Chapter 1_2

Question 1

what are proteins made of?

Answer 1

proteins are made of one or more polypeptide molecules

Question 2

what are the basic repeat units of polypeptides?

Answer 2

amino acids

Question 3

what is a hydrogen bond?

Answer 3

hydrogen bond:

> weak electrostatic bond between positively charged hydrogen atoms and negatively charged atoms

> e.g. oxygen atoms in the case of water

Question 4

in which direction is a DNA strand usually described?

(and read out)

Answer 4

5’ to 3’ direction

Question 5

which enzyme is used to unwind the DNA helix?

(in DNA replication)

Answer 5

helicase

Question 6

genes contain … and …

> which functions?

Answer 6

exon segments: genetic instructions for making mRNA or noncoding RNA

intron segments: separate exon segments, do not contribute genetic information to the final product

Question 7

what is the GT-AG rule?

Answer 7

dinucleotides at the ends of introns are highly conserved:

> vast majority of introns start with GT and end with AG

> GT - AG rule

Question 8

RNA splicing is mediated by?

Answer 8

RNA splicing is mediated by the spliceosome

> a large RNA protein complex

Question 9

what is 5’ capping?

Answer 9

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

Question 10

what are the functions of capping?

Answer 10

1. protection
2. facilitation of

> transport

> RNA splicing

> attachment to ribosome during translation

Question 11

what are untranslated regions in mRNA?

why?

Answer 11

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

Question 12

how are polypeptides made from RNA?

Answer 12

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

Question 13

genetic code is degenerate: what does this mean?

Answer 13

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

Question 14

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?

Answer 14

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

Question 15

transcription: how many basepairs does polymerase cover?

Answer 15

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

Question 16

how is the end of transcription signaled?

Answer 16

end of transcription is signaled by an upstream AAUAAA signal

> in combination with a GU rich region

Question 17

what happens after transcription?

why?

Answer 17

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

Question 18

what are 4 steps in RNA processing?

Answer 18

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

Question 19

what are 2 examples of non-coding RNA?

Answer 19

non coding RNA

1. rRNA = ribosomal RNA

> is the RNA component of a ribosome

> provides mechanism for decoding mRNA into amino acids

2. tRNA = transfer RNA

> transfer a specific active amino acid to a growing polypeptide chain (during translation)

Question 20

peptide bond direction?

Answer 20

peptide ponds go from N-terminal to C-terminal

Question 21

tRNA: what does

> acceptor arm?

> anticodon arm?

Answer 21

acceptor arm: amino acids attached

anticodon arm: forms basepairs with mRNA

Question 22

in which direction does polymerase run?

Answer 22

from 3’ to 5’

> basepairs get attached to 3’ end of new RNA/DNA strand

Question 23

how many levels of protein structure are there?

Answer 23

4:

> primary - quartenary

Question 24

what is a proteome?

Answer 24

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

Question 25

5’ capping: which base is added using which bond?

Answer 25

5’ capping:

5’-5’ phosphodiester bond is used to attach m7G

> 7-methylguanosine

Question 26

3’ polyadenylation, what is added to 3’ end of RNA transcript?

Answer 26

about 200 bases adenylate are attached

Question 27

RNA polymerase 1/2/3

> differences in transcription termination?

Answer 27

-> RNA polymerase 1/3 recognize transcription terminate site in code (AAUAAA)

> RNA polymerase 2 terminates transcription when exonuclease reaches the RNA polymerase