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Lesson 1 Flashcards

Making proteins (67 cards)

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1
Q

What do proteins mediate?

A

Everything in a cell is mediated by proteins.

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2
Q

Protein shape?

A

Protein shape matters; they can all be different shapes and sizes, and they are all very important and specialized for their functions.

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3
Q

An amino acid consists of what groups?

A

All amino acids are organic molecules with both an amino group and a carboxyl group.

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4
Q

The side chain is…

A

The side chain is variable.

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5
Q

Proteins are made of…?

A

Proteins are made of amino acid chains.

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6
Q

How many amino acids make up proteins?

A

Proteins are made up of 20 amino acids, which have different physical and chemical properties.

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7
Q

What are the three types of amino acids?

A

There are hydrophobic, hydrophilic, and charged (- or +) amino acids.

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8
Q

Polypeptides consist of…?

A

Polypeptides are amino acid polymers.

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9
Q

What is the covalent bond between amino acids called?

A

The covalent bond between amino acids is called a peptide bond.

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10
Q

How do peptide bonds form between amino acids?

A

Amino acids join together in a peptide bond by a dehydration reaction - this involves losing a water molecule.

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11
Q

What is the primary structure?

A

Primary structure consists of the amino acid sequence - folds on its own in water.

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12
Q

What is the secondary structure?

A

Secondary structure consists of hydrogen bonds between amino acids form alpha helices or beta sheets.

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13
Q

What is the tertiary structure?

A

Tertiary structure is the 3D structure of the protein - structure of a single polypeptide chain.

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14
Q

What is quaternary structure?

A

Quaternary structure is when two or more polypeptides come together to form a protein complex.

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15
Q

What is the central dogma of cell biology?

A

The central dogma of cell biology is that information to form amino acids comes from the DNA.

DNA -> RNA -> Protein

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16
Q

What is transcription?

A

Transcription occurs when RNA polymerase uses DNA as a template to produce a pre-mRNA (transcript).

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17
Q

Where does transcription occur?

A

Transcription occurs in the nucleus. RNA polymerase uses a two stranded DNA and converts it into one strand of RNA.

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18
Q

What is translation?

A

Translation is a process in which a ribosome builds the protein molecule (polypeptide) from a mature mRNA.

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19
Q

Where does translation occur?

A

Translation occurs in the cytoplasm.

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20
Q

What does the ribosome do?

A

The ribosome makes the peptide bonds between the amino acids.
- It scans through each part of the mRNA and translates each codon into an amino acid.

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21
Q

The protein is encoded in….?

A

The protein is encoded in a gene.

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22
Q

How many membranes does the nucleus have?

A

The nucleus has two membranes (inner and outer)

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23
Q

What is chromatin?

A

Chromatin is compacted DNA.

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24
Q

What does the nucleolus do?

A

The nucleolus encodes ribosomal RNAs.

