Week 3

Question 1

types of rna

Answer 1

mRNA—code for proteins

rRNA—Core of ribosome

Question 2

in vitro

Answer 2

in glass, in test tube

Question 3

in vivo

Answer 3

in life, without disrupting organism

Question 4

Nirenberg experiments

Answer 4

make a cell free extract from E. coli

added different parts at different times (similar to electrophoresis)

use 14C as a tracer to label proteins (allows to track very small amounts)

show protein synthesis in vitro (add amount of soluble RNA, show that more proteins occur, add ribosomal rna—necessary)

mRNA—needed for protein production in a dose dependent manner

mRNA—needed for protein synthesis once endogenous rna removed by DNAse (can stimulate, once DNA destroyed)

Question 5

x-ase

Answer 5

short way to say an enzyme that destroys x

penicillinase—enzyme that destroys penicillin, etc.

DNase—enzyme that destroys dna, etc.

Question 6

how did scientists find genetic code?

Answer 6

idea: take simple synthetic rna (UUU poly-U), then see what this codes for

poly U results in poly phenylalanine peptide

very simplified system

make poly C, poly A, etc, in each case only single amino acid made

can’t make poly G, since makes secondary and tertiary structures—not really translatable

UC… gives 2 amino acids, so triplicate code, etc.
UA… gives 4 amino acids

Question 7

Khorana

Answer 7

did experiments on genetic code, chemically synthesized nucleotides

Question 8

wobble base

Answer 8

third base in nucleotide sequence, changes

UC together, AG together for wobbling

Question 9

directionality of mRNA synthesis

Answer 9

5’ terminus of mRNA first, then 3’ terminus last

during protein synthesis, same direction

but reading of dna is 3’ to 5’

Question 10

correspondence between tRNA and codon

Answer 10

not a clean (one to one) correspondence, always

Question 11

UAA, UAG, UGA

Answer 11

stop codons—mean stop, terminator, nonsense

Question 12

if mutation changes base of codon

Answer 12

1) no change—e.g wobble base, synonymous mutation
2) change one amino acid to another—nonsynonymous mutation
3) changes amino acid to stop—nonsense mutation, or stop gain

Question 13

dna structure

Answer 13

dna is wrapped around histones in large coils in the cell

• special enzymes needed to uncool and recoil dna
• dna is very long molecule that is highly condensed

Question 14

chromosome

Answer 14

highly packed structure of dna

each species has a characteristic number of chromosomes (46 for humans)
-22 autosome pairs, 2 sex chromosomes x and y

when cell divides, chromosomes are visible

nondividing cell—tangled mess

two parts—chromatid and centromere

Question 15

chromatin

Answer 15

when eukaryotic cell is not dividing, dna is tangled mass of thin threads

material from which chromosomes of eukaryotes are composed

consists of protein, rna, dna

Question 16

the cell cycle

Answer 16

organization of how dna and life of cell is organized

most of cell happens during interphase (dna replication as chromosomes duplicate, protein production, etc.)

then growth phase, and prepares to divide (mitosis, cytokinesis—movement into 2 cells)

orderly sequence of events that occurs in time

stages: G1 (cell increases in size), S (copies it’s dna), G2 (prepares to divide), and M (divides)
- interphase —G1, S, G2

Question 17

mitotic phase

Answer 17

where cell division occurs

four phases: prophase, metaphase, anaphase, telephase

Question 18

interphase

Answer 18

majority of time for cell

late interphase—when chromosomes begin to compact

end of interphase—two copies, so four copies of each gene (one on each chromosome)

G1, S, G2

no observable changes under the microscope

Question 19

early and late prophase

Answer 19

early prophase—nuclear membrane becomes in distinct, chromatin fibers more packed and condensed

late prophase—nuclear membrane and nucleosus vanish completely

Question 20

metaphase

Answer 20

short moment during which chromosomes look like we see (in well known shape)

chromosomes become attached to spindle fibers

then anaphase, then telophase

Question 21

karyotype

Answer 21

number of chromosomes

species specific

chromosomes can be very small of very late, different shapes

species differing by chromosome number cannot interbreed

Question 22

diploid number

Answer 22

number of chromosomes found in somatic (non sex) cells

Question 23

haploid number

Answer 23

one chromosome of each kind

Question 24

autosome

Answer 24

non-sex chromosome

22 autosome pairs (not sex chromosomes)

receive one of each autosome from father, one of each from mother, X chromosome from m, etc.

