and nucleic acids presented in lecture 2.
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5' is the Phosphate end
3' is the Hydroxyl group end 1' is the nitrogenous base |
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What is a genotype?
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the genetic makeup of an organism, potential properties but not properties themselves. The information that codes for all the particular characteristics of the organism. .
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What is phenotype?
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the actual, expressed properties, such as an organism's ability to perform a particular chemical reaction. Manifestation of the genotype.
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The phosphate group of a nucleotide is attached to which carbon?
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5' (prime)
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Molecular Formulas
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actual ratio of atoms in a unique compound
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The nitrogenous base of a nucleotide is attached to which carbon?
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1' (prime)
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What is the difference between the chromosomal structure and number of chromosomes between prokaryotes and eukaryotes?
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A prokaryotic chromosome consists of a single molecule of DNA in the form of a closed loop. The chromosome is described as circular. A prokaryotic cell has only one chromosome.
A eukaryotic chromosome is linear, not circular, in other words it has two ends, like a sausage. Eukaryotic cells have more than one chromosome. A further difference: prokaryotic chromosomes consist only of a naked DNA molecule, but eukaryotic chromosomes also contain many molecules of proteins (mostly histones). The DNA is wound around these proteins. |
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What does the term "antiparallel" mean in regards to the DNA molecule?
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it means that they run parallel to each other but in opposite directions. One chain 5'-3', the other chain 3'-5'
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Be able to explain and draw the steps in DNA replication at the level discussed in class. Know all the functions of enzymes and molecules involved. Note: directionality is extremely important!
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Draw an example
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What are the functions of DNA polymerase?
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"reads" an intact DNA strand as a template and uses it to synthesize the new strand. The newly-polymerized molecule is complementary to the template strand and identical to the template's original partner strand. Has proofreading ability to correct errors. Moves in a 5'-3' direction.
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What is the direction of movement for DNA polymerase?
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5' to 3'
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What is an exonuclease?
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cut DNA backbone in a strand of DNA; facilitate repair and insertion.
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What does it mean to have exonuclease activity?
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???
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Why is one new DNA strand made continuously and the other one is made discontinuously?
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Because the lagging strand is 3' to 5' direction wich is backwards. So on lagging strand DNA is copied by smaller sections (all at the same time) that are then pieced together to make continuous strand.
Lagging strand has many RNA primers, one per Okazaki fragment generated while the leading strand only has one RNA primer. |
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What are Okazaki fragment?
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A relatively short fragment of DNA (with an RNA primer at the 5' terminus) created on the lagging strand during DNA replication.
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Why do the new DNA strands have an RNA primer?
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since the DNA polymerase can only add new nucleotides to the 3' end, a short piece of RNA primer starts the synthesis of a new DNA strand.
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What does DNA ligase do?
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joins Okazaki fragments and new segments in excision repair.
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What does helicase do?
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Unwinds double-stranded DNA.
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What do topoisomerase and/or gyrase do?
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Relaxes super coiling ahead of the replication fork.
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What is the replication fork?
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site of DNA replication. Double stranded DNA unwinds and RNA Polymerase begins process.
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What is the replication bubble?
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Each replication bubble actually consists of two replication forks, one at each end of the bubble, and traveling in opposite directions.
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Can DNA replication occur bidirectionally? If so, how?
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Yes. Via the leading strand and lagging strand. Each having replication occurring in opposite directions.
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What is the nature of DNA replication?
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one "parental" double-stranded DNA molecule is converted to two identical "daughter" molecules.
semi-conservative replication...because each new double-stranded DNA molecule contains one original (conserved) strand and one new strand. |
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When does DNA replication occur?
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replicates before cell division.
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What is the central dogma of molecular biology?
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originally proposed by Francis Crick, states that the flow of the genetic information in a cell is always from DNA to RNA to protein.
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What is transcription?
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genetic information in DNA is copied, or transcribed, into a complementary base sequence of RNA.
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What is translation?
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Protein synthesis. Decoding the language of nucleic acids and converting that information into language of proteins. mRNA from transcription into proteins.
