Molecular and cellular biology

Objective assessment study material. Study and failed PRE assessment

How are monomers bonded together to form macromolecules?

Monomers are bonded together to form macromolecules through dehydration reactions, where a water molecule is removed.

How are the bonds between monomers of macromolecules disrupted?

The bonds between monomers of macromolecules are disrupted by hydrolysis, where a water molecule is added.

What are the four basic biological macromolecules?

Carbohydrates, lipids, nucleic acids, and proteins.

What are the four levels of protein structure?

Primary, secondary, tertiary, and quaternary structure.

What are the steps in the cell cycle and what occurs in each step?

G1, S, G2, and M phase. G1 involves cell growth and preparation for DNA replication. S phase involves DNA replication. G2 involves further growth and preparation for mitosis. M phase involves mitosis and cytokinesis.

How do the major checkpoints of the cell cycle help regulate cell division?

The major checkpoints of the cell cycle are G1-S, G2-M, and metaphase-anaphase. These checkpoints ensure that the cell cycle progresses correctly and prevent errors.

How are cyclins and cyclin-dependent kinases involved in the regulation of the cell cycle?

Cyclins and cyclin-dependent kinases regulate the cell cycle by phosphorylating target proteins that promote cell cycle progression.

How are disruption of mitosis and cell cycle checkpoints involved in the development of cancer?

Disruption of mitosis and cell cycle checkpoints can lead to uncontrolled cell division and the development of cancer.

What are the steps in DNA replication?

DNA replication involves the unwinding of the DNA double helix, synthesis of new DNA strands using DNA polymerase, and proofreading to ensure accuracy.

What are the roles of leading strand, lagging strand, Okazaki fragments, ligase, DNA polymerase, DNA helicase, and RNA primer in replication?

Leading strand: synthesized continuously; Lagging strand: synthesized discontinuously in Okazaki fragments; Ligase: joins Okazaki fragments; DNA polymerase: synthesizes new DNA; Helicase: unwinds DNA; Primase: synthesizes RNA primers.

What are the steps that occur during transcription?

Initiation, elongation, and termination.

What are the roles of RNA polymerase, promoter, and transcription factors in transcription?

RNA polymerase: synthesizes RNA; promoter: region where RNA polymerase binds; transcription factors: proteins that help RNA polymerase bind to the promoter.

What are the roles of 5' cap, 3' poly(A) tail, introns, exons, and spliceosome in mRNA processing?

5' cap: protects mRNA from degradation; 3' poly(A) tail: increases mRNA stability; introns: non-coding regions; exons: coding regions; spliceosome: removes introns.

What are the steps that occur during translation?

Initiation, elongation, and termination.

What are the roles of codon, anticodon, ribosome, A site, P site, E site, tRNA, and amino acid in translation?

Codon: a sequence of three nucleotides that codes for an amino acid; anticodon: sequence on tRNA that binds to mRNA codon; ribosome: site of protein synthesis; tRNA: carries amino acids to ribosome.

Carbohydrates monomer

Carbon

Hydrogen

Oxygen

Simple Carbohydrates

Easily broken down: 1-2 linked sugars ( monosaccharides): fruits, vegetables, dairy, honey

Complex carbohydrates

Long to digest: 3-10 linked sugars (oligosaccharides), 11+ (polysaccharide):

starches found in grains, potatoes, and vegetables

Lipids

Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

Lipids functions

Promoting brain function, providing insulation and protective cushioning for organs. Support body's immune system.

Nucleic acids

Long polymer chains of ribonucleic acids (RNA) or DNA

Nucleic acid monomer

Phosphate, a sugar (nucleotide), and a nitrogenous base

5 nucleotides are

(A) adenine

(T) thymine

(C) cytosine

(G) guanine

(U) uracil

DNA nucleotide

Thymine

RNA nucleotides

Uracil

DNA and RNA nucleotides

Adenine

Cytosine

Guanine

Nucleotides function

Responsible for all genetic coding in living organisms

Types of protein molecules

Globular (compact, soluble, + spherical)

Fiberous (elongated + insoluble)

Primary protein structure

Unique sequence of amino acids are linked together to form a protein.

A carbon + hydrogen + carboxyl group + amino acid group = a variable group or "R" group

secondary protein structure

coiling or folding of a polypeptide due to H-bonding between amino acids

Types of secondary protein structure

alpha helix and beta pleated sheet

Tertiary protein structure

3D folding pattern of a protein due to side chain interactions

hydrophobic interactions

a type of weak chemical interaction caused when molecules that do not mix with water coalesce to exclude water. Avoid water.

hydrogen bonding

the intermolecular force in which a hydrogen atom that is bonded to a highly electronegative atom is attracted to an unshared pair of electrons of an electronegative atom in a nearby molecule.

Helps to stabilize protein structure

disulfide bonds

Strong chemical side bonds that can only be broken by chemical solutions

Quaternary protein structure

association between two or more polypeptide chains within one protein.

Ex: hemoglobin contains 4 subunits= 2 alpha + 2 beta

Prophase

first and longest phase of mitosis in which the genetic material inside the nucleus condenses (so that it's easier to distribute to daughter cell with less tangling) and the chromosomes become visible.

sister chromatids

Identical copies of a chromosome; full sets of these are created during the S subphase of interphase.

mitotic spindle

a structure that separates the duplicated chromosomes during anaphase

Prometaphase

The second stage of mitosis, in which the nuclear envelope fragments and the spindle microtubules attach to the kinetochores of the chromosomes. Units of the nuclear envelope are reserved in vesticles to be used later to assemble nuclear envelope for daughter cells.

Metaphase

the duplicated chromosomes line up on the mid plane and spindle fibers connect to the centromeres

Metaphase to anaphase

The remaining cohesion proteins joining the sister chromatids at their centromere

Anaphase (Mitosis)

sister chromatids are pulled apart

Chromatids into chromosomes

Telophase (mitosis)

chromosomes arrive at the poles and begin to uncoil, spindles break down, new nucleur membrane forms.

Cytokinesis

Begins in Telophase. division of the cytoplasm to form two separate daughter cells. Last step in M phase.

G1/S checkpoint (restriction point)

1st key checkpoint

Checks:

Enough nutrients?

Receiving reproductive signal (growth factor)?

Sufficient cell size?

DNA undamaged?

Will not allow synthesis to begin

G2-M checkpoint

The second cell-division control point, at which division can be delayed if DNA has not been properly replicated or is damaged.

4 phases of cell cycle

G1- gap 1 phase

S- synthesis

G2- gap 2 phase

M- mitosis

metaphase to anaphase checkpoint

ensures that all the chromosomes are attached to the spindle and aligned properly at the equator of the cell

protein kinase

enzymes that activate or inactivate other proteins by phosphorylating them

Cyclin

Cyclin dependent kinases active only when they bind tightly to regulatory proteins

G2 to M phase: control system triggers

1. Cyclin is synthesized and accumulates

2. Cyclin dependent kinases (cdk)associates with cyclin, forming Mitosis (cdk) and a cdk complex

3.M-cdk phosphorylates proteins, activating those that facilitate mitosis and inactiving those that inhibit mitosis.

4.an activated enzyme complex recognizes a specific amino acid sequence in cyclin and targets it for destruction.

5. When cyclin is degraded M-cdk activity is terminated and the cells formed by mitosis enter G1

6. Cdk is not degraded but is recycled and reused

DNA replication steps

1) Helicase- unwinds the parental double helix

2) DNA topoisomerase - upstream of helices alleviating torsional strain

3) Single-strand binding proteins (SSBP) stabilize unwound DNA, aided by DNA gyrase.

4) Primase synthesizes a short RNA primer for DNA polymerase to bind to in the 5' to 3' direction to start replication on each strand.

5) DNA polymerase synthesizes the leading strand in 5' to 3' direction while the lagging strand is made discontinuously by primase making short pieces and then DNA polymerase extending these to make Okazaki fragments.

6) DNA ligase joins the Okazaki fragments together

origin of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

DNA primase

synthesizes a short RNA primer to provide a 3'-OH group for the attachment of DNA nucleotides

DNA helicase

An enzyme that unwinds the DNA double helix during DNA replication

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

Introns

Noncoding segments of nucleic acid that lie between coding sequences.

