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PHGY 170 Midterm > Module 1 > Flashcards

Module 1 Flashcards

1
Q

What is cell theory?

A

Cell theory is the scientific theory that describes the properties of cells. has 3 tenets.

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2
Q

What is the First Tenet?

A

All living organisms are composed of one or more cells

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3
Q

What is the second tenet?

A

The cell is the basic unit of structure and organization in organisms.

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4
Q

What is the third tenet?

A

All cells come from pre -existing cells.

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5
Q

What are prokaryotic cells?

A

No true nucleus or membrane-bound organelles
Smaller cells (~1-5 μm)
Always unicellular
Binary fission for cell division
Always asexual reproduction
Examples: Bacteria like E. coli

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6
Q

What are eukaryotic cells?

A

Have a true nucleus and membrane-bound organelles
Larger cells (~10-30 μm)
Usually multicellular
Mitosis/meiosis for cell division
Sexual or asexual reproduction
Examples: Plants and animals

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7
Q

What is human cell diversity?

A

All the cells in the body have the same DNA, they are vastly diverse in structure and function

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8
Q

What are the 8 primary cells in the human body?

A

Epithelial cells, Muscle cells, Bone cells, Nerve cells, Connective tissue cells, secretory cells, red blood cells, adipose cells.

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9
Q

what are epithelial cells?

A

Barriers in tissues
Can absorb or secrete compounds
form protective barriers in tissues and may be specialized to absorb or secrete specific compounds
Epithelium generally lines pathways that are open to the external environment, such as your respiratory tract and digestive system.

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10
Q

What are muscle cells?

A

responsible for movement of the skeleton, heart, and many internal organs (e.g., stomach).

skeletal

cardiac

smooth

These cells have specialized structures and proteins that allow them to generate motion

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11
Q

what are nerve cells?

A

Nerve cells conduct electrical signals throughout the body
control the contraction of muscles
responsible for senses including taste, touch, smell, sight, and hearing.

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12
Q

what are connective tissues?

A

create extracellular material
holds cells together in tissue.

They may be specialized to absorb or resist external forces (e.g., tendons, vertebral discs).

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13
Q

what are bone cells?

A

form the bones of the skeletal system
give strength and support to the body

These cells include osteoclast cells that degrade bone

osteoblast cells that create new bone

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14
Q

what are secretory cells?

A

Secretory cells form glands and secrete substances (e.g., mucous, hormones, enzymes, etc.)

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15
Q

what are adipose cells?

A

Adipose cells are located throughout the body
Store fat
This fat is in the form of triglycerides
Released when the body is in a period of fasting

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16
Q

what are red blood cells?

A

Cells formed primarily in the bone marrow
Released into the circulation where they move and deliver oxygen throughout the body
NO nuclei or mitochondria
They have limited lifespans
Must be continuously replaced

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17
Q

why are red blood cells considered eukaryotic?

A

Specialized cells like red blood cells are formed from a precursor cell, known as a stem cell
These cells can differentiate into many more cell types called blasts (immature cells),
Then becomes mature cells in the body
Since red blood cells = matured stem cells that have these organelles,
they are still considered a eukaryotic cell, even though when they are matured they do not have these organelles
Red blood cells come from eukaryotic organisms
When red blood cells are matured the nucleus is lost (enucleation)

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18
Q

Plasma Membrane

A

The plasma membrane is like the city limit and border police.
It is a semi -permeable phospholipid bilayer that keeps all of the cell’s organelles contained
regulates what can come in or leave the cell using specialized proteins

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19
Q

Nucleus

A

The nucleus is the leader of the cell
Making the ‘laws’ of
The nucleus stores these ‘laws’ as DNA
Protects it with specialized structures like a double membrane, nuclear pores, and a unique fluid called nucleoplasm.

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20
Q

Mitochondria

A

Mitochondria are the power plants in Eukaryopolis
They produce energy for the cell to use in all of its processes, in the form of A T P ; a kind of cellular energy ‘currency.’
The number of mitochondria in a cell depends on its function
(muscle cells have the most)

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21
Q

Endoplasmic Reticulum ( ER )

A

the endoplasmic reticulum ( ER ) acts as a highway system
Carrying molecules around the cell, and as a factory warehouse that makes lipids and proteins, and stores ions.

