Genetics Exam 1

Mendelian genetics (transmission)

addresses how traits are passed in a family

replication fork

area where the DNA is still winded ip

When you see an electron micrograph of a DNA undergoing transcription, you will notice a Christmas-like structure. What does each part of this structure represent?

Main branch: DNA strand Side branch: RNA strand

list the basic components of an operon and explain their function

promoter operator structural genes terminator

DNA polymerase

reads the template DNA and assembles dNTPs into a complementary strand

DNA polymerase I

removes RNA primers and replaces them with DNA nucleotides

DNA ligase

seals the nick

gene

segments of DNA that code for specific traits

primers

short complementary RNA sequences mark the region to be replicated

Okazaki fragments

short pieces of the lagging strand that aren't synthesized continuously

template strand

single stranded DNA to be copied

trait

specific feature or characteristic of an organism (eye color)

what is the function of the sigma factor?

to help RNA polymerase to bind to the promoter?

What is a telomere?

Their job is to stop the ends of chromosomes from fraying or sticking to each other, much like the plastic tips on the ends of shoelaces. Telomeres also play an important role in making sure our DNA gets copied properly when cells divide.

what is transformation?

a process where bacteria takes up DNA from their environment and expresses a new trait. Transformation is one of the ways bacteria exchange plasmid DNA.

mRNA

carries info for protein synthesis

phenotype

versions of a trait (different types of eye color)

operons are common in prokaryotes. Can you find them in eukaryotes?

yes

in which direction does RNA polymerase read the template strand?

3 to 5

One strand of a DNA double helix has the following sequence. Write the sequence of the complementary strand and show the number of H-bonds between the complementary bases using vertical lines. Include the 5' and 3' ends of the new strand. 5'-GAT ACC GTA-3'

3' -CTA TGG CAT-5' A and T are double bonds and G and C are triple bonds.

What does the 5' and 3' notation in DNA and RNA indicate?

3' end has a hydroxyl group and 5' has the phosphate group.

in which direction does RNA synthesis take place?

5 to 3

Explain the results of the Griffith experiment?

Griffith determined a substance in the heat-killed virulent bacteria genetically transformed the Type IIR bacteria into live, virulent Type IIIS bacteria.

What are histone proteins? List the types of histone proteins in eukaryotes.

H1 H2A - H2B - H3 - H4 -

We refer to Gregor Mendel as the father of genetics because he was the first to accurately predict inheritance of genetic traits. What was the organism Mendel used in his genetics experiments and what were the major traits he studied?

He used a pea plant: 1. seed (endosperm color) 2. seed shape 3. seed coat color 4. flower positions (axial vs terminal) 5. stem length 6. pod color 7. pod shape

What is a model organism?

a non human species that are extensively studied to understand certain biological processes with the expectation that knowledge gained from them will provide insight into how these processes work in other organisms

variation

difference in the DNA sequence

replication bubble

forms around the origin, is where the replication happens

describe some of the difference between DNA replication in prokaryotes and eukaryotes

in prokaryotes its circular and in eukaryotes its linear replication

compare and contrast DNA replication and transcription

transcription uses DNA to create RNA to send to ribosomes to create proteins replication unwinds one DNA into two separate strands to then create two whole DNA strands.

Explain why DNA replication progresses in the opposite direction on the two strands of DNA

Antiparallel structure, so 5' of one end has to attach the 3' end of the other (and vise versa)

A gene and its associated control elements (promoters, etc.) constitute a transcription unit. The following diagram shows the general structure of a transcription unit. Make sure you understand the function of each component.

Exon: segment of a gene that codes for amino acids Intron: segments that are removed

DNA has primary and secondary structures. What is the difference between the two?

Primary structure is the order in which what amino acid is bound the other with a peptide bond. This is coded for by the order of codons in a gene. Secondary structure is how the chains on amino acids interact with each other to form beta barrels and alpha helixes.Primary = one strand (nucleotide sequence) Secondary structure = doubles stranded DNA

What is the benefit of packaging DNA into a chromosome?

The double helix of DNA is then wrapped around certain proteins known as histones. This allows the DNA to be more tightly wrapped and therefore take up less space within the cell. The DNA can condense even further by the histones coming into close proximity to each other

The major challenges of replicating eukaryote DNA include (a) large size, (b) linear structure, (c) the DNA is complexed with histones, and (d) slow replication speed. Discuss how eukaryotes overcome each of these challenges and replicate their before the cell divides

The large size was conquered by breaking it into smaller sections by lagging strands and having multiple origins. For the linear structure, telomerase helps protect the ending so it doesn't gradually get shorter over time. With the histones, it has a process of unwinding itself from them. For slow replication speed, it has multiple origins.

Griffith used two strands of streptococcus bacteria. What is the difference between these strains?

Type IIR is good and nonvirulent. Type IIIS is bad and virulent.

T or F: DNA pol reads the template strand in a 5′→ 3′ direction.

false

T or F: DNA pol synthesizes the new DNA strand in a 3′→ 5′ direction.

false

T or F: Proofreading occurs in a 5′→ 3′ direction.

false

What is an operon?

genes that control the same metabolic pathway are transcribed as a group called operons

Why do we say genetics is not new?

genetics has been around for thousands of years - germ-plasm theory: all cells contain a complete set of genetic information - cell theory: all life is composed of and cells arise only from cells - Mendelian inheritance (particulate hypothesis): parents pass on a discrete heritable units (particles) to offspring according to principles promised by Mendel

other proteins

help in DