6315 Lesson 3 (p. 1 & 2) Flashcards
What are the 3 basic components of a nucleotide?
Nitrogenous bases
Pentose sugar
Phosphate group
What composes the nitrogenous bases? and Pentose Sugar?
Purine bases – Adenine and Guanine
Pyrimidine bases – Thymine and Cytosine
In RNA: Uracil instead of Thymine
Pentose: Deoxyribose in DNA; In RNA: Ribose
What is the Composition and Structure of DNA?
Nucleoside – Pentose sugar + Nitrogen base
Nucleotide – Phosphate group + Pentose sugar + Nitrogen base
What did Watson and Crick demonstrate?
How the 3 components are physically assembled to form DNA
Double helix model – DNA is like a twisted ladder with chemical bonds as its rungs
Nucleotides are joined to form what?
a polynucleotide chain
What is a phosphodiester bond?
Covalent bond that links adjacent nucleotides
5’-phosphate group of the new nucleotide is linked to the free 3’-OH group of the existing nucleotide
What orientation of the phosphodiester bond linkages continues throughout the chain?
The 5’ – 3’ – 5’ – 3’ orientation
What holds the DNA strands together?
Hydrogen bonds
In a DNA duplex, the 5′ end of one strand is opposite the 3′ end of the other. They have opposite orientations so they are________.
antiparallel
What is the important attachment sites of DNA Binding Proteins involved in replication and transcription?
Major and Minor Grooves
What are the components of the central dogma of molecular biology?
Replication, Transcription, Translation
Why is replication important in duplicating the DNA?
So that there will be sister chromatids at anaphase stage and at the end of cytokinesis, each daughter cell would have the genetic material.
DNA replication is described as what?
Semiconservative
Why is replication semiconservative?
Parental DNA strand separates into two
What are the major steps in replication?
- Unwinding of the double stranded DNA
- DNA synthesis
- Rewinding of the double helix
What unwinds the two DNA strands at the replication fork?
Helicase
What are the components of the replication machinery?
Helicase
Single-strand DNA binding proteins (SSB)
DNA Gyrase
What stabilizes ssDNA as it forms so it will not anneal to reform the double helix?
SSB
What does DNA gyrase do?
Releases the tension (positive supercoils) ahead of the replication fork caused by the unwinding of the DNA helix
What are the processes in Replication?
- Unwinding of parental strands through Helicase protein binding creating a replication fork
- Stabilizing the ssDNA through the single-strand DNA binding proteins (SSB) at the replication fork
- Primase binding at the replication fork to synthesize short RNA primer, needed at the start of DNA synthesis, since it provides the 3’-OH group, to which new nucleotides are added
- DNA polymerase binding at the DNA template which adds DNA nucleotide at the RNA primer
- Adding of nucleotides by DNA polymerase in a 5’ to 3’ direction to both Parental DNA template
- The other strand produced short fragments (Okazaki fragments), known as discontinuous synthesis
- DNA polymerase proofreading the newly synthesized DNA and replacing incorrect bases
- Annealing helicase rewinding the DNA double helix and ligase sealing the sugar phosphate
Major steps in transcription?
Initiation
Elongation
Termination
__________ is the process by which an RNA sequence is formed from a DNA template.
Transcription
What are the roles of two complementary DNA strands in transcription?
Template strand and Coding strand
Aka: sense strand
Coding strand
Has the same sequence as the RNA produced, with exception of U replacing T
Coding strand
Aka: antisense strand
Template Strand
Template strand used in the synthesis of?
RNA
Non-template strand
Coding strand
What is the type of RNA produced by the transcription process?
Messenger RNA (mRNA)
What is the process of transcription?
- One of the RNA polymerase enzymes (RNA polymerase II for mRNA) binds to a promoter site on the DNA
- RNA Pol pulls a portion of the DNA strands apart from each other, exposing unattached DNA bases
- One of the two DNA strands provides the template for the sequence of mRNA nucleotides
- The RNA sequence is synthesized only in 5’ to 3’ direction
- Transcription continues until a group of bases called termination sequence is reached
- DNA strands and RNA Pol separate from the transcribed single mRNA strand (primary transcript)
What is the antisense strand and sense strand?
