Chapter 1_2 Flashcards
what are proteins made of?
proteins are made of one or more polypeptide molecules
what are the basic repeat units of polypeptides?
amino acids
what is a hydrogen bond?
hydrogen bond:
> weak electrostatic bond between positively charged hydrogen atoms and negatively charged atoms
> e.g. oxygen atoms in the case of water
in which direction is a DNA strand usually described?
(and read out)
5’ to 3’ direction
which enzyme is used to unwind the DNA helix?
(in DNA replication)
helicase
genes contain … and …
> which functions?
exon segments: genetic instructions for making mRNA or noncoding RNA
intron segments: separate exon segments, do not contribute genetic information to the final product
what is the GT-AG rule?
dinucleotides at the ends of introns are highly conserved:
> vast majority of introns start with GT and end with AG
> GT - AG rule
RNA splicing is mediated by?
RNA splicing is mediated by the spliceosome
> a large RNA protein complex
what is 5’ capping?
5’ capping:
> in RNA synthesis of primary RNA transcript (before splicing)
> methylated nucleoside is added by a 5’-5’ phosphodiester bond and the 5’ end of the transcript
what are the functions of capping?
- protection
- facilitation of
> transport
> RNA splicing
> attachment to ribosome during translation
what are untranslated regions in mRNA?
why?
untranslated regions 5’UTR and 3’UTR
> those regions are not translated into polypeptides (only a central segment of mRNA is)
> they assist in binding and stabilizing mRNA on the ribosomes and promote efficient translation
how are polypeptides made from RNA?
RNA is scanned from 5’ to 3’ in groups of 3 nucleosides (codons)
> each codon specifies 1 amino acid
> proces is mediated by tRNA molecules
genetic code is degenerate: what does this mean?
genetic code is a 3 letter code with 4 possible bases to choose: 4³ = 64 possiblities
> only 20 major types of amino acids
> many amino acids are coded for by multiple codons
there are more than 60 codons that specify an amino acid, but there are less cytoplasmic tRNA molecules and only 22 types of mitochondrial tRNA to read them
> how is this possible?
base pairing in RNA is more flexible than in DNA
> first two base positions in codon follow the normal AU and GC rule
> third base pair, there is some flexibility >>> GU base pairs tolerated
transcription: how many basepairs does polymerase cover?
about 30 bp of the template DNA
> including the transcription bubble
>>> which holds the growing transcript to the template strand for about 8 RNA-DNA basepairs
how is the end of transcription signaled?
end of transcription is signaled by an upstream AAUAAA signal
> in combination with a GU rich region
what happens after transcription?
why?
end of transcription:
> poly A tail is added by poly A polymerase
function:
> helps transport mRNA to cytoplasm
> stability of the mRNA molecule
> enhance recognition of mRNA by ribosomal machinery
what are 4 steps in RNA processing?
RNA processing:
1) end-modification > poly A tail and capping
2) splicing - removal of introns
3) cutting events - molecule is cut into pieces
4) chemical modification - addition of new chemical groups
what are 2 examples of non-coding RNA?
non coding RNA
- rRNA = ribosomal RNA
> is the RNA component of a ribosome
> provides mechanism for decoding mRNA into amino acids
- tRNA = transfer RNA
> transfer a specific active amino acid to a growing polypeptide chain (during translation)
peptide bond direction?
peptide ponds go from N-terminal to C-terminal
tRNA: what does
> acceptor arm?
> anticodon arm?
acceptor arm: amino acids attached
anticodon arm: forms basepairs with mRNA
in which direction does polymerase run?
from 3’ to 5’
> basepairs get attached to 3’ end of new RNA/DNA strand
how many levels of protein structure are there?
4:
> primary - quartenary
what is a proteome?
proteome: final product of all genome expression
> all proteins present in a cell at a given time
> different types of human cells have different proteomes
> most proteins are “housekeeping” proteins
> proteins that specialize cells are rare
5’ capping: which base is added using which bond?
5’ capping:
5’-5’ phosphodiester bond is used to attach m7G
> 7-methylguanosine
3’ polyadenylation, what is added to 3’ end of RNA transcript?
about 200 bases adenylate are attached
RNA polymerase 1/2/3
> differences in transcription termination?
-> RNA polymerase 1/3 recognize transcription terminate site in code (AAUAAA)
> RNA polymerase 2 terminates transcription when exonuclease reaches the RNA polymerase