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22
Q

Smooth ER

A

makes lipids for plasma membrane

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23
Q

Rough ER

A

has ribosomes
makes proteins
“protein processing”

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24
Q

Golgi Apparatus

A

processes and packages proteins
then sends them across the cell

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25
Q

Cytoskeleton

A

holding cell together
3 types = microfilaments, microtubules, intermediate filaments

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26
Q

Actin

A

proteins that form microfilaments in the cytoskeleton

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27
Q

what are the motor proteins

A

Myosin, kinesin, and dynein

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28
Q

what are motor proteins function

A

(force) proteins that generate force, or motion throughout the cell

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29
Q

what are the 3 smaller bound organelles that contain enzymes and proteins?

A

lysosomes, endosomes, peroxisomes

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30
Q

Lysosomes

A

recycling plants that break down proteins, lipids, and nucleic acids
Use acid hydrolases to break down waste into reusable parts

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31
Q

Perixosomes

A

deal with hazardous waste, such as hydrogen peroxide.

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31
Q

Endosomes

A

waste collection vehicles that sort and start breaking things down from outside the cell

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32
Q

what are the two building blocks of cells?

A

carbon and water

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33
Q

how does water support cells?

A

polarity and specific heat capacity

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34
Q

polarity

A

excellent solvent
This facilitates the delivery of nutrients and removal of wastes
Provides an environment that allows cells to exist within a network
facilitates the movement of chemical messengers within and between cells

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35
Q

specific heat capacity

A

high specific heat capacity allows for thermoregulation
critical for warm - blooded organisms, such as humans, that must regulate their body temperature
Water can absorb or release a large amount of heat without significantly changing its own temperature.

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36
Q

importance of carbon

A

four covalent bonds
This flexibility in bond formation allows it to form a large variety of molecules important to cellular life

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37
Q

LIPIDS

A

The building blocks for oils and fats
They are made of hydrocarbon chains
Usually quite hydrophobic and are therefore often insoluble in water
Lipids are commonly amphipathic
3 types in the body

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38
Q

Cholesterol:

A

Regulates cell membrane fluidity
forms compounds such as steroid hormones, bile acids, and certain vitamins.

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39
Q

Phospholipids:

A

Are amphipathic lipids that form cell membranes
They have a hydrophilic head and a hydrophobic tail that enables them to form the phospholipid bilayer of cells

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40
Q

Triglycerides:

A

Are the main component of body fat in animals
used to store energy

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41
Q

CARBOHYDRATES

A

4 classes
main nutrients in foods
body breaks carbs down into glucose (blood sugar)

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42
Q

sugar

A

simple building block of carbohydrates

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43
Q

Monosaccharides

A

Single carbohydrate molecules containing only carbon, hydrogen, and oxygen
glucose

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44
Q

Disaccharides

A

2 monosaccharides bonded together connected by a glycosidic bond
An example = sucrose, which is composed of a glucose connected to a fructose
Table sugar is crystallized sucrose

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45
Q

Oligosaccharides

A

composed of three to ten monosaccharides linked together
ex. Raffinose

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46
Q

Polysaccharides

A

longer chains, are even more complex, and play many important roles in the cell
glycogen

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47
Q

NUCLEOTIDES

A

building blocks of nucleic acids
ex. deoxyribonucleic acid ( DNA) and ribonucleic acid ( RNA )
Form adenosine triphosphate ( ATP ), the main form of cellular energy used to power reactions within an organism.
The basic molecular structure of a nucleotide = DNA or RNA sugar attached to a phosphate group and nitrogenous base

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48
Q

AMINO ACIDS

A

building blocks of peptides and proteins
The structure of amino acids =
an amino group, a central alpha carbon with an R -group, and a carboxylic acid group

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49
Q

The Carboxylic Acid Group

A

can also exist as a negatively charged carboxylate ( -COO -) group.

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50
Q

The R -group

A

unique to each amino acid
gives it its distinct molecular characteristics.

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51
Q

The Amino Group

A

can also exist as a positively charged -NH 3+ group.

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52
Q

how many amino acids are there? and what are they grouped into?

A

20 amino acids are grouped into categories based on their R -groups
aliphatic hydrophobic amino acids, aromatic hydrophobic amino acids, Charged Hydrophilic Amino Acids, Polar Amino Acids, Aromatic Amino Acids

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53
Q

Aliphatic:

A

The R -group consists of carbon chains which can be straight, branched, or non -aromatic rings.