- Antisense strand – template DNA strand
- Sense strand – other DNA strand that doesn’t serve as template
RNA Pol moves in ____ direction along the DNA template strand while assembling mRNA strand from _____.
3’ to 5’ ; 5’ to 3’
What are modifications that occur in a primary mRNA molecule before it leaves the nucleus?
Post-transcription Modifications
T or F: RNA products of transcription are functional RNAs
F, RNA products of transcription are not necessarily functional RNAs
What are the processes in Post-transcription Modifications?
Splicing
Capping
Polyadenylation
5’ end of RNA is capped by the addition of a methylated guanine nucleotide
Capping
In splicing, _______ are excised, and the exons are __________ to form a shorter mature mRNA
Introns in the precursor mRNA ; spliced together
In polyadenylation, 3’ end acquires a ____that contains approx. _______adenine residues.
poly(A) tail ; 200 adenine residues
Major steps in translation?
Initiation
Elongation
Termination
Translation is the process in which _______.
mRNA provides a template for the synthesis of a protein
Structures involved in translation are?
mRNA
rRNA
tRNA
Ribosomes
Component of ribosome (structural support and catalytic activity)
rRNA
tRNA is an adaptor molecule that provides what?
physical and informational link between mRNA and the polypeptide being synthesized
Carries code for protein synthesis
mRNA
Ribosomes are the site for?
Protein synthesis
How many subunits are ribosomes made out of?
2 (small and large)
Small or large unit: decoding site; mediates interaction between mRNA and tRNA
Small
What does the large subunit of the ribosome do?
It is an active site; catalyzes peptide bond formation
What is the process of translation?
The ribosome finds the initiation site on the mRNA sequence
The ribosome binds the tRNA to its surface so that base pairing can occur between tRNA and mRNA
The ribosome moves along the mRNA, codon by codon, in the 5’ to 3’ direction
As each codon is processed, an amino acid is translated by the interaction of mRNA and tRNA
The ribosome provides an enzyme that catalyzes the covalent peptide bonds between adjacent amino acids, resulting in a growing polypeptide – catalyzed by enzyme peptidyl transferase
Termination of translation occurs when the ribosome arrives at a stop codon on the mRNA sequence
Upon completion of synthesis, the mRNA, ribosome and polypeptide separate from one another
The polypeptide is released into the cytoplasm
What are post-translational modifications?
Modifications that occur in newly synthesized polypeptides to become functional proteins
Examples of post-translational modifications?
Proteolytic cleavage into smaller polypeptide units
Combination with other polypeptides to form larger proteins
Addition of carbohydrate or lipid moieties
Modification of amino-acid side chains
What are the types of protein by structure?
Primary
Secondary
Tertiary
Quaternary
What are the types of protein by composition?
Simple and Conjugated
What are the types of protein by function?
Enzymes
Structural
Storage
Protective
Regulatory
Nerve Impulse Transmission (Hormones)
Movement (Contractile)
Transport
What kind of protein: local folded proteins that occur inside a polypeptide due to atom interactions (alpha-helix and beta-pleated sheets)
Secondary
What kind of protein: Amino acid residues plus prosthetic groups
Conjugated
What kind of protein: three-dimensional framework of the polypeptide, due to interactions between the R groups of the AA sequence of the protein
[Hydrophobic interactions, H bonds (non- covalent bonds), sulfur bridges]
Tertiary
What kind of protein: bind to DNA to switch the gene on or off
Regulatory
What kind of protein: Contain a series of amino acids only
Simple
What kind of protein: linear sequence of amino acids
Primary
What kind of protein: association of two or more polypeptides into a multi-subunit complex ; assembly of individual polypeptides into a larger functional cluster
(contains more than one subunit – hemoglobin)
Quaternary
What kind of protein: serves as antibodies that protect the body from antigens ; serves as coagulation factors
Protective
What do storage proteins store?
store amino acids or ions
Hormones carry what?
carry extracellular signals from cell to cell
The cell cycle represents what?
a self-regulated sequence of events that controls cell growth and cell division
What is the goal of the cell cycle?
to produce two daughter cells, each containing chromosomes identical to those of the parental cell
What are the 2 principle phases of the cell cycle?
Interphase and M phase (mitosis)
The cell membrane contains what?
cholesterol, cardiolipin, sphingomyelin; also contains carbohydrates known as oligosaccharides and membrane proteins
What is the core of the cell membrane?
based on the fluid-mosaic model, the lipid bilayer is the core of the membrane
Which side of the layer is hydrophobic and hydrophilic?
Hydrophobic - inside
Hydrophilic - outside
What are the membrane proteins of the cell membrane?
Integral proteins
Lipid-anchored proteins
Peripheral proteins
Where are organelles suspended?
Cytosol
How many Svedberg units are the small and large units in the ribosomes?
40S (small) ; 60S (large)
Where is rRNA synthesized?
In the nucleolus
Where can ribosomes be found?
free flowing, on the RER, attached to the perinuclear membrane
What is the double membrane-bound organelle?
ER (RER, SER)
Which ER is responsible for protein synthesis because of the ribosomes embedded in this membrane?
RER
What is SER responsible for?
This is responsible for glucose and lipid synthesis.
T or F: RER is situated very near the nuclear membrane.
T, for the translation to occur
Where are the newly synthesized proteins processed and modified?
Golgi body
What organelle: smooth membranes consisting of flattened, disc-like cisternae with dilated rims and associated vesicles and tubules
Golgi
What does the mitochondria provide to the cell?
ATP via cell respiration
Mitochondria contains several enzymes and proteins embedded in its inner membrane called _______.
cristae
What makes chloroplast special?
a type of plastid which is found in plant cell
contains chlorophyll located at the thylakoid membrane
thethylakoids are stacked together to form granum (plural grana) suspended in stroma
responsible for photosynthesis
What is the complex structure that contains two barrel- shaped centrioles surrounded by amorphous, electron dense pericentriolar material (PCM)
Centrosome
What organelle: generally small and help sequester waste products
Vacuole
in plant cell, the vacuole is a fluid filled structure that is made up mostly of_______.
water
What provides structural support and internal framework responsible for positioning various organelles within the interior of the cell?
Cytoskeleton
Cytoskeleton has an elaborate interactive network composed of three well defined filamentous structures which are?
microtubules, microfilaments, and intermediate filaments
________ are found in the interior of the cell where they maintain cell shape by resisting compressive forces.
Microtubules
__________ are found throughout the cell and hold organelles in place.
Intermediate filaments
___________ thicken the cortex around the inner edge of a cell; they resist tension.
Microfilaments
What do peroxisomes form?
formation of hydrogen peroxide thru substrate oxidation
Peroxisomes are also known as?
Microbodies
What is the nucleus made up of?
̶ Nuclear membrane
- Chromosomes
̶ Nucleolus
How many layers makes up the nucleus?
2 (inner and outer)
Each of the nuclear membranes contains?
two layers of phospholipids, arranged with their tails pointing inward (forming a phospholipid bilayer)
Chromosomes are threadlike strands of nuclear DNA with proteins called ______.
histones
in mitosis, the chromosomes condensed from chromatin to _____ becoming more visible under the light microscope
meta-chromosome
T or F: Chromosomes do not come in pairs.
F, homologous
What is found inside the nucleus suspended in nucleoplasm?
Nucleolus
What is the ribosome-producing organelle?
Nucleolus
When is the nucleolus prominent?
interphase
T or F: Human cells have cell wall.
F, only in plants
Cell wall is made up of?
pectin, glycan and cellulose microfibrils
The Cell Cycle Is Regulated by?
Protein Kinases.
The key enzymes that control the transitions between the different states of the cell cycle, and the entry of nondividing cells into the cell cycle, are the?
cyclin-dependent protein kinases, or CDKs
T or F: Cell division is a vital process that requires orderly progression.
T
_______ are among the most important core cell cycle regulators.
Cyclins
What are cyclins?
