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UKCD Biochem Lec 4
Terms from Biochem lecture 4
| Question | Answer |
|---|---|
| Transcription/Translation | Genes are transcribed to form an RNA message (mRNA) which is in turn translated to form proteins. |
| Ribose | There are several differences between RNA and DNA, the two classes of nucleic acids. The most obvious one is the difference in the sugar used in the backbone of the molecule: ribose in RNA, and |
| Deoxyribose | deoxyribose in DNA (note the oxygen missing from each sugar in DNA). |
| Nucleoside | A base attached to a sugar (of either RNA or DNA) |
| Nucleotide | Nucleosides attached to one or more phosphate groups by an ester linkage |
| Semi-Conservative | data can be explained if DNA replication is semi-conservative – that is, each new double-stranded DNA consists of one of the parent strands and one newly-synthesized daughter strand. |
| Uracil | pyrimidine uracil, which substitutes for thymine in RNA. |
| Template | Each strand of DNA can act as a template for the other strand. |
| Hypochromism | Melting DNA can be followed by monitoring the absorption of light at 260 nm - stacked bases absorb less light than unstacked bases. |
| Tm | In replication the two strands of DNA must be separated, at least locally. In the laboratory, DNA can be separated into single strands by heating – what we refer to as melting DNA. The point at which a given double helical molecule has become 50% unwound |
| Primer | If the DNA is single stranded, a short stretch of RNA known as a primer must be bound to the template, and the polymerases will add nucleotides to the primer in the 5’ to 3’ direction. |
| Reverse Transcriptase | When an RNA virus infects a cell, a copy of its RNA is used as a template to make a corresponding DNA, which can then integrate into the host’s genome. This is done by a viral enzyme called reverse transcriptase. |
| snRNA and miRNA | small nuclear RNA (snRNA) is important for mRNA splicing and micro RNA (miRNA) is important for controlling gene expression at the translational level. |
| Degenerate Coding | There are 64 possible codons (the 3 base sequence that specifies an amino acid or stop signal); since there are only 20 amino acids, there is some redundancy – the term used is degenerate (codons that encode the same amino acid are called synonyms). |
| Exon | “regions of the DNA that are expressed in mRNA”, and are not necessarily expressed as protein. |
| Intron | Introns are stretches of DNA sequence that do not code for protein that are interspersed within a gene. These can contain regulatory information, or even other genes (they can be very large). |
| Shine-Dalgarno Sequence | to help distinguish the start codon from internal methionine (or valine) residues, the initiator codon is further distinguished by this preceding purine rich region, which base pairs with a complementary sequence in the ribosomal RNA. |
| Frameshift Mutation | An insertion or deletion of a single base within a coding sequence |
| Exon Shuffling / Skipping | splicing out an exon that is necessary for the function of a protein – this is different from alternative splicing, which leads to different versions of the same protein, with slightly different properties. |
| Alternative Splicing | adv of exons possibility of generating a series of related proteins by splicing nascent mRNA in different ways, allows organism to generate a set of related proteins that can have variant specificities without requiring an entirely new gene for each one. |
| Enamelin | protein only found in enamel, and in no other tissues. |
| Missense Mutation | change in a single codon resulting in a change in its meaning. |
| 3’-5’ Phosphodiseter Linkage | Connections along the backbone, b/w 3’ of one sugar and 5’ of next, 3’-5’ phosphodiester linkage gives chain directionality, amino acid sequence of which is read in the N- to C-terminal direction, a nucleic acid sequence is read from the 5’ to the 3’ end. |
| Nucleic Acids | The bond between the sugar and the base is a beta-glycosidic linkage, which occurs between the N-9 of a purine or N-1 of a pyrimidine, is attached to the C-1’ of the sugar. |
| Anneal | separated strands will spontaneously associate (anneal) to form a double helix when cooled |
| Supercoiling | Circular DNA can be twisted like a rubber band, leading to supercoiling, which results in a more compact form of storage (space is limited within a cell, after all). |
| DNA Polymerase | enzymes that synthesize the new DNA strand(s) by catalyzing the formation of phosphodiester bonds. DNA polymerases require a template - a single strand or a double strand with one chain broken – in order to begin |
| RNA Polymerase | similar to DNA polymerases require a template, activated precursors (ATP, GTP, CTP and UTP) and Mg2+, does not require a primer in order to begin synthesis. Also, RNA polymerase lacks the ability to excise mismatched pairs, leading to a higher error rate. |
| mRNA | messenger RNA |
| rRNA | ribosomal RNA |
| tRNA | carries amino acids to the ribosome for addition to a new protein chain |
| Promoter / Terminator | discrete start/stop signals for transcription contained w/in DNA sequence. A promoter site specifically binds RNA polymerase and determines where transcription begins, will continue until encounters termination signal |
| Codon | the 3 base sequence that specifies an amino acid or stop signal / Anti-Codon- template recognition site is a set of three bases |
| Release Factors | Proteins known as release factors, which cause the ribosome to release the newly synthesized protein. |
| fMet | The start codon is AUG (or, rarely, GUG); AUG also codes for Met (GUG codes for Val). Protein synthesis starts with the modified amino acid fMet (formylmethonine); this is carried by a special tRNA known as the initiator. |
| 5’ / 3’ UTRs | first exon and the last exon contain the 5’ and 3’ untranslated regions (UTRs) of the mRNA. The UTRs contain important regulatory elements that control the efficiency of translation (the 5’ UTR) and how long the message persists in the cell (the 3’ UTR). |
| Splicing / Spliceosomes | removal of Introns that are transcribed into mRNA during mRNA processing after synthesis (before leaving the nucleus), involves the recognition of splice signals w/in RNA, formation of lariat-like intermediate, cut out, ends of exon ligated together |
| Amelogenesis Imperfecta | genetic heterogeneous disorder affecting the normal development of enamel in the teeth, through changes in several critical proteins. |
| Cryptic Splicing | use of a splice site that doesn’t really exist, leads to problems – inclusion of parts of an intron with the next exon, missing part of an exon, etc. This can also result in a frameshift, which can change the entire meaning of the codons in the next exon. |
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wiechartm
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