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

DNA polymerase

Links nucleotide subunits to form a new DNA strand complementary to a DNA template

initiation of transcription

RNA polymerase attaches to the promoter region on the DNA and begins to unzip the DNA into two strands.

elongation (transcription)

Additional nucleotides are added to the 3' end of RNA molecules. DNA double helix re-forms following transcription.

termination of transcription

The third, and last, phase of transcription in which the mRNA transcript is released when RNA polymerase reaches the terminator sequence

initiation of translation

Protein (initiation factor) becomes attached to the small ribosomal subunit

1. Methionine of the initiator tRNA is not modified

2. small subunit with 10 protein initiation factors, forms an initiation complex that binds to the 5'cap of the mRNA

elongation (translation)

amino acids are added one by one to the preceding amino acid to make a polypeptide chain.

1. The polypeptide chain is covalently bonded to the tRNA that carries the amino acids most recently added to the chain. The tRNA is in the P site of the ribosomes

2. An aminoacyl tRNA binds to the A site by complementary base pairing between the tRNAs anticodon and the mRNAs codon

3. The growing polypeptide chain detached from the tRNA molecules in the P site and becomes attached by peptide bond to the amino acid linked to the tRNA. At the A site

4. The ribosome moves one codon toward the 3' end of the mRNA. The growing polypeptide chain is transferred to the P site. The uncharged tRNA in the E site exits the ribosome.

termination of translation

The synthesis of the polypeptide chain is terminated by a release factor, a protein that recognizes the stop codon at the end of the coding sequence.

RNA polymerase in transcription

runs along the DNA strand unzipping it and copying the DNA while zipping back after the DNA's nitrogenous bases have been copied allowing the new RNA strand to peel away.

Promoter (transcription)

DNA sequence where RNA polymerase attaches and initiates transcription

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

5' cap

At the end of the 5' end of the mRNA chain. The cap is formed of 7-methylguanosine, which is linked to the mRNA transcript by three phosphate groups

3' poly (A) tail

Near the 3' end of a completed message usually lies a sequence of bases that serves as a signal for adding many adenine-containing nucleotides (poly-A tail) enzymes recognizes the signal for poly-A tail and cut the mRNA molecule at the site.

Exons

expressed sequence of DNA; codes for a protein

Ribosome

Cytoplasmic organelles at which proteins are synthesized.

tRNA in translation

The molecule that bridges the gap between mRNA and proteins. DNA contains genes that are transcribed to form tRNAs

Role of tRNA in translation

tRNA molecules deliver exactly the right amino acid called for by each codon on the mRNA; anti-codons

Role of ribosomes in translation

Proteins and rRNA contains 3 binding sites for tRNA molecules (A, E, P, binding sites)

P site (peptidyl-tRNA binding site)

One of a ribosome's three binding sites for tRNA during translation. The P site holds the tRNA carrying the growing polypeptide chain.

A site (aminoacyl-tRNA binding site)

holds the tRNA carrying the next amino acid to be added to the chain

E site (exit site)

One of a ribosome's three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.)

amino acids in translation

The amino acids on one end of the polypeptide chain has a free amino group (the amino end) and the amino acid at the other end has a free carboxyl group.

Codon translation

set of 3 RNA nucleotides which code for a specific amino acid

- AUG = methionine

- CUG = leucine

Release factor at the end of a coding sequence

stop codon

UAA, UAG, UGA - stop translation and polypeptide is released

Any of the 3 codons in mRNA that do not code for amino acids but signal termination of translation.

start codon

codon that signals to ribosomes to begin translation; codes for the first amino acid in a protein

AUG methionine

Anti-codon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

Cell Cycle: G1

5 hrs

Growth and normal metabolism occurs. Cells not dividing

Toward end: enzymes for DNA synthesis become more active

Cell Cycle: Synthesis Phase

4.5 hrs

DNA replication

cell cycle: G2 phase

2 hrs

Increased protein synthesis occurs as final steps in the cells prepare for division to take place

Cel cycle: mitosis

30 minutes

Mitosis and cytokinesis

The nuclear division that produces two nuclei containing chromosomes identical to the parental nucleus ( begins at end of G2)

Translation order of events

1. mRNA codon matches with tRNA anticodon

2. Peptide bond forms between amino acids

3. Ribosomes shift position

4. Unchanged tRNA ejected from ribosome

glycerol and fatty acids

nucleotide, DNA, RNA

amino acid, polypeptide