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Biochem > 04 > Flashcards

04 Flashcards

1
Q

What are the types of biomolecules

A

DNA
RNA
PROTEINS

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2
Q

What are DNA

A

chains of deoxyribonucleotides
double stranded
reside in the nucleus

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3
Q

What are RNA

A

chains of ribonucleotides
single stranded
transcribed in nucleus, translated in cytoplasm or orugh endoplasmic reticulum

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4
Q

What are proteins

A

chains of aa
present in all parts of the cell, both inside and outside

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5
Q

What do DNA and RNA do

A

source of genetic info for all humans, animals and plants (some bacteria and viruses too)

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6
Q

How does DNA differ in eukaryotes and prokaryotes

A

euk: have nuclei within their cells where the DNA is found

prok: do not have a separate organelle (their DNA is in the cytoplasm)

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7
Q

Where is there a small amount of DNA

A

within the mitochondria or chloroplast
- DNA not housed in a separate compartment (it’s more like a prokaryotic DNA)

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8
Q

What are bacteriophage

A

viruses that infect bacteria
(can infect euk or prok)

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9
Q

How do viruses differ from euk and prok

A

may use DNA or RNA for genetic info but can’t replicate it on their own

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10
Q

What are plasmids

A

circular DNA molecules that can enter bacterial cells and replicate independently of the genomic DNA

not infectious but confer antibiotic resistance to bacteria they enter

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11
Q

What is the nucleotide structure

A

nitrogenous base
ribose sugar
1-3 phosphate groups

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12
Q

what is a nucleoside

A

when a sugar is bound to a base

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13
Q

When do you call a nucleoside a nucleotide

A

after phosphate added to the molecule

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14
Q

TF ATP is a nucleotide

A

true

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15
Q

How are the carbons in sugars number

A

1-5 from the most oxidized carbon
- once first is numbered, rest is 2-5 in order

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16
Q

How does ribose differ from deoxyribose

A

ribose: sugar in RNA
- carbon at position 2
- has an -OH group

deoxyribode: sugar in DNA
- has an -H at position 2 instead of OH

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17
Q

What are pyrimidines

A

cityosine
thymine

smaller bases

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18
Q

What are purines

A

adenine
guanine

larger bases

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19
Q

How many hydrogen bonds pair the bases together

A

a & t = 2 h bonds
g & c = 3 h bonds

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20
Q

What bodns the 3’ and 5’ or different carbonds together

A

two ester bonds (phosphodiester bond)

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21
Q

How are ester bonds formed

A

acid and an alochol
condensation reaction that released water

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22
Q

TF ester bonds are weak adn easily degraded

A

FALSe
strong covalent bonds that are not easily degraded

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23
Q

Describe DNA structure

A

phosphates and sugars form the backbone of the molecule

two oxygen mol on the phosphate group from phophosiester bond
remaining hydroxyl group (-OH) loses its hydrogen at physiological pH
–> DNA carries a negative charge

negative charge proteins bind to DNA (to aa with a positive charge)

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24
Q

what is the forward direction of DNA/RNA

A

5’–>3’

strands are opposite (antiparallel)

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25
Q

TF opposite DNA strands are different

A

FALSE

strands run in opposite directions and a pyrimidine is always hydrogen bonded to the same purine (complemntarity) –> each strand is the same but in opposite directions

each strand has the same information and can serve as a template for the other strand

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26
Q

What are the grooves on DNA structure

A

major groove is a larger space
minor groove is a smaller space

  • spaces can be accessed by proteins
  • proteins can form hydrogen bonds with specific DNA bases in the grooves
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27
Q

What is DNA packaging

A

DNA is over 2m in length if spread out
DNA must be packed into each cell, inside the nucleus

eukaryotic DNA binds to an equal weight of histone proteins

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28
Q

What are histones

A

small proteins that contain many arginine and lysine aa

2 each of 4 diff histones make up the nucleosome core
H1 attaches to the linker DNA between each nucleosom

positive charge

29
Q

What do you call a histone core further wrapped

A

solenoid structure

30
Q

What is a further wrapped solenoid

A

chromatin (then chromosomes in mitosis)

31
Q

What are the types of RNA

A
  1. mRNA: provides instruction for protein synthesis
  2. rRNA: combines with proteins to form the ribosomes which synthesize proteins
  3. tRNA: molecules that carry the individual aa to the ribosomes (according to the instructions on the mRNA to be incorporated into the growing protein)
32
Q

Why can RNA strands bind to DNA strands and other RNA strands (including itself)

A

bases are still complementary with other RNA bases and DNA bases

33
Q

Which strand does mRNA transcribe

A

antisense (template)

34
Q

where is mRNA exported

A

into the cytoplasm (through the nuclear pore) where it can direct the synthesis of a protein

35
Q

What is ribosomal RNA

A

uses an mRNA as instructions to make a protein

ribosome is a complex of rRNA and proteins

36
Q

What is the difference in rRNA in euk and prok

A

euk: 80S ribosome that conducts the synthesis of proteins
- consists of 60S and 40S

prok: have ribosomes to carry out protein synthesis –> their structures are slightly different from euk (70S)

37
Q

How many different tRNAs are there

A

one or more for each of the 20 aa

38
Q

Which end is the aa matching the codon attatched to

A

3’ end

39
Q

What is an anticodon

A

complementary to the mRNA sequence so the code can be “read” and the correct aa added to the polypeptide chain

