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Biology 108 > Quiz 3 > Flashcards

Quiz 3 Flashcards

1
Q

genome

A

set of DNA in a living organism

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2
Q

genes

A

sequences of DNA that encode specific proteins

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3
Q

gene expression

A

transcription plus translation

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4
Q

How is DNA replicated?

A
  1. unwind helix
  2. Add complementary base pairs
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5
Q

phosphodiester bonds

A

phosphate groups are linked together by these bonds and the phosphate groups link carbon 5’ in on sugar to another 3’ in another sugar

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6
Q

Origins of replication (ORI)

A

-must unwind the DNA first
multiple points of origins of replication
-replication in both directions in bubble until the bubbles meet each other
-unwound and replication proceeds in both directions, which form replication forks

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7
Q

DNA helicase

A

uses energy from ATP hydrolysis to unwind the DNA

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8
Q

Single-strand binding proteins

A

keep the strands from getting
back together

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9
Q

Topoisomerase

A

prevents twisting, relieves pressure by cutting DNA and putting it back together

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10
Q

leading strand

A

continuous synthesis of DNA

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11
Q

lagging strand

A

discontinuous

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12
Q

DNA polymerase

A

requires a primer which is a short RNA starter. primer is complementary to the DNA template and is synthesized by an enzyme called primase.

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13
Q

okazaki fragments

A

Synthesis of the lagging strand
occurs in small, discontinuous
stretches. Each fragment requires its own primer

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14
Q

DNA polymerase III

A

adds nucleotides to the 3’ end until reaching the primer of the previous fragment

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15
Q

chromosome

A

lots of DNA packed together in a strand

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16
Q

translation

A

-nucleotide to amino acids
-process of which info from mRNA is used to build proteins

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17
Q

codon

A

sequence of 3 bases that code for/specify for an amino acid

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18
Q

genetic code

A

specifies which amino
acids will be used to build a protein.
- given a codon we can determine which specific amino acid is made/used
- multiple codons for one amino acid but theres no multiple amino acids for the same codon

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19
Q

start codon

A

AUG

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20
Q

tRNA

A

binds to specific amino acid
-anticodon= complementary to mRNA codon
- each is charged by a specific enzyme (amino acid has been added to tRNA which makes it charged)
- once it gives up one amino acid, it can attach to a new one

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21
Q

ribosome

A
  • associate with mRNA
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22
Q

initiation

A
  • an initiation complex forms around mRNA (small subunit of ribosome)
    -first amino acid is always methionine which can be removed after translation
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23
Q

elongation

A

labelled as A, P, and E site
- large subunit catalyzes two reactions

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24
Q

P site

A

first RNA is located
- amino acid is then transferred and taken to the new tRNA that is in the A site