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54
Q

Aromatic

A

The R -group contains an aromatic ring that has double bonds similar to benzene

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55
Q

Hydrophobic Amino Acids

A

non polar
can be aliphatic or aromatic

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56
Q

Aliphatic Hydrophobic Amino Acids

A

7 OF THEM
glycine, alanine, valine, leucine, isoleucine, methionine, and proline

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57
Q

Aromatic Hydrophobic Amino Acids

A

2 OF THEM
phenylalanine, tryptophan

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58
Q

what does Charged Hydrophilic Amino Acids mean?

A

carry a positive or negative charge, hydrophilic
charge is found on the outside of proteins where they can interact with water

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59
Q

positively charged R -groups

A

3 OF THEM
Lysine, arginine, and histidine

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60
Q

negatively charged R -groups

A

2 OF THEM
Aspartic acid and glutamic acid

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61
Q

Polar Amino Acids

A

hydrophilic
can form hydrogen bonds that stabilize proteins
6 OF THEM
serine, threonine, tyrosine, asparagine, glutamine, and cysteine

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62
Q

Cysteine:

A

sulfur -containing thiol (R−SH) that can form a covalent bond called a disulfide bond with another cysteine
needed for forming and maintaining three - dimensional protein structures

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63
Q

Aromatic Amino Acids

A

have ring structures with double bonds
very large amino acids

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64
Q

Aromatic Hydrophilic Amino Acid

A

tyrosine is polar (hydrophilic).

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65
Q

PEPTIDES AND PROTEINS

A

Proteins are made up of long chains of amino acids
normally more than 20 amino acids
form polypeptides
polypeptides fold into a 3D structure (tertiary) that is required for protein function

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66
Q

Types of proteins:

A

3 TYPES:

Enzymes
Receptors
structural proteins like keratin, which makes up nails and hair
hemoglobin, which carries oxygen in red blood cells.

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67
Q

Genome:

A

The complete set of genetic material in an organism; all of the DNA in a cell

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68
Q

Gene

A

A sequence of nucleotides in DNA that determines certain characteristics

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69
Q

FIVE CARBON SUGAR

A

contain a central five -carbon sugar, or monosaccharide.
The carbons of cyclic sugar rings are numbered, so the carbons are named from 1 to 5
Because of this numbering system, each sugar in a nucleotide will have a 5’ (i.e., five prime) and 3’ (i.e., three prime) end.

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70
Q

5 prime and 3 prime of carbon ring

A

The 5’ end of the sugar is where the phosphate group is attached in a single nucleotide
The 3’ end is where a phosphate group of a different nucleotide can form a bond.

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71
Q

ribose sugar

A

extra oxygen on the 2’ carbon.

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72
Q

deoxyribose sugar

A

DNA contains a lone hydrogen at the 2’ carbon and lacks the additional oxygen.

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73
Q

PHOSPHATE GROUP

A

1-3 phosphates attached to the 5’ carbon in nucleotides when it is not forming DNA
In DNA at the 5’ there is only one phosphate group
form high energy bonds and are why ATP can be used for energy
Phosphates are part of what is called the DNA sugar -phosphate backbone
Phosphates are attached to the 5’ carbon of one sugar and the 3’ carbon of another by a phosphodiester bond

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74
Q

Phosphodiester Bond:

A

covalent bond that joins a phosphate group to the 5’ carbon of one sugar and the 3’ carbon of another sugar

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75
Q

NITROGENOUS BASES

A

purines and pyrimidines found in both RNA and DNA

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76
Q

purines

A

two rings in their structure
in DNA are adenine (A) and guanine (G).

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77
Q

pyrimidines

A

only one ring in their structure
The three pyrimidines are cytosine (C), thymine (T), and uracil (U).
Thymine (T) is a pyrimidine that exists only in DNA
uracil (U) is a pyrimidine that exists only in RNA .

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78
Q

From nucleotides to DNA

A

nucleotide was 3 phosphates before getting joined to other nucleotides to form the phosphate backbone in DNA

2 phosphates are released to produce energy needed to form phosphodiester bonds

Now there is just one phosphate in the sugar phosphate backbone.

