Biology Modules 5-7

Two important features of DNA

• Molecules are passed down from parent to offspring.

• DNA contains instructions for creation, growth and development.

Francis Crick and James Watson

The two-scientist responsible for figuring out the exact structure of DNA

DNA (Deoxyribonucleic acid)

A nucleic acid, a macromolecule, made of individual nucleotides. Its structure is often referred to as a “double helix.”

Double Helix

Two sugar -phosphate backbones that spiral around each other, forming the vertical structures of DNA. Connected by the bases sticking out from their sugar molecules

Nucleotide

The unit of DNA molecule has three components: a phosphate group, a sugar, and a nitrogen-containing base.

Base Pairs

Connected with hydrogen bonds. They pair predictably. One strand of DNA compliments the other side. (A=T, G=C)

DNA structure

• Two strands of DNA

• A sugar

• Phosphate group

Chromosome Eukaryotic Definition

Long Linear strands of DNA

Genome

The full set of DNA present in an individual organism, in eukaryotes this information can be found in the nucleus of every cell.

Chromosome

One or more unique piece of DNA. Vary length and can consist of hundreds of base pairs. Circular in prokaryotes and linear in eukaryotes.

Gene

A specific sequence DNA on average about 3,000 bases pairs long and contains the information necessary for protein synthesis.

Locus

The position or location of a gene on a chromosome

Alleles

Alternate, different versions of a gene that codes for the same trait.

Noncoding DNA

Noncoding regions take the form of sequences that are repeated. Some DNA sequences can make copies of themselves, and these copies move throughout the genome.

Introns

A noncoding region of DNA

Exons

The portion of gene’s DNA sequence that codes for amino acids

Pseudogenes:

Sequences that evolved from actual genes but accumulated mutations that made them lose their protein-coding ability.  

Genotype

Organisms that carry a particular trait. An organism’s genetic composition. 

Phenotype

The manifested structure, function, and behaviors of an individual. The expression of the genotype of an organism.

Transcription and Translation

The process involved in building an organism

Transcription

The gene sequence is copied from DNA to go-between molecule called mRNA

Translation

The gene sequence is now encoded in mRNA, which directs the production of a protein.

Transcription Process

• Recognize and Bind

• Transcribed

• Terminate

• Cap and Edit

Transfer RNA

interprets the mRNA code, translating the language of DNA-coded in the linear sequence of bases-into the language of proteins-coded in the linear sequences of amino acids.  

Anti-Codon

A three-base sequence that matches up with a three-base sequence on the mRNA 

Codon

A three-base sequence on mRNA that matches with a tRNA that carries one amino acid. For every possible codon, one type of tRNA molecule will recognize and bind to the mRNA at the point, and it always carries the same amino acid.  

Translation Process

• Recognize and Initiate protein building.

• Elongate

• Terminate

Gene Expression

Production of the protein that the gene’s sequence codes for.

Gene Regulation

The processes by which cells “turn on” or “turn off” genes, influencing the amount of gene products formed.

Microarray

Small chip that looks like a microscope slide and can be used to monitor the expression levels of thousands of genes simultaneously.  

Transcription Factors

A regulatory protein that binds to a specific sequence in the DNA called regulatory site before the promoter site of genes. The regulation takes either positive or negative control. Positive control = initiates or speeds up gene expression, Negative Control: Protein slows or blocks gene expression.  

Regulatory proteins

can be produced by the same cell whose DNA they are regulating, or they come from nearby cells.  

Gene Regulation

is extremely important in directing cells to differentiate into one type of tissue.  

Prokaryotic gene control

The bacteria E. Coli adjust its diet depending on which sugars are available in its environment. E. coli prefers glucose, however in the absence of glucose, it will use lactose as an energy source.  

Operon

The regulation of gene expression uses a set of regulatory sequences, which includes several genes and the elements that control their expression as a unit

Promoter

The region of DNA that RNA polymerase recognizes and binds to produce an mRNA transcript of the genes

Operator

The region of DNA that a repressor protein can bind to and by doing so, block RNA polymerase

Genes

The region of DNA that is transcribed by RNA polymerase

Eukaryotic Gene Control

Uses associated sequences called enhancer sequences and when a regulatory protein binds to the enhancer sequence, the transcription rate for the associated gene is increased-positive control.  

Regulation of mRNA in eukaryotic cells

can be regulated by altering its processing and transport or by altering the rate at which it is broken down in the cytoplasm

Epigenetic changes

Alterations to chromosomes that do not change the DNA sequence but may influence the long-term activity of some genes and may be passed on to an organism’s offspring.  

Mutation

An alteration in the base-pair sequence of an individual’s DNA; may arise spontaneously or following exposure to a mutagen. Very rarely they are beneficial to the organism 

How is Breast Cancer a Mutation

Genes called BRCA1 and BRCA2 help reduce breast cancer risk by helping to repair DNA damage, which prevents accumulation of changes that might lead to cancer. However, if the DNA sequence of either of these genes is altered through mutation and the gene’s normal function is lost, that person carrying the allele has significantly increased risk of developing breast cancer. 

Mutations in gametes

do not have any adverse health effects on those carrying them however these mutations can be passed to offspring and the individual inheriting the mutation can be at risk for diseases.  

Mutation in non-sex cells

Mutation in non-sex cells can have bad consequences, such as skin and lung cancer. Non-sex-cell mutations are not passed down to children.  

Mutations in evolutionary processes

as heritable mutations that reduce an organism’s ability to survive and reproduce, to those that have no impact on an organism’s survival and reproduction.   

Point Mutations

A mutation in which one, ONLY ONE, base pair in DNA is replaced with another, or a base pair either inserted or deleted 

Chromosomal Aberrations

Changes to the overall organization of the genes on a chromosome. Aberrations can involve the deletion of a gene, the relocation ofa gene, or the duplication of a gene 

Spontaneous Mutations

May arise by accident as DNA is duplicating itself, when dividing. DNA repair enzymes correct more errors but not all  

Radiation-induced mutations

Ionizing radiation has enough energy to disrupt atomic structure and even break apart chromosomes by removing tightly bound electrons. 

Chemical Induced mutations

Chemicals such as those found in cigarette smoke and vaping emissions can also induce mutations. 

Tay Sachs Disease

an individual inherits genes with a mutation that causes an inability to produce a critical lipid-digesting enzyme in the lysosomes, which function cellular garbage disposal. The diseased organelles can’t digest certain lipids. Therefore, the lipids accumulate, undigested. The lysosomes sell until they eventually choke the cell to death

How does a mutation turn into an illness?

1. A mutated gene codes for a nonfunctioning protein, commonly an enzyme 

2. The nonfunctioning enzyme can’t catalyze the reaction as it normally would  

3. The molecules that typically would've been modified as part of the reaction accumulate in the cell 

4. The accumulating chemical causes sickness or death (Tay Sachs disease) 

Faulty Enzymes can interfere with….

metabolism including administering medications that contain the normal-function version of the enzyme.  

1. i.e. Lactose Intolerant individuals reduce their consumption of lactose-containing foods to keep the chemical from accumulating, reducing the problems.  

Telomere

A noncoding, highly repetitive section of DNA at the tip of every eukaryotic chromosome that shortens with every cell division. If it becomes too short, additional cell division can cause the loss of functional, essential DNA and almost certain cell death. Keeps track of cell divisions by shortening every time the cell divides.

Function of Telomere

Cellular “odometer”. Limits cells to fixed number of divisions. 

Hutchinson-Gilford progeria syndrome

Genetic condition that causes the cell’s telomeres to be much shorter at birth. The normal functioning of many genes is disrupted. Therefore, the cells and tissues begin to appear aged very soon after birth. Children with the disorder rarely live beyond the age of 13.

Cancer

Immortal cells that are unable to stop dividing.

Chromosomes:

Linear or circular strands of DNA compromising specific sequences of base pairs.  

Eukaryotic chromosomes…

Most important part of this molecule is the DNA molecule which carries information about how to accomplish the process needed to support the life of an organism.  

Eukaryotic chromosomes are made of….

Chromatin

Chromatin

A linear DNA strand bound to and wrapped tightly around proteins called histones. This keeps DNA from getting tangled and enables it to be tightly and efficiently packed inside the nucleus. (Plants and animals usually have between 10 and 50 chromosomes)  

Histones

Proteins around which the long, linear strands of DNA are wrapped; serve to keep the DNA untangled and to enable orderly, tight, and efficient packing of the DNA within the cell.  

Prokaryotic Chromosome:  

have less DNA than eukaryotes do. They carry their genetic information in a single, circular chromosome, a closed loop of double-stranded DNA that is attached at one site to the cell membrane.  

Binary Fission:

Type of asexual reproduction in which the parent cell divides into two genetically identical daughter cells. Bacteria and other prokaryotes reproduce by binary fission.  Begins with replication.  

Replication

Method by which a cell creates an exact duplicate of each chromosome. Begins as the double stranded DNA molecule that unwinds from its coiled-up configuration. The strands are uncoiled and split apart. As the double-stranded molecule unzips, enzymes bind to DNA and attaches free-floating nucleotides to growing DNA backbone, matching A to T and G to C, creating two identical double-stranded DNA molecules.  

Eukaryotic Cell Cycle:

Describes the series of phases in somatic cell division. With two main phases: interphase, where the cell grows and prepares to divide and the Mitotic phase where division occurs.  

Gap 1

The cell’s primary growth phase. Normal cellular functions may take place (making proteins, getting rid of waste, etc.)  

G0

Some cells pause in G1 phase and enter in a state called G0 which is a resting phase outside the cell cycle. Cells may stay in this phase for days or years.  

S Phase (DNA Synthesis)

The cell begins preparations for division. Every chromosome creates an exact duplicate of itself using the replication process. Each chromosome’s DNA has become a pair of identical long linear molecules, held together at the center.  

Gap 2

Second period of growth and preparation for cell division. High rates of protein synthesis in preparation for division. Shorter duration and its genetic material now exist in duplicate.   

Mitotic Phase

Mitosis

Cytokinesis

Mitosis

The parent cell’s nucleus, with duplicated chromosomes, divides.

Cytokinesis

The cytoplasm is divided into two daughter cells, each of which has a complete set of the parent cell’s DNA and other cellular structures. 

Somatic Cells

The cells forming the body of the organism

Reproductive Cells

Sex cells---gametes (sperm and eggs).  

Cell-Cycle Control System

Group of molecules, mostly proteins, within a cell that coordinates the events of the cell cycle. Functions through a system of checkpoints.  

Checkpoints

Critical points in the cell cycle at which progress is blocked and cells are prevented from dividing-until specific signals trigger continuation of the process.

G1/S Checkpoint

Assesses DNA damage and cell growth. It occurs near the end of G1 phase. Decides if a cell will proceed to the S phase and complete cell division, delays division or enter an extended resting phase. Malfunctions in this checkpoint can allow damaged cells to continue their division. Leading to uncontrolled cell division and cancer.  

G2/M Checkpoint

Assess DNA synthesis: Serves as a mitosis-readiness assessment. Indicating that no damage was detected. If not, the cell typically undergoes repair of damaged DNA.  

Spindle assembly checkpoint

Assesses anaphase readiness during mitosis. Cell-cycle controlled mechanisms assess whether the chromosome has aligned properly as the metaphase plate and whether there is appropriate tension on them. If the checkpoint is passed, then the cell continues division. 

DNA complementary

Complementary base pairing makes it possible to produce two identical strands by separating the parent molecule and using each strand as a template to build a new complementary strand.  

Complementarity

in the double stranded DNA molecule, the base on one strand always has the same pairing partner called a complementary base. With the consistent pattern of pairing one strand carries all the information needed to construct its complementary strand.  

Sugar-Phosphate Backbone

DNA molecules are made of nucleotides which contain: a base, a phosphate group, and a molecule of five carbon sugars. Each sugar is given a number. The nitrogenous base is attached to the 1’ (one prime) carbon. An –OH group is attached to the 3’ carbon. And the phosphate group is attached to the sugars 5’ carbon atom.  

DNA replication

Process of DNA replication occurs in two steps:

- Unwinding and Separation

-Reconstruction and Elongation

Unwinding and Separation

The coiled, double stranded DNA molecule unwinds and separates into two strands  

Reconstruction and Elongation

Enzymes connect the appropriate nucleotides to the growing new strands and the nucleotides are added to the 3’ end of the new strands.  

Define Mitosis

Enables existing cells to generate new, genetically identical cells. Is required for growth and replacement. Prior to , the parent cell replicates its DNA creating a duplicate copy of each chromosome

Interphase

The genetic material is replicated during the DNA synthesis portion:

1. Chromosome condenses 

2. Chromosomes line up in the middle of the cell 

3. Each chromosome is pulled apart from its duplicate 

4. New nuclear membranes form around each complete set of chromosomes 

5. Cytokinesis: The cell divides into two identical daughter cells. 

Apoptosis

Cell suicide. Programed cell death which takes place particle in parts of the body where the cells are likely to accumulate significant genetic damage over time and therefore at high risk of becoming cancerous.

Two important events occur before mitosis

1. Chromosomes replicate, becoming two identical linear DNA molecules that are held together at the centromere. Throughout mitosis, until the centromeres sperate, each of the identical DNA molecules is called a chromatid: together, the two become sister chromatids.  

2. The sister chromatids begin the process of condensation, in which they coil tightly and become compact 

Chromatid

One of two strands of replicated chromosome  

Sister Chromatids

The two identical strands of a replicated chromosome  

Condensation

The cell cycle just before mitosis, the process in which sister chromatids coil tightly and become compact-in contrast to the uncondensed and tangled state of the chromosome prior to replication, during most of interphase. 

Genetic Material During the Cell Cycle: 

1. Eukaryotic chromosomes are uncoiled and spread out in a diffuse way 

2. Chromatids: After replication each chromosome appears as two identical linear DNA molecules, held together at the centromere. Until the centromere separates, each of the identical DNA molecules is called a chromatid, together the two are called sister chromatids. 

Spindle

Part of the cytoskeleton, formed in prophase (in mitosis) or prophase I (in meiosis), from which extend the fibers that organize and separate the sister chromatids 

Microtubules

One of three types of protein fibers, that make up the eukaryotic cytoskeleton, providing it with structure and shape. These are the thickest elements in the cytoskeleton. They resemble rigid, hollow tubes, functioning as tracks to which molecules and organelles within the cell may attach and be moved along; also help pull chromosomes apart during cell division.

Centrosomes

The threads originate and spread out at each pole from structures, which contain pairs of centrioles. 

Centrioles

Mass of proteins that anchor microtubules.

Spindle Fibers

Fibers that extend from one pole of a cell to the other, which pull the sister chromatids apart in anaphase of mitosis or anaphase II of meiosis.