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25
What is the function of nuclear pores?
Nuclear pores allow mRNA to pass through the membranes of the nucleus to the cytoplasm.
26
Nuclear membrane proteins?
The nuclear membrane has plenty of proteins that allow for selective permeability.
27
What does the RNA Polymerase catalyze?
RNA polymerase catalyzes the chemical reactions that synthesize RNA from a DNA template.
28
How many RNA polymerases are there?
We study three different types if RNA polymerases.
29
RNA polymerase?
RNA polymerase synthesize rRNA genes
30
RNA polymerase II?
RNA polymerase II synthesizes mRNA, miRNA, snRNA, and snoRNA genes
31
RNA polymerase III?
RNA polymerase III synthesizes tRNA and 5S rRNA genes.
32
mRNAs?
Messenger RNAs, code for proteins.
33
rRNAs?
Ribosomal RNAs, form basic structure of ribosome; catalyze protein synthesis.
34
tRNAs?
Transfer RNAs, adaptors between mRNA and amino acids.
35
snRNAs?
Small nuclear RNAs, function in nuclear processes.
36
What does the active site of RNA polymerase contain?
The active site of RNA polymerase has two DNA stands and an RNA strand.
37
What does RNA polymerase's active site look like?
1. Two DNA strands form a double helix at the top 2. RNA polymerase separates the two DNA strands in the middle and builds an RNA strand 3. the two DNA strands come back together
38
Where is the TATA box located?
The TATA box is typically located about 30 nucleotides upstream from the transcription start site
39
What is the TATA box composed of?
TATA box is a DNA sequence primarily composed of T and A nucleotides - helping locate where TATA binding protein should bind.
40
What recognizes the TATA box?
TATA binding proteins recognize the TATA box. They are drawn to the high concentrations of T and A.
41
What proteins are required by RNA polymerase II?
RNA Polymerase II Requires a Set of proteins called General Transcription Factors
42
Where does everything assemble?
RNA polymerase and the rest of the general transcription factors assemble at the promoter.
43
What is shown in the electron microscope?
Transcription of two genes as observed under the electron microscope. The micrograph shows many molecules of RNA polymerase simultaneously transcribing each of two adjacent genes. Molecules of RNA polymerase are visible as a series of dots along the DNA with the newly synthesized transcripts (fine threads) attached to them.
44
How does mRNA leave the nucleus?
mRNA leaves the nucleus through the Nuclear Pore Complex
45
What is able to leave through the nuclear pore complex, what comes in through the NPC, and how is it regulated?
* Particle movement by the NPC is controlled * mRNA, ribosomes, and proteins leave the nucleus through the npc * Protein import also happens through the npc
46
How does the ribosome translate the mRNA?
* The two subunits lock together with a mRNA trapped inside * The ribosome then walks down the messenger RNA and translates the nucleotides into amino acid chains * Three nucleotides (codon) = one amino acid
47
What does the ribosome do?
The ribosome read mRNA and translates the information into a polypeptide.
48
Ribosome composition?
It is composed of a large catalytic subunits and a small subunit.
49
Large subunit?
Contains the active site of the ribosome: the site that creates the new peptide bonds when proteins are synthesized.
50
Small subunit?
Finds a messenger RNA strand and ensures that each codon pairs with the anticodon
51
Role of tRNA?
Transfer RNA (tRNA) translate the mRNA into amino acids * tRNAs are a link between the mRNA molecule and the growing chain of amino acids. * They consist of anticodons and codons
52
Anticodon?
Anticodon consists of 3 exposed nucleotides - find codon of mRNA and bind to it.
53
How is the growing chain added?
The growing chain is added onto the next tRNA molecule's amino acid that its expressing.
54
Ribosomes read...?
The ribosome read mRNA and translates the information into a polypeptide
55
How does the mRNA get read?
* The two subunits lock together with a mRNA trapped inside * The ribosome then walks down the messenger RNA and translates the nucleotides into amino acid chains * Three nucleotides (codon) = one amino acids
56
Start and stop codons?
The start codon is the first codon of a mRNA transcript translated by a ribosome. Stop codon signals the termination of the translation process.
57
Start codon?
Methionine
58
Stop codon?
no aa
59
Stop tRNA?
There is no stop tRNA but a protein that stops translation (translation termination factor).
60
Bacteria nucleus?
* Bacteria don’t have nucleus * Bacteria make proteins faster than eukaryotes * Moving mRNA out of the cytoplasm is complex and energy-demanding
61
So why do we have a nucleus?
We need a nucleus to do splicing of the RNA!
62
What does RNA splicing do?
RNA splicing removes untranslated regions from mRNA. This allows us to make different proteins from one gene.
63
Where is splicing common?
Splicing is common in eukaryotes.
64
What are Exons and Introns?
- Exons are that part of the RNA that code for proteins - Introns are regions that resides within a gene but does not remain in the final mature mRNA
65
How is mature mRNA exported?
Mature mRNA is exported by the nuclear pore complex after splicing occurs in the nucleus.
66
What do spliceosomes do?
Spliceosomes cut up the exons and reconnect them to produce the mRNA molecules that are used to make proteins.
67
Splicing allows us to encode...?
Splicing allows multiple proteins to be encoded in a single gene. There are strands 1,2,3,4,5 on gene. Spliced proteins are: Protein A: 1,2,3 Protein B: 1,2,5 Protein C: 1,3,4,5
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