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25
A site
new amino acid is located here (incoming tRNA - after amino acid from P site is transferred, growing polypeptide bond starts forming
26
E site
for exit, tRNA leaves from e site
27
termination
stop codon in A site - no amino acid matches up with stop codon - stop codon binds to release factor which is a protein (cuts polypeptide off of tRNA)
28
What happens to a protein after translation?
1. Proteins have specific functions, so it has to go to the right location 2. Some proteins are modified (post-translational modification)
29
signal sequence
allows for protein to get to the right place in the cell - translation starts from mRNA - moved to rough ER
30
post translational modification
- phosphorylation: Addition of phosphate groups catalyzed by protein kinases. - Glycosylation: Addition of sugars to form glycoproteins. - Proteolysis: Polypeptide is cut by proteases (e.g., signal sequence is removed)
31
32
how/when can gene expression be regulated ?
Before transcription * During transcription * After transcription but before translation * At translation * After translation
33
transcriptional control
are we starting transcription or not? best time to figure out if we are going through transcription - allows for control of making of certain proteins
34
Constitutive genes
expressed in all cells at a constant rate
35
inducible genes
genes can be turned on/turn on expression of these genes - control catabolic pathways - genes turned on when needed to make protein
36
repressible genes
- genes can be turned off - controls anabolic pathways - turned off when product/protein production is sufficient
37
prokaryotic gene regulation
- regulation occurs when environmental changes need to be responded to (adapt to nutrients available in environment) - Coordinate expression of genes with related functions - Conserve energy by making certain proteins only when needed
38
sigma factors
-bind to RNAP and direct it to certain promoters -separate genes can have the same promoter sequence - help regulate/start transcription with certain promoters
39
operon
-several genes can come together an be controlled by one promoter (make proteins needed for a certain function, might as well make them all together) - includes, operator, promotor, and structural genes
40
structural genes
- 2 or more structural genes are part of the operon -make proteins that do the thing that we want to do -core of operon
41
operator
- all about regulation of proteins - part of DNA that is the binding site for regulatory proteins
42
regulatory gene
makes regulatory proteins - proteins are separate from operon - can be active or inactive
43
lac operon
-An inducible operon regulated by a repressor protein (turn on when needed) - ex. e. coli must quickly adjust in the intestine and quickly adjust to changes in food supply. they need lactose to use as energy source. Three proteins that e coli needs are only present if lactose is - made up of 3 beta galactoside (structural genes). Must know z, y, and a genes
44
trp operon
A repressible operon regulated by a repressor protein - the genes code for enzymes that synthesize tryptophan (anabolic pathway) - 5 enzymes needed to make tryptophan and when it is present the operon can be turned off
45
repressor protein
has two binding sites: one for operator that can block transcription ex. if lactose is absent, the repressor prevents binding of RNA polymerase
46
What happens if lactose is present?
-binds to repressor and changes the repressors shape -repressor can’t bind to operator -RNA polymerase can bind to the promoter, and the genes are transcribed.
47
how does lactose get broken down?
when lactose is present, there is a lot of it. It creates proteins and then those proteins will continue to break down the rest of the lactose. - must know that whenever lactose is present you must break it down (catabolic reaction)
48
co repressor
when repressor is made it is inactive. the co repressor activates the repressor - ex. tryptophan is the co repressor and activates repressor then binds to operator, then RNA polymerase cant bind and then no transcription occurs
49
allosteric regulation
allows for rapid changes in pathways
50
TATA box
Many eukaryote promoters contain this sequence
51
general transcription factors
RNA polymerase can only bind to the promoter after general transcription factors bind to the TATA box
52
Basal transcription apparatus
group of proteins that bind to DNA to start transcription
53
activators
increase transcription
54
repressors
decrease transcription
55
DNA sequences
enhancers (activators bind to and activate transcription) or silencers (DNA sequence that repressors bind to and repress transcription)
56
what determines rate of transcription?
The combination of factors present determines the rate of transcription
57
How do eukaryotes coordinate expression of sets of genes?
EUKARYOTIC GENES ARE NOT ORGANIZED IN OPERONS -Most genes have their own promoters, and may be far apart in the genome. -If the genes have common regulatory sequences within promotors, they can be regulated by the same transcription factors.
58
Epigenetic modification:
how we change the DNA structure and the accessibility of the DNA
59
histones
Protein that DNA wraps around - there is an attraction between DNA and protein -positively charged amino acids which attract the DNA negative charges from phosphates
60
nucleosome
made up of DNA wrapped around a core of eight histone proteins
61
How DNA is packaged influences gene expression
Expression depends on 1. Modification of histone proteins 2. Methylation of bases
62
heterochromatin
tightly packed and not expressed
63
euchromatin
loosely packed and expressed
64
What is a HAT?
Reduces ionic attraction and weakens association of histone and DNA, and “opens” the chromatin
65
Histone acetylation
promotes transcription
66
Histone deacetylases
can repress transcription by removing acetyl groups
67
DNA methylation
natural process of adding methyl groups to parts of DNA -Methylated DNA is not expressed -gives a stable long term silencing of genes
68
alternative splicing
take out introns but can also take out exons as well - allows for different proteins -complexity, more proteins we can make - introns always spliced out

Biology 108 (4 decks)

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