Nucleotides, Genetics/Pedigrees and Evolution/Biodiversity - Final Exam

I am so sorry for how many flashcards this contains (THIS IS STILL A WORK IN PROGRESS)

Transcription

the process of making an RNA copy of a gene's DNA sequence. RNA Polymerase goes into the nucleus, finds the gene and transcribes the code from DNA to RNA language

Translation

process in cells in which proteins are produced using RNA molecules as templates; the generated protein is a sequence of amino acids which is determined by the sequence of nucleotides in the RNA (nucleotides are read 3 at a time).

gather the new code (mRNA), raw materials (Amino Acids) and machinery (tRNA) on the ribosome and begin constructing polypeptide

The Process of Gene Expression

1. Trigger of Gene Expression (hormones, nutrients, environment) arrives at cell/chromosome/gene

2. Transcription bubble forms

3. RNA Polymerase builds mRNA code

4. Get mRNA to raw materials and building machinery in cytoplasm

5. TRANSLATION: Construct POLYPEPTIDE (Amino Acid chain)

Finished!

What is each cell designed to detect?

Different stimuli or triggers of Gene Expression

What happens when the trigger for Gene Expression arrives?

A gene opens up its DNA sequence and protein synthesis begins

Protein synthesis process

DNA → mRNA → Polypeptide → Transcription → Translation

Codon

a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genomic information encoding a particular amino acid

Anti-codon

a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence

What happens to completed polypeptide sequences after there are no more amino acids to add onto the polypeptide chain?

This combination will be folded and shaped into the final protein, like an enzyme, antibody, structure or “portal”

What are the 3 triggers for Gene Expression?

1. Hormones (cortisol/progesterone etc.)

2. Nutrients (lactose/fructose etc.)

3. Environment (sun/light/temperature)

SnRNPs (Small Nuclear Ribonucleoproteins)

a large RNA-protein complex that cuts out unnecessary sections of the pre-mRNA

Spliceosomes

removes intronic sequences from primary transcripts to generate functional messenger and long noncoding RNAs (lncRNA)

Regulate

control or maintain the speed or rate of a machine or process so that it operates properly

Denature

destroy the characteristic properties of a protein or other biological macromolecule by heat, acidity, or other effects that disrupt its molecular conformation

Lac Operon

a set of structural genes that code for proteins to metabolize (digest) lactose, which can be turned on or turned off

E. coli

a bacteria which is generally found in the intestines. they benefit their hosts by producing vitamin K₂ or by preventing the colonization of the intestine by harmful pathogenic bacteria

Mutation

a permanent change in a cell’s DNA; inheritable

Point mutation

substitution, insertion, or deletion of one or very few molecules

Substitution

a type of mutation in which one nucleotide is replaced by a different nucleotide. has a relatively minor effect overall

Insertion

a type of mutation that involves the addition of one or more nucleotides into a segment of DNA. usually results in a frameshift mutation

Deletion

occurs when part of a DNA molecule is not copied during DNA replication. usually results in frameshift mutation

Frameshift mutation

Insertion or deletion that results in a change to the reading frame of a gene

What feature of the genetic code helps protect a cell from the effects of nucleotide substitution?

The redundancy of genetic code (changes in a gene’s code may result in the same amino acid)

Mutagen

anything that causes a change (mutation) in a cell. increases the mutation rate in a cell

Carcinogen

a substance, organism or agent capable of causing cancer

Somatic Cell Mutation

a mutation that occurs in the body cells

Germ Line Mutation

a mutation that occurs in the reproductive cells

What 2 types of point mutations can cause a disturbance in how codons are read?

Insertion and deletion

Silent point

a type of substitution, or point, mutation, wherein the change in the DNA sequence of the gene has no effect on the amino acid sequence

Mis-sense point

a DNA change that results in different amino acids being encoded at a particular position in the resulting protein

Nonsense point mutation

a change in DNA that causes a protein to terminate or end its translation earlier than expected

3 traits of a physical mutagen

• Structure of DNA is altered

• Replication is interfered with

• Point mutations or chromosome loss

3 traits of a chemical mutagen

• Induce mutations via DNA reacting to chemical reactions

• Can cause incorrect nucleotides to be used during replication

• Often associated with cancer

DNA Ligase attaches…

DNA to DNA

Ligase

an enzyme that joins together fragments of newly synthesized DNA to form a seamless strand

List in sequence the three stages of the replication process

1. Initiation

2. Elongation

3. Termination

Initiation

a sequence in protein synthesis that consists of the recruitment of a ribosome initiator tRNA complex to the initiation codon of a messenger RNA

Elongation

a key step of protein synthesis, during which the polypeptide chain extends by one amino acid residue during one elongation cycle

Termination

process in protein synthesis in which a stop codon becomes positioned in the ribosomal A-site and is decoded by a protein

Helicase

cuts the hydrogen bonds between nucleotides

Okazaki fragments

short segments of DNA built moving away from the replication fork toward the replication origin

What molecule replaces RNA primers during replication?

DNA Polymerase

DNA polymerase reads the  _____ strand of DNA

3 to 5

From the diagram above, what is structure 5?

SSBP - Single strand binding proteins

From the diagram above, is structure 1 the lagging strand or the leading strand?

Leading strand

From the diagram above, is structure 2 the lagging strand or the leading strand?

Lagging strand

What is enzyme E?

DNA Polymerase

What is structure 4 being built by enzyme B?

Primer

What is structure 3 called?

Okazaki fragment

What is the name of enzyme F?

Ligase

Which enzyme is used to prevent supercoiling and DNA damage?

Gyrase

Gyrase

an enzyme that reduces/stops the super-coiling effects of DNA during replication

Chargoff’s Rule

The amount of Cytosine is equal to the amount of Guanine in a DNA molecule, and the amount of Adenine is equal to that of Thymine in a DNA molecule (A=T, C=G)

Describe DNA’s structure

• Double helix (2 strands twisted)

• Complementary base pairing (purine to a pyrimidine)

• Antiparallel (strands run in opposite directions same distance apart)

Gene vs Genome

• Both refer to the genetic makeup of an organism/DNA

• Gene = 1 DNA instruction along 1 part of a chromosome

• Genome = the collection of all the DNA instructions on all the chromosomes of an organism

The building machinery of a replication fork can only function by…

1. Reading template nucleotides that read in a 3 to 5 direction

2. Adding new nucleotides to the new DNA in a 5 to 3 direction

(Meaning there are some delays in the building process)

Poly A tail

the section of the mature mRNA added to the 3’ end of the mature mRNA

Cap

the section of the mature mRNA that is added to the 5’ end of the mRNA

Chromosomal mutation

changes in the number or structure of chromosomes

What is label number 1?

Lac Operon

What is label 2?

The operator

What is label 3?

The promoter region

What is label 4?

The structural genes

What is label 14?

The chromosome

What is label 5?

The regulator gene

What is label 6?

The mRNA

What is label 7? (ignore the one off to the right)

The repressor protein

What is label 8?

RNA Polymerase

What is label 10?

RNA Polymerase

What is label 9?

Transcription

What is label 11?

mRNA

What is label 12, and what do they do?

Proteins (digest lactose)

What is label 13?

Lactose

Methionine

the starter amino acid of a codon sequence. encoded as AUG

DNA vs. RNA

• Both carry genetic information/are essential for genetic processing

• DNA encodes genetic information, forms a double helix, and is typically housed in a cell’s nucleus

• RNA decodes genetic information, is single stranded, and different types of RNA can be found in multiple locations (mRNA: nucleus, tRNA: cytoplasm, rRNA: ribosomes)

What does RNA and DNA stand for?

• RNA: Ribonucleic Acid

• DNA: Deoxyribonucleic Acid

What is the literal translation of Semi-Conservative replication?

• Semi → half or partial

• Conservative → saving/reserving something

• Replication → Copy + paste, duplication

True or False: the leading strand of DNA is built toward the replication fork

True

True or False: the lagging strand of new DNA is built in one continuous piece

False

True or False: the lagging strand of DNA is made of Okazaki fragments

True

True or False: primase is the only enzyme that makes RNA primers

True

True or False: An RNA primer is made of nucleotides that use Ribose sugars and have bases like A, C, G, and T

False

True or False: when A bonds to C, two hydrogen bonds are formed

False

Polymerase Chain Reaction (PCR)

A method invented by biochemist Kary Mullis that amplifies the trace amounts of DNA and RNA from a sample. Here are the following steps:

1. Denaturation - solution in a tube is heated to 94 degrees Celsius; the heat breaks down hydrogen bonds, separates DNA into single strands

2. Annealing - sample is cooled to 50-60 degrees Celsius which allows DNA primers and DNA polymerase to bind to individual DNA strands

3. Extension - a new complementary strand of DNA is formed. temperature cycles from 95 to 50 to 60 degrees (this is repeated 35-40 times). this continues the replication amplification process

4. Analysis - once the process is complete, the resulting generated sequences can be compared to other nucleotide segments. scientists use electrophoresis to test the nucleotide segments

Taq Polymerase

a thermostable DNA polymerase often used in PCR because of it’s resistance to unwinding in extreme heat

Genetics

a branch of biology that attempts to predict the outcome of sexual reproduction through understanding gene-to-gene actions and meiosis

Evolution

change in inheritable traits (genes) in living things, over time

Macro-evolution

big changes over longer periods of time

Micro-evolution

small changes over a short period of time

Early Philosophies

• Plato and Aristotle believed life was unchanging

• This belief carried on to western culture

• “All life was created independently of one another and has remained unchanged ever since”

Buffon

• Challenged the idea species never changed

• Wrote Histoire Naturelle, a book detailing his understandings of the world

• Noted ape and human similarities

• Suggested Earth was older than 6000 years

• Essentially kick-started evolution theories

Cuvier

• Largely credited for developing paleontology

• Each rock layer contains unique fossil species; the farther down you go the older they get

• Proposed Earth experienced “revolutions,” destructive natural disasters that caused mass extinctions

• Rejected the evolution theory

Lyell

• Rejected the “revolution” theory

• Geological processes operated at the same rate in the past as they do today

• Slow, continuous processes means Earth is older than 6000 years

• These slow processes result in big changes

Lamarck

• Wrote Philosophie Zoologique, detailing the changes of animals over time

• Line of descent (series of fossils leads to modern species)

• Inheritance of acquired characteristics (traits, or an animal’s adaptation to the environment, are passed down to offspring)

• His theory was ultimately rejected as biologists learned about cells, genes and heredity

Darwin and Wallace

• The Beagle Expedition/Galapagos Islands

• The study of many species and the comparison of similarities between them on different landmasses

• Made records and took notes of species all over the world

• Developed artificial selection theory

• On the Origin of Species (book about evolution theory)

Darwin’s Two Main Ideas (On the Origin of Species)

1. Present life forms have arisen by descent and modification from an ancestral species

2. The mechanism for moderation is natural selection working for long periods of time

Artificial selection

selective breeding to obtain varieties of plants or animals with desired traits

Fossil record

remains or traces of a past life preserved in sedimentary rock, which reveal the history of life on Earth

Index fossils

fossils that are known to be common during a particular time, and so indicate the age of the rock they are found in

Radiometric dating

method of dating rocks and minerals that uses measurements of certain radioactive isotopes to calculate the absolute age in years