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79
Q

base pairing and bonding

A

Hydrogen bonds between opposite (complementary) bases on each strand form cross -linkages
The purines in one D N A strand will always base -pair with the pyrimidines in the opposing DNA strand
Adenine always pairs with thymine and guanine always pairs with cytosine
This bonding leads to the formation of a double -stranded DNA molecule
Each strand of the DNA is antiparallel to the other, because they run in opposite directions

80
Q

How and WHY does the double helix form

A

nitrogenous bases are hydrophobic
the sugar phosphate backbone is hydrophilic
when places in a cell (lots of water) the bases will go to the middle and the sugar phosphate backbone goes to the outside
this forms folding into the double helix shape

81
Q

Cytoplasm

A

he contents of the cell outside the nucleus that are contained by the plasma membrane.

82
Q

HOW RNA STRUCTURALLY DIFFERS FROM DNA

A

single stranded, uracil, ribose sugar

83
Q

single stranded

A

less stable than DNA

84
Q

uracil

A

pyrimidine uracil is used instead of thymine
base pairs with adenine

85
Q

ribose

A

The nucleotides in R N A contain ribose rather than deoxyribose. Recall that ribose has an extra oxygen on the 2’ carbon compared to deoxyribose.

86
Q

RNA purpose

A

to transport small copies of genes around the cell for a variety of uses.

87
Q

types of RNA

A

rRNA, mRNA, tTRNA

88
Q

Messenger RNA (mRNA )

A

carries instructions for making proteins in the cell

89
Q

Transfer RNA (tRNA )

A

brings amino acids for protein synthesis during translation.

90
Q

Ribosomal RNA (rRNA )

A

rRNA and ribosomal proteins make up ribosomes
which are in charge of translating RNA into protein
Ribosomes are an example of ribozymes -RNA that has the ability to catalyze chemical reactions

91
Q

genes

A

small pieces of DNA that contain specific instructions for the synthesis of a functional product, a molecule, needed to perform a job in the cell
that code for specific proteins

92
Q

where are genes located in eukaryotes?

A

on chromosomes

93
Q

types of genes

A

exons, introns, and regulatory sequences.

94
Q

Exons

A

Exons are the sections of a gene
Contain the information that is used to make a protein, called coding sequences, or coding DNA.

95
Q

Introns

A

Introns are sections of DNA that are not used to make a protein, called non -coding sequences, or non - coding DNA.

96
Q

Regulatory sequences

A

Control when a gene is turned on, or used
“regulate the gene”

97
Q

what is the central dogma?

A

explains that there are three key processes that need to occur for information to be converted from DNA to protein:
Replication, transcription, and translation

98
Q

semi conservative

A

each newly made DNA molecule has one original and one new strand of DNA

99
Q

why do we need to do DNA replication

A

before cell devision
so that each new cell has a copy of the parent genome

100
Q

Steps of DNA replication

A

initiation, elongation, and termination

101
Q

What is DNA Initiation

A

double -stranded DNA needs to be separated into single strands to begin replication
At regions in the DNA called the origin of replication (Orc) with the help of special proteins

102
Q

Initiation part 1

A

Protein Binding = A group of proteins binds to the ORC to begin replication

the most important = DNA helicase

ORC = where there a lot of A-T bonds because these ones only have 2 HYDROGREN BONDS

103
Q

Initiation part 2

A

DNA Unwinding = DNA helicase unwinds DNA into two single strands

Forming a structure that is called the replication fork

This is where the rest of replication occurs

As helicase moves down the DNA strand, so does the replication fork
This step requires energy
RNA Primers

104
Q

DNA Helicase

A

unwinds the DNA double helix by breaking the hydrogen bonds between the complementary bases

105
Q

RNA primers

A

short segment of single-stranded RNA used as a binding site for DNA polymerase to initiate DNA replication
needed to start replication

106
Q

DNA polymerase

A

enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA

107
Q

primase

A

an enzyme that synthesizes short RNA sequences called primers

108
Q

replication fork

A

a very active area where DNA replication takes place. It is created when DNA helicase unwinds the double helix structure of the DNA

109
Q

Initiation part 3

A

DNA can now be copied = Each single strand will act as a template for synthesis of a new complementary strand

The enzyme that accomplishes this is DNA polymerase

However, it needs several existing nucleotides at the beginning of the complementary strand to begin adding nucleotides with phosphodiester bonds

The solution to this is the enzyme primase

which adds a short number of RNA nucleotides at the beginning of the strand, called an RNA primer