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Be able to transcribe a gene given a sequence
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Answer: Be able to transcribe a gene given a sequence
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What is the sense DNA strand?
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A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein.
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What is the antisense DNA strand?
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In double-stranded DNA, only one strand codes for the RNA that is translated into protein. This DNA strand is referred to as the antisense strand. The strand that does not code for RNA is called the sense strand. Another way of defining antisense DNA is that it is the strand of DNA that carries the information necessary to make proteins by binding to a corresponding messenger RNA. Although these strands are exact mirror images of one another, only the antisense strand contains the information for making proteins. The sense strand does not.
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The RNA transcripts are most similar to which DNA strand?
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The sense strand
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What is the direction of RNA transcription?
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5' to 3'
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What is the promoter site?
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a sequence that determines transcription (RNA synthesis).
Always located at 5' end of the sense strand. |
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What is the terminator site?
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transcription termination sequence that is always located at the 3' end of the transcribed region
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What are regulatory elements?
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Sequences that are not promoter but can also regulate transcription.
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What is upstream v.s. downstream?
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upstream is towards the 5', downstream is towards the 3'
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What is cistron, monocistron, polycistron?
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Cistron: an old name for a gene
Polycistronic: 1 promoter directs synthesis of 1 mRNA that can be translated to more than one polypeptide (Prokaryotic genes) Monocistronic: 1 promoter directs synthesis of 1 mRNA that translates to only 1 gene. (Eukaryotic genes) |
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Monocistronic versus polycistronic mRNA
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Prokaryotes:
- plycistronic genes are usually involved in the same biochemical pathway - such an arrangement of genes in a functional group is referred to as an Operon - Allows for simple regulation of the whole pathway - 1 mRNA has many sites for translation to start - Allows for more and faster translation - Allow for fast growth Eukaryotes: - monocistronic genes allow for more control / regulation -do not mind a bit of slowness |
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What is the function of DNA dependent RNA polymerase?
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Transcription requires an enzyme called DNA dependent RNA polymerase and a supply of RNA nucleotides (A,U,C,G).
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Can many RNA polymerase transcribe the same gene at the same time?
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Yes
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What are the three types of transcripts that can be made from transcription?
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mRNA - messenger RNA's code for protein
rRNA - ribosomal RNAs, form the basic structure of the ribosome and catalyze protein synthesis tRNAs - transfer RNAs, central to protein synthesis as adapters between mRNA and amino acids. |
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What is the function of mRNA?
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mRNA - messenger RNA's code for protein
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What is the function of rRNA?
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rRNA - ribosomal RNAs, form the basic structure of the ribosome and catalyze protein synthesis
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What is the function of tRNA?
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tRNAs - transfer RNAs, central to protein synthesis as adapters between mRNA and amino acids.
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What is pre-mRNA?
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pre-mRNA exists only briefly before it is fully processed into mRNA. Pre-mRNAs include two different types of segments, exons and introns.
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What happens to the pre-mRNA molecule in eukaryotes?
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Pre-mRNAs include two different types of segments, exons and introns. Exons are segments that are retained in the final mRNA, while introns are removed in a process called splicing, which is performed by the spliceosome
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What is the spliceosome?
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removes introns from a transcribed pre-mRNA segment. This process is generally referred to as splicing.
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What are the names of the 3 sites on the 50S subunit and what happens at these sites?
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A site
P site E site P site holds the tRNA with growing polypeptide attached A site holds an aminoacyl tRNA E site holds a tRNA that will exit. |
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What does peptidyl transferase do? Which molecule has this activity?
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the primary enzymatic function of the ribosome which forms peptide links between adjacent amino acids using tRNAs during the translation process of protein biosynthesis.
In eukaryotic cells, the 60S (28S component) ribosome subunit contains the peptidyl transferase component and acts as the ribozyme. |
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What binds to the 30S subunit?
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mRNA
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What is the structure of tRNA?
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3 loops kind of looks like a cross.
