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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
TF opposite DNA strands are different
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
26
What are the grooves on DNA structure
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
27
What is DNA packaging
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
28
What are histones
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
What do you call a histone core further wrapped
solenoid structure
30
What is a further wrapped solenoid
chromatin (then chromosomes in mitosis)
31
What are the types of RNA
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
Why can RNA strands bind to DNA strands and other RNA strands (including itself)
bases are still complementary with other RNA bases and DNA bases
33
Which strand does mRNA transcribe
antisense (template)
34
where is mRNA exported
into the cytoplasm (through the nuclear pore) where it can direct the synthesis of a protein
35
What is ribosomal RNA
uses an mRNA as instructions to make a protein ribosome is a complex of rRNA and proteins
36
What is the difference in rRNA in euk and prok
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
How many different tRNAs are there
one or more for each of the 20 aa
38
Which end is the aa matching the codon attatched to
3' end
39
What is an anticodon
complementary to the mRNA sequence so the code can be "read" and the correct aa added to the polypeptide chain
40
How do viruses replicate
dont have all the proteins or mol --> cant replicate hikacl a host's proteins to do so
41
What is the central dogma
outlines how info flows in a biological system DNA transcribed to RNA translated to protein
42
TF DNA has same info on either strand
TRUE either strand can be used to make a copy of the DNA original sequence
43
What is semi-conservative replication
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
which direction is DNA synthesized
5' --> 3' phosphate group at the 5' added to the hydroxyl group at the 3' carbon
45
what is bi-directional replication
each strand is synthesized in the opposite direction because DNA is antiparallel and each strand is going in the opposite orientation
46
How are bacterial DNA replicated
have a single origin of replication circular DNA origin of replication is where DNA replication begins in both direction
47
What are the two differences in euk and prok DNA replication
cicular nature single origin (in prok)
48
What are the steps to DNA replication
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
What is a topoisomerase
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
What is topoisomerase in bacteria called
gyrase
51
what happens to replication on the lagging strand
new RNA primers need to be added as more of the DNA helix is unwound --> generates RNA:DNA fragments termed okazaki fragments
52
What does DNA polymerase I do
fills in gaps between okazaki fragments
53
what are the phases of euk cell division
resting phase: g0 interphase: - g1: growth and metabolism - S: DNA replication - G2: preperation for cell division mitosis: m phase
54
which phase of cell divison is dna reolication
s phaase --> histone and other protein synthesis is greatly increased
55
What happens after replication and division of cells
can either further divide or enter resting phase g0
56
why are there multiple origins of replication in DNA of eukaryotes
multiple origins of replication in DNA to speed up replication
57
Which direction are DNA read
3'->5'
58
Describe DNA proofreading
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
What happens at the ends of the DNA after replictation (the issue)
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
What is telomerase What does it do
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
What are the steps to repair DNA
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
What repairs damaged DNA bases caused by toxins and UV radiation
nucleotide excision and base excision repair
63
How do DNA recognize which side to repair in a mismatch
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
How are double stranded breaks repaired
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
How does CRISPR-Cas9 work
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
How do retroviruses replicate
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
What are reverse transcriptase How does it work
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
What can convert RNA template into a DNA copy
reverse transcriptase telomerase RNA-containing viruses contain RT

Biochem (11 decks)

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