110
Q

ELONGATION OF REPLICATION

A

DNA polymerase elongates the new complementary strand beginning at the primer
making a new strand in the 5’ to 3’ direction

and moves along the 3’ to 5’ on the parent strand

111
Q

Direction of elongation

A

DNA polymerase can only add nucleotides to the 3’ end of a D N A strand
Therefore can only move along the parent strand of DNA in the 3’ to 5’ direction
Creating a new strand that is in the 5’ to 3’ orientation

112
Q

Catalysis of elongation

A

DNA polymerase catalyzes the new phosphodiester bonds between an incoming nucleotide and the existing nucleotide on the backbone
ensures new nucleotide is the correct base pair to match the parent strand

113
Q

Leading Strand

A

runs in the 3’ to 5’ direction along the parent strand
DNA polymerase creates a new strand that is in the 5’ to 3’ orientation, in the same direction that the replication fork is moving, synthesis = continuous.
The leading strand can be elongated from one RNA primer alone

114
Q

lagging strand

A

built in the 5’ to 3’ direction running away from the replication fork
Because DNA polymerase can only build continuously in the 3’ to 5’ direction, this strand has to be made in fragments because as the DNA unwinds needs to jump back to where it is unwinding

As DNA polymerase moves away from the fork, it must repeatedly release and reattach. Each time DNA polymerase reattaches, it needs primase to make a new RNA primer, thereby creating a new DNA fragment.

These fragments are known as Okazaki fragments

115
Q

single stranded binding proteins ( SSBP s )

A

bind to single stranded DNA To mitigate potential damage to the lagging strand while it is not yet being replicated
cannot fight off damage forever

116
Q

OKAZAKI FRAGMENTS

A

on the lagging strand
not continuous

117
Q

LIGASE

A

goes through the new strand of DNA and catalyzes the phosphodiester bonds
By sealing these gaps in the DNA backbone, ligase joins the Okazaki fragments on the lagging strand.

Once all of the RNA primers have been replaced with DNA and ligase has joined the backbones of the Okazaki fragments, the new DNA double helices are almost complete

118
Q

TERMINATION OF DNA REPLICATION

A

All RNA primers have been removed, leading to a new problem.
When the replication fork reaches the end of a DNA molecule, a section of the lagging strand cannot be replicated.
DNA polymerase requires an RNA primer to initiate DNA synthesis.
At the end of the lagging strand, there is insufficient space for primase to add an RNA primer.
DNA polymerase is unable to begin DNA synthesis.
This results in a single-stranded stretch of uncopied DNA, known as an overhang.

119
Q

OVERHANG: SHORTENING OF CHROMOSOMES

A

If the overhang on the lagging strand were to be left as it is, there would be a very small region of the parent (lagging) strand DNA that is left unreplicated and unpaired (the 3’ overhang)
This overhang would be degraded, since single strand DNA is very unstable.
Therefore, after every cycle of DNA replication, there would be a gradual loss of DNA at this end, causing chromosomes to shrink over time, which would be very damaging to a cell.

120
Q

how does the cell stop the negative affects of overhang?

A

the cell has a mechanism in place to prevent the loss of DNA. TELOMERES AND TELOMERASE

121
Q

TELOMERES

A

extend the ends of DNA.
Telomeres are long, non -coding sections of DNA that are added to the ends of each chromosome.
Since they are non -functional, they can be degraded over cell cycles without affecting cell function.

122
Q

Telomerase

A

adds telomeres is called telomerase

It carries a short piece of RNA within the enzyme that binds to the 3’ overhang and extends past the DNA

RNA Template Telomerase is an RNA -dependent DNA polymerase, so it can make DNA using RNA as a template

The RNA carried by the telomerase is then used as a template to add a corresponding DNA strand to this extension

123
Q

overhang after telomeres are used

A

There is now an extra long 3’ overhang that contains repetitive, non - functional DNA.
An RNA primer is added, and DNA polymerase adds DNA like usual until there is not enough of a 3’ lead for the enzyme to proceed

124
Q

TRANSCRIPTION

A

Transcription is the process by which information is rewritten

125
Q

what are the 3 steps in transcription?

A

initiation, elongation and termination

126
Q

RNA Polymerase

A

synthesizes/makes RNA from DNA

127
Q

The 3 types of RNA polymerase in eukaryotes?

A

RNA polymerase I, RNA polymerase II, RNA polymerase III

128
Q

RNA polymerase I

A

responsible for synthesizing most of the rRNA required for a functional ribosome

129
Q

RNA polymerase II (RNA pol II)

A

synthesizes messenger RNA (mRNA)

130
Q

RNA polymerase III

A

synthesizes transfer RNA (tRNA)
and some other RNA molecules.