One of the loops contains an anticodon region that complements the codon in mRNA. - Amino acid attaches covalently to the 3' tail. (acceptor stem) |
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Where does the amino acid attach to the tRNA?
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covalently attached to the acceptor stem at the 3' tail.
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Where is the anticodon on tRNA?
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at the bottom loop or anticodon region that complements the codon in mRNA.
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What does aminoacyl-tRNA synthetase do (ARS)?
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enzyme complex named aminoacyl-tRNA syntetase, which is specific for each of the twenty aminoacids, that is able to recognize the specific tRNA based on sequence match of the anticodon.
ARS can proofread and remove incorrect Amino Acids. |
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What is the anticodon?
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a tRNA sequence of 3 bases that is complementary to a codon on mRNA.
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What is the codon?
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groups of 3 nucleotides, such as AUG, GGC, or AAA. Determines the sequence of amino acids that will be in protein being synthesized.
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What is the difference between sense and non-sense codons?
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Sense codons: code for amino acids
Nonsense codons: also called stop codons, do not code for amino acids. |
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What is the genetic code?
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the set of rules that determines how a nucleotide sequence is converted into the amino acid sequence of a protein.
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What does it mean that the genetic code is degenerate?
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Degeneracy allows for a certain amount of change or mutation in the DNA without affecting the protein ultimately produced. Example...most amino acids are signaled by several alternative codons - UUU & UUC bote = Phe.
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What is the start codon?
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AUG (Met or Methionine))
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How many codons are possible?
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64 possible codons but only 20 amino acids.
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What does it mean that the genetic code is non-overlapping?
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This means that successive triplets are read in order. Each nucleotide is part of only one triplet codon.
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What are the 3 general steps of translation?
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1) Initiation - finding the start codon and assembling the ribosomal subunits
2) Elongation - reading the mRNA sequence and polymerizing the addition of corresponding amino acids to growing polypeptide chain. 3) Termination - recognition of the stop codon and release of the new polypeptide. |
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What is always the first amino acid in translation?
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Methionine
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In translation, what happens to the first amino acid in Prokaryotes?
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It's later removed.
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Where does translation occur in prokaryotes and eukaryotes?
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prokaryotes: It occurs in the cytoplasm of the cell. Transcription and translation occur in prokaryotes at the same time because of the lack of nuclear membrane.
Eukaryotes: at the ribosomes |
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What is the Shine Delgarno sequence?
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a ribosomal binding site in the mRNA located upstream of the start codon AUG. Only in prokaryotes. The six-base consensus sequence is AGGAGG; in E. coli, for example, the sequence is AGGAGGU. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon.
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Which molecule recognizes and binds to the Shine Dalgarno sequence?
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Ribosome
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Be able to explain and draw the series of events in prokaryotic translation.
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A.Be able to explain and draw the series of events in prokaryotic translation.
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What is a peptidyl transferase?
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primary enzymatic function of the ribosome which forms peptide links between adjacent amino acids using tRNAs during the translation process of protein biosynthesis.
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If a protein is 10 amino acids long, how many nucleotides make up the gene? And how many nucleotides make up the mRNA strand?
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?
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What is post-translational processing AND why does it occur?
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The process of translation uses an mRNA pattern to produce a string of amino acids technically known as a polypeptide. To turn a polypeptide into a protein with the shape that is crucial to its function requires several more steps. Sugars, lipids, phosphate groups, or other molecules may be added to the amino acids in the chain. The polypeptide may be "trimmed" as well; the first few amino acids may be removed. Some proteins, like insulin, only become functional after cleavage by an enzyme. Because of this ability to create variations from the basic polypeptide chain, a given gene may code for several different functional structures. This helps to explain the unexpectedly small size of the human genome. Our 35,000 or so genes actually code for several hundred thousand different proteins.
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What is the term used to label the DNA template strand?
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Antisense strand
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Where does the small ribosomal subunit bind on the mRNA? and is this Ribosome the 70S or 80S ribosome?
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to the Shine Delgarno sequence.
It's the 70S Ribosome since the Shine Delgarno sequence only exist on prokaryotes. |