Cyclins are a group of related proteins, and there are four basic types found in humans and most other eukaryotes: G cyclins, G /S cyclins, S cyclins, and M cyclins.
Which cyclin: bind Cdks at the end of G1 and commit the cell to DNA replication
G1/S
Which cyclin: promote the events of mitosis
M-cyclin
Which cyclin: binds Cdks during S phase and are required for the initiation of DNA replication
S-cyclin
Which cyclin: help to promote passage through “ Start” or the restriction point in late G1
G1-cyclins
What enzyme phosphorylates proteins using ATP?
Protein kinases
The transition from G1 to S requires ________.
a set of cyclins ( G1 cyclins)
CDKs possess two tyrosine phosphorylation sites: What are these?
One causes activation of the enzyme; the other causes inactivation.
Specific kinases carry out what?
stimulatory and the inhibitory phosphorylation
________ can remove phosphate from CDKs, either stimulating or inhibiting their activity, depending on the position of the phosphate.
Protein phosphatases
What plays an important role in regulating the cell cycle in animals?
Cyclin inhibitors
How is CDK activity regulated?
(1) cyclin synthesis and destruction and
(2) the phosphorylation and dephosphorylation of key amino acid residues within the CDK protein.
CDKs are inactive until?
they are associated with a cyclin.
T or F: It takes time for most cyclins turn over.
F, it is rapid
Where are cyclins degraded and by what structure?
proteasome
Before destruction, what marks the cyclins?
ubiquitin, this process requires ATP
What are checkpoints?
internal quality control mechanisms represented by biochemical pathways that control transition between cell- cycle stages
monitor and modulate the progression of cells in response to intracellular or environmental signals
Who discovered cell checkpoints?
Leland Hartwell and Ted Weinert (1988)
What is mitotic catastrophe?
The failure to arrest the cell cycle before or at mitosis, resulting in aberrant chromosome segregation
What causes mitotic catastrophe?
The malfunction of cell cycle checkpoints and may lead to cell death and tumor cell development
Malfunction of the restriction checkpoint may be facilitated by________.
the viral proteins of several cancer- causing viruses
How long does the G1 phase last?
9-12 hrs
When does the G1 phase begin?
at the end of M phase
What happens in the G1 phase?
the cell gathers nutrients and synthesizes RNA and proteins necessary for DNA synthesis and chromosome replication
What monitors the integrity of newly replicated DNA?
G1 DNA - damage checkpoint
What is mediated by interactions between pRb and a family of E2F with target promoters?
Restriction checkpoint
What is the restriction checkpoint sensitive to?
the size of the cell, the state of the cell’s physiologic processes, and its interactions with extracellular matrix
How long does the S phase last?
7.5-10hrs
What happens in the S phase?
DNA is replicated
Chromosome replication is initiated at many different sites along the chromosomal DNA - replicon
What is the checkpoint of the S phase?
S DNA-damage checkpoint
How long does the G2 phase last?
3.5 - 4.5 hours
What happens to the cell in the G2 phase?
the cell prepares for cell division and examines its replicated DNA in preparation for cell division
period of cell growth and reorganization of cytoplasmic organelles before entering the mitotic cycle
What is the checkpoint of the G2 phase?
G2 DNA-damage checkpoint and the unreplicated-DNA checkpoint
How long does the M phase last?
about 1hr
Mitosis almost always includes?
Karyokinesis (division of nucleus) and Cytokinesis (division of cell)
Checkpoint of M phase?
spindle-assembly checkpoint and the chromosome-segregation checkpoint
What is the resting phase?
G0
What happens in the G0 phase?
reserve stem cell population
What are the stages of Mitosis?
PMAT
In prophase, sister chromatids are held together by the ring of proteins called ____ and ______.
cohesins and the centromere
What is the late prophase called?