131
Q

Transcription Factors

A

group of proteins that binds to specific DNA sequences

By doing so controls the rate of transcription from DNA to RNA

Transcription factors can promote (as an activator) or block (as a repressor) the transcription of genes

132
Q

where do transcription factors bind?

A

to regulatory regions of a gene
Signal to transcriptional machinery, including RNA polymerase, which genes need to be transcribed

133
Q

STAGE 1: INITIATION OF TRANSCRIPTION

A

binding of transcription factors to a specific DNA sequence

This sequence is a regulatory region of DNA located upstream to the beginning of the gene

The regulatory region controls whether a gene is turned on or off

Once this happens, RNA pol II can bind to the DNA of the gene

It attaches to a specific location called the promoter

The promoter region is the “start site” for transcription

Contains the nucleotide sequence 5’-TATAAA -3’, known as the TATA box

134
Q

promoter region

A

is the start site for transcription

135
Q

tata box

A

sequence of DNA found in the core promoter region of genes in eukaryotes.

136
Q

STEP 1: THE TRANSCRIPTION COMPLEX

A

RNA polymerase II (transcribes eukaryotic mRNAs) cannot bind to a promoter by itself

Requires other transcription factors that are added in a specific order to the promoter and interact with RNA polymerase II to efficiently transcribe the mRNA.

137
Q

3 steps for transcription to start

A
  1. Guiding R N A pol II to the correct DNA strand.
  2. Unwinding the double -stranded DNA is enough for RNA pol II to access the gene being transcribed.
  3. Activating the enzyme function of RNA pol II by phosphorylating it twice.
138
Q

What might happen if there was a mutation in the promoter region of a gene?

A

initiation of transcription depends on the binding of transcription factors to the promoter region

A mutation in the sequence could result in silencing the expression of the entire gene.

139
Q

STAGE 2: ELONGATION OF TRANSCRIPTION

A

The moving of the transcription complex (made up of RNA pol II and the transcription factors) synthesizes the mRNA molecule

140
Q

How is mRNA synthezised in elongation

A

RNA pol II uses the DNA template strand to synthesize the mRNA

141
Q

how does elongation work?

A

elongation is the stage when the RNA strand gets longer, thanks to the addition of new nucleotides.
During elongation, RNA polymerase “walks” along one strand of DNA, known as the template strand, in the 3’ to 5’ direction. For each nucleotide in the template, RNA polymerase adds a matching (complementary) RNA nucleotide to the 3’ end of the RNA strand.

142
Q

The transcription bubble

A

formed by RNA pol II, unwound DNA, and the formation of the mRNA molecule

143
Q

Template strand:

A

The template strand is the one that RNA polymerase uses as the basis to build mRNA

144
Q

STAGE 3: TERMINATION OF TRANSCRIPTION

A

The stopping of transcription

145
Q

Transcription typically ends when:

A

RNA is cleaved from RNA pol II by a separate enzyme, well past the coding sequence of the gene.
The transcription bubble collapses.
The RNA molecule dissociates from the DNA template.
RNA pol II detaches from the DNA.

146
Q

DNA polymerase vs RNA pol II

A

RNA pol II does NOT have proofreading abilities

147
Q

How does RNA pol II make sure the right base pairings are happening and that mRNA is getting formed?

A

RNA pol II produces several short RNA molecules until one correctly forms complementary hydrogen bonds with the DNA template strand

148
Q

POST -TRANSCRIPTIONAL RNA PROCESSING

A

Only in eukaryotes

The cell has now finished synthesizing an mRNA molecule

RNA is designed to be short -lived in the cell since the changing demands of the cell need different proteins to be made at different times

However, the cell needs a way to keep the newly made mRNA around long enough to produce the proteins it needs

To preserve the newly produced mRNA molecule, make it functional, and deliver it to its final location, some modifications are made after transcription

149
Q

How does the cell preserve the newly produced mRNA molecule?

A

Three post -transcriptional mRNA modifications are made:

5’ methylguanosine cap
3’ polyadenylation (poly(A) tail)
Splicing

150
Q

what is the 5’ methylguanosine cap? when does it occur?