40
Q

How do viruses replicate

A

dont have all the proteins or mol –> cant replicate

hikacl a host’s proteins to do so

41
Q

What is the central dogma

A

outlines how info flows in a biological system

DNA transcribed to RNA translated to protein

42
Q

TF DNA has same info on either strand

A

TRUE

either strand can be used to make a copy of the DNA original sequence

43
Q

What is semi-conservative replication

A

DNA splits while being replicated –> each strand used to make a copy at the same time

results in 2 copies of the double-stranded DNA

one original and one new strand

44
Q

which direction is DNA synthesized

A

5’ –> 3’

phosphate group at the 5’ added to the hydroxyl group at the 3’ carbon

45
Q

what is bi-directional replication

A

each strand is synthesized in the opposite direction because DNA is antiparallel and each strand is going in the opposite orientation

46
Q

How are bacterial DNA replicated

A

have a single origin of replication
circular DNA

origin of replication is where DNA replication begins in both direction

47
Q

What are the two differences in euk and prok DNA replication

A

cicular nature
single origin
(in prok)

48
Q

What are the steps to DNA replication

A
  1. DNA helix is opened and unwound
    - helicase opens
    - single-stranded binding proteins: keeps DNA from re-annealing
    - topoisomerases: relieve supercoiling by breaking the phosphodiester bond in DNA and rejoining it
  2. original strand of DNA used to make a copy
    - primase (RNA polymerase) adds a small RNA primer onto the strand of DNA being copied
    - DNA polymerase III adds complementary base the DNA catalyzes the formation of the phosphodiester bond on the free 3’ (OH) group
  3. RNA primers are removed and replaced by DNA
    - RNA primer is removed from the DNA strand by RNase H and DNA POlymerase i
  4. DNA fragments on the lagging strand are attached
    - DNA ligase forms the final phosphodiester bond between DNA fragments
49
Q

What is a topoisomerase

A

an enzyme that can break and rejoin the strands to relieve tension from twisting

wraps around the strand and cuts the phosphodiester bond to allow the helix to spin freely and relax

topo rejoins the phosphodiester bond so that strands can be opened by the helicase for the replication machinery to work

50
Q

What is topoisomerase in bacteria called

A

gyrase

51
Q

what happens to replication on the lagging strand

A

new RNA primers need to be added as more of the DNA helix is unwound –> generates RNA:DNA fragments termed okazaki fragments

52
Q

What does DNA polymerase I do

A

fills in gaps between okazaki fragments

53
Q

what are the phases of euk cell division

A

resting phase: g0

interphase:
- g1: growth and metabolism
- S: DNA replication
- G2: preperation for cell division

mitosis: m phase

54
Q

which phase of cell divison is dna reolication

A

s phaase –> histone and other protein synthesis is greatly increased

55
Q

What happens after replication and division of cells

A

can either further divide or enter resting phase g0

56
Q

why are there multiple origins of replication in DNA of eukaryotes

A

multiple origins of replication in DNA to speed up replication

57
Q

Which direction are DNA read

A

3’->5’

58
Q

Describe DNA proofreading

A

DNA polymerase have 3’->5’ exonuclease activity that removes incorrect bases

correct mistakes before moving on and lower the error rate in replication

also have mismatch repair system that corrects mistakes missed by DNA polymerase

59
Q

What happens at the ends of the DNA after replictation (the issue)

A

DNA polymerase needs a 3’ OH to add the next base on
- primers are removed and DNA is shorter

*when chromosomes are replicated, the lagging strand becomes shorter each time
- important genes can be lost

60
Q

What is telomerase
What does it do

A

RNA dependent DNA polymerase

complex of proteins (an RNA primer specific to the telomere & an enzyme that can lengthen the ends of chromosomes)

  • composed of an RNA template that is coppied (A and U) to legnthen
61
Q

What are the steps to repair DNA

A
  1. damaged DNA is recognized by a protein
  2. enzymes (endo- and exonucleases) are recruited to break the phosphodiester bond and remove the damaged area of DNA
  3. DNA polymerase rebuilds the damaged area
  4. DNA ligase re-seals the phosphodiester bonds
62
Q

What repairs damaged DNA bases caused by toxins and UV radiation

A

nucleotide excision and base excision repair

63
Q

How do DNA recognize which side to repair in a mismatch

A
  1. nucleases remove the bases in the area around the un-methylated DNA mismatch
  2. DNA polymerase rebuilds the damaged area
  3. DNA ligase re-seals the DNA
64
Q

How are double stranded breaks repaired

A

homologus recombination (HR)
- the other chromosome or another piece of DNA is used as the template
- error free

nonhomologous end joining
- error prone
- incorporates many mutations

65
Q

How does CRISPR-Cas9 work

A

Cas9 (nuclease) cuts the DNA and causes double-stranded break that must be repaired by the cell
- can tell the nuclease where to cut using guideRNA (gRNA)

66
Q

How do retroviruses replicate

A

use the enzyme reverse transcriptase to convert their RNA into DNA and insert that into a host’s chromosome
- “highjacked” the transcription and translation machinery of the host

67
Q

What are reverse transcriptase
How does it work

A

DNA polymerases enzymes that can convert an RNA template into a DNA copy
- form complementary DNA (cDNA)
- RNA is removed and DNA is double stranded
- Double stranded DNA integrated into the host genome

DOes not have proof-reading so makes many errors

68
Q

What can convert RNA template into a DNA copy

A

reverse transcriptase
telomerase
RNA-containing viruses contain RT

Biochem (11 decks)

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