Prometaphase
What phase of mitosis: marked by the reconstitution of a nuclear envelope around the chromosomes at each pole
Telophase
What phase of mitosis: begins at the initial separation of sister chromatids
Anaphase
What phase of mitosis: replicated chromosomes condense and become visible
Prophase
In pro metaphase, a highly specialized protein complex called a_______appears on each chromatid opposite to the _______.
kinetochore ; centromere
What phase of mitosis: begins as the mitotic spindle, consisting of three types of microtubules, becomes organized around the microtubule- organizing centers (MTOCs) located at opposite poles of the cell
Metaphase
What phase of mitosis: chromosomes uncoil and become indistinct except at regions that will remain condensed in the interphase nucleus
Telophase
What are the 3 kinds of microtubules present in metaphase?
A. astral microtubules
B. polar microtubules
C. kinetochore microtubules
What phase in mitosis: the nuclear envelope begins to disintegrate into small transport vesicles and resembles the sER
Prometaphase
T or F: Cytoplasmic events are markedly different in males and females
T
What are similar between male and female?
Nuclear events
What is meiosis I known as (what kind of division)?
Reductional division
Meiosis II is what kind of division?
Equatorial
Equatorial or Reductional: No DNA replication
Equatorial
Equatorial or Reductional: the amount of DNA is reduced from the (4d) to (2d).
Reductional
In reductional division, chromosome number is reduced from?
diploid (2n) to haploid (1n)
In equatorial division, what happens to the number of chromosomes?
remains at (1n), although the amount of DNA represented by the number of chromatids is reduced to (1d).
In what phase is DNA replicated, forming sister chromatids?
S phase
What are the phases of Meiosis I?
- Prophase I
Five Stages:
A. Leptotene
B. Zygotene
C. Pachytene
D. Diplotene
E. Diakinesis - Metaphase I
- Anaphase I
- Telophase I
What are the phases of Meiosis II?
Prophase II
Metaphase II
Anaphase II
Telophase II
In metaphase I, homologous chromosomes are still held together by what?
chiasmata
What phase of meiosis I: homologous chromosomes condense and shorten to reach their maximum thickness
Diakinesis
What phase of meiosis I: Sister chromatids also condense and become connected with each other by meiosis-specific cohesion complexes.
Leptotene
In diplotene, what dissolves and what further develops after?
Early in this stage, the synaptonemal complex dissolves, and the chromosomes condense further.
What phase of meiosis I: crossing over occurs early in this phase and involves transposition of DNA strands between two different chromosomes and synapsis is complete
Pachytene
What phase of meiosis I: formation of a synaptonemal complex
Zygotene
What phase of meiosis I: pairing of homologous chromosomes of maternal and paternal origin is initiated
Leptotene
What phase of meiosis I: pairing of homologous chromosomes, synapsis and recombination of genetic material on homologous chromosomes is observed.
Prophase I
What phase in Meiosis I: nucleolus disappears
and nuclear envelope disintegrates
Diakinesis
What phase in Meiosis I: The sister chromatids, held together by cohesin complexes and by the centromere, remain together and centromeres do not split
Anaphase I and Telophase I
What phase provides genetic diversity?
Anaphase I and Telophase I
What meiosis I phase: Once the nuclear envelope has broken down, the spindle microtubules begin to interact with the chromosomes through the multilayered protein structure which is usually positioned near the centromere
Metaphase I
In metaphase I, where are the chromosomes located?
paired chromosomes are aligned at the equatorial plate with one member on either side
In which phase do sister chromatids still remain closely associated with each other?
Diplotene
What are Barr bodies?
inactivated X chromosomes seen in female somatic cells present adjacent to the nuclear membrane.
stains intensely with nuclear dyes
absent in male nuclei
CYCLIN AT G1/S CHDCKPOINT?
CYCLIN E
CYCLIN AT M CHECKPOINT
D
CYCLIN AT G2 CHECKPOINT
B
WHAT CONTAINS THE CODON?
MRNA
WHAT HAS THE ANTICODON?
TRNA
WHAT IS FOUND IN THE CYTOPLASM ONLY
RRNA AND TRNA
WHAT IS IN THE NUCLEUS AND CYTOPLASM
RRNA
WHERE AA ATTACHES
TRNA
HAS ACTIVE SITE
RRNA