A

occurs shortly after mRNA synthesis

To protect the mRNA molecule from premature degradation by nucleases, which degrade nucleotides 5’ methylguanosine cap is added to the m R N A molecule

Guanosine Triphosphate
A guanosine triphosphate (GTP) is added to the 5’ end of the mRNA via an unusual 5’ to 5’ triphosphate linkage

151
Q

why is GTP added to 5’ end of the mRNA?

A

This makes it more stable and protects it from being broken down

152
Q

Methylation

A

Immediately after capping, this GTP has a methyl group added to the 7 position of the guanine base

153
Q

RNA MODIFICATION: 3’ POLYADENYLATION

A

5’ methylguanosine cap is added
2 modifications occur in the same time period
The first modification is 3’ polyadenylation
A different type of polymerase called poly(A) polymerase adds around 200 adenosines to the 3’ end of the mRNA immediately after it is cut from the RNA pol II
This creates a structure called a poly(A) tail

154
Q

Why is 3’ POLYADENYLATION essential?

A

for binding proteins that are necessary to transport the m R N A out of the nucleus and to start the process of translation

155
Q

RNA MODIFICATION: RNA SPLICING

A

same time as the poly(A) tail

Introns do not correspond to protein production

Therefore, they need to be removed from mRNA before it is translated into a protein

Splicing is the mechanism that cells use to remove the introns from the m RNA sequence, leaving only the mRNA that codes for protein (exons).

This is performed by a protein/ RNA complex called the spliceosome
The splicing event requires breakage of the exon - intron junctions and joining of the ends of the exons

156
Q

spliceosome

A

protein/RNA complex that breaks the exon - intron junctions and joins the ends of the exons back together

157
Q

What might be the consequences of a mutation in the splicing sites of a gene?

A

mutations at the splicing sites can lead to incorrect splicing that may lead to improper protein translation.

158
Q

TRANSPORT THROUGH THE NUCLEAR PORE COMPLEX

A

after post -transcriptional modifications are completed, the mRNA needs to exit the nucleus to be translated into protein in the cytoplasm

mRNA exits through the nuclear pore of the nucleus

159
Q

TRANSLATION

A

mRNA is modified, spliced, and in the cytoplasm, translation from an mRNA transcript to a protein can begin.

160
Q

FROM NUCLEOTIDES TO AMINO ACIDS

A

Proteins are composed of long chains of amino acids that are held together by peptide bonds
mRNA encodes these amino acids

161
Q

mRNA

A

Cells decode mRNA by reading their nucleotides in groups of three, called codons .

162
Q

Amino acids

A

1 codon

163
Q

I codon

A

3 nucleotides long (AUG)

164
Q

How many possible codons are there?

A

64 possible different codons.

165
Q

THE STANDARD GENETIC CODE

A

The full set of relationships between codons and amino acids

166
Q

Stop codons

A

UGA, UAG, and UAA

167
Q

Start codon

A

AUG (met)

168
Q

what does starting sequence of the mRNA show?

A

if mRNA will either stay in the cytoplasm, or it will be directed to the endoplasmic reticulum.

169
Q

tRNA

A

deliver the correct amino acid to a growing peptide

tRNA will recognize a codon by containing a complementary sequence to the codon, termed the anticodon

170
Q

Ribosome

A

composed of a large and small subunit, both made of rRNA

171
Q

The small subunit

A

responsible for binding to mRNA

172
Q

The large subunit

A

has three important sites: The A site, P site, and E site.

173
Q

3 steps of translation

A

initiation, elongation, and termination

174
Q

STAGE 1: INITIATION OF TRANSLATION

A

when the ribosome assembles around the mRNA

Requires the initiation factors to help the small ribosomal subunit find the correct AUG site (start codon) to begin the translation of mRNA into protein.

175
Q

Initiation Factors

A

bind to the mRNA molecule, including the 5’ cap binding factors, the poly(A) binding protein (PABP) and the poly(A) tail

proteins that bind to the small subunit of the ribosome during the initiation of translation

176
Q

Once initiation factors binded to mRNA

A

initiation factors guide the small ribosomal subunit complex to attach to the mRNA molecule at the 5’ end near the methyl - guanosine cap

then the small ribosomal subunit and initiator tRNA moves along the mRNA to find the start codon

then The small ribosomal subunit attaches to the initiator tRNA, which carries the amino acid methionine.