Question 25

meiosis

Answer 25

reduced the chromosome number such that each daughter cell (egg or Sperm) has only one of each kind of chromosome

ensures that the next generation…

two nuclear divisions, result will be four haploid nuclei (each is different but complementary)

germ cell (sperm/egg) combine to form zygote, then make somatic cells and germ line cells

M1 and p1 side by side, etc.

increases diversity in offspring

Question 26

chiasma

Answer 26

maternal and paternal chromosomes exchange material

point at which paired chromosomes remain in contact during first metaphase of meiosis

Question 27

genetic recombination during meiosis

Answer 27

1) crossing over—non sister chromatids exchange material
- happens on average once or twice on each chromosome arm
2) independent assortment—homologous chromosomes distributed to daughter cells randomly

Question 28

meiosis vs mitosis

Answer 28

before each, dna separation occurs only once during interphase

Mitosis requires one division
Meiosis 2 divisions

2 diploid daughter cells from mitosis
-generically identical to parent cells
4 haploid daughter cells from meiosis
-not genetically identical to parental cells

…

human life cycle requires both

meiosis—spermatogenesis in males
—oogenesis in females

mitosis involved in growth of child and repair of tissues

Question 29

zygote

Answer 29

cell made from 2 germ cells

46 chromosomes

23 pairs of homologous chromosomes

Question 30

dna replication

Answer 30

semi conservative
- each new dna molecule consists of half of the old, half of the new dna

every time, split in half and one half in one cell, other half in another cell

since dna strands antiparallel, only one strand will form a continuous copy

Question 31

dna synthesis

Answer 31

always occurs 5’ to 3’

DNA polymerase involved in replication

requires energy—phosphate

Question 32

lagging strand of dna

Answer 32

forms a series of short pieces with gaps
During synthesis

Okazaki fragments, require use of other enzymes to complete process

Question 33

Okazaki fragments

Answer 33

ligation ties several Okazaki fragments together

other strand just polymerase (continuous)

Question 34

origins of dna replication

Answer 34

where dna replication is originated

bubbles—open up in both directions

replication forks

Okazaki fragments in bubbles

Question 35

polymerases

Answer 35

DNA polymerase requires a primer to start polymerization reaction

primer—dna primase makes primer, made out of rna

Question 36

dna helicase

Answer 36

unwinds dna, enzyme

Question 37

telomerase

Answer 37

adds additional repeats to template strand

helps with end replication problem on lagging strand

Question 38

end replication problem

Answer 38

telomerase solves this

using rna template, elongates parent strand and makes lagging strand longer

Question 39

error rates of DNA polymerase

Answer 39

very low, but large genome so

proofreading: several mechanisms eliminate most of these

end error rate 1/10^9 (only a few mistakes)

Question 40

pcr purpose

Answer 40

isolate and amplify a specific piece of dna from a given mixture
-eg gene in full genome (circ. Rhythm), gene in mix of bacteria, presence of viral dna)

identify presence of dna in a mix

introduce subtle changes into piece of dna

amplify all dna from small amount

sequence piece of dna

amplify selectively one pice if dna for genotyping, etc.

Question 41

pcr history

Answer 41

1983: recombinant dna technology existed

realized principle of dna replication
-> can be used to target specific DNA sequence for exponential amplification and further analysis

Question 42

pcr process, chain reaction

Answer 42

double stranded dna

heat to separate strands

hybridization of primers (primers on each strand, going in opposite directions)

add dna polymerases, etc

dna synthesis from primers

then do same on each new strand—second cycle. Then continue—exponential

Question 43

needed for pcr reaction

Answer 43

dna starting material

primer set (2 primers)—min length of 16

Dntps

Enzyme

Buffer, salt