177
Q

what are the key components required for translation inititaion

A

mRNA, ribosomal large and small subunit and initiator tRNA (amino acid and complementary anticodon), GTP (required energy source for initiation complex), initiation factors

178
Q

initiator tRNA

A

only reads the start codon AUG on the mRNA to start translation

179
Q

Large ribosome subunit in initiation

A

Once the initiator tRNA is bound to the start codon

The large ribosomal subunit encloses the mRNA, with the initiator tRNA in the P site

The formation of the complex of the small and large ribosomal subunits completes initiation of translation.

180
Q

What are the key components required for peptide chain elongation?

A

tRNA that carries amino acids and anticodons, elongation factors, release factors and GTP

181
Q

elongation translation overview

A

multi step process that moves forward in a continuous loop

Each cycle adds one amino acid to the growing chain of amino acids, called a peptide.

This process requires energy

These steps are coupled with the consumption of GTP which is an energy -rich molecule similar to ATP

This is needed to drive the process forward.

182
Q

tRNA Binding

A

The A site of the ribosome is where aminoacyl tRNA is first attached to the ribosome
The new tRNA is charged with GTP and will have an anticodon complementary to the A site codon

183
Q

Peptide Bond Formation

A

The GTP on the aminoacyl tRNA in the A site is converted to GDP, and peptidyl transferase

An enzyme within the large ribosomal subunit, moves the growing peptide in the P site onto the tRNA amino acid in the A site.

The P site is where the amino acid chain is removed from the tRNA and added to the next amino acid by a peptide bond in the A site.

184
Q

Translocation

A

The ribosome next translocates down one codon on the mRNA moving the mRNA and tRNAs down from the A and P sites to the P and E sites
This also requires GTP.

before it moves peptide bonds need to be formed between amino acids on P and A site. Amino acids all attach to A site and then when ribosome is moves the tRNA is moved to the E site were it exits

Moves to the right

185
Q

E site

A

The E site is where spent tRNA is ejected from the ribosome.

The ribosome is now ready for the next charged tRNA to enter the A site.

186
Q

A site

A

acceptor site for new tRNA carrying amino acids

187
Q

P site

A

where the polypeptides are being made

188
Q

STAGE 3: TERMINATION OF TRANSLATION

A

The growing peptide chain ends when a stop codon is reached (i.e., U A A, U A G, U G A).

Stop codons are not connected to a tRNA molecule.

189
Q

how do we know when termination of translation starts?

A

when the stop codon appears on the mRNA

These codons are recognized by release factors

190
Q

what do release factors do?

A

recognize stop codons

release factors go to the A site of the ribosome and hydrolysis which is linking the peptide chain and tRNA

This releases the peptide chain

191
Q

how do you release release factors from the ribosome

A

energy consuming process

and the whole ribosomal complex dissociates

This results in the release of the large and small ribosomal subunits from the mRNA
which can be recycled for more translation.

192
Q

Repair During DNA replication

A

DNA polymerase has a proofreading function and can check to ensure no mistakes have been made.

193
Q

Repair Throughout The Cell Cycle

A

DNA repair proteins are continually scanning DNA for errors and making repairs
Some check immediately after replication, fixing the newly synthesized strand of DNA, whereas others check at different points throughout the cell cycle.

194
Q

TYPES OF MUTATIONS

A

Point Mutations, INSERTION, deletion,

195
Q

Point Mutations:

A

a single nucleotide is changed, resulting in one of three outcomes:

  • Silent Mutation *: The mutation does not cause the amino acid to change.
  • Missense Mutation *: The mutation does cause the amino acid to change.
  • Nonsense Mutation *: The mutation replaces an amino acid codon with a stop codon, ending translation, and preventing the production of the rest of the amino acid. This is very detrimental, especially near the start of a sequence.
196
Q

INSERTION

A

extra base pair is added to DNA.

This shifts the 3 -base pair reading frame down by one

can alter every amino acid produced
Insertions may also involve the addition of multiple base pairs

A similar reading frameshift effect is seen with two base pairs, but three will add a new amino acid and keep the reading frame intact

This is a type of frameshift mutation

197
Q

Deletion

A

a base pair or more is removed from the D N A sequence.

Deletions may involve the removal of multiple nucleotides

This is another form of frameshift mutation.

198
Q

LARGE SCALE DELETION, INSERTION, RECOMBINATION

A

Multiple deletions, insertions, or recombinations of nucleotides can involve entire chromosomes or just parts of chromosomes.
These changes are often lethal

PHGY 170 Midterm (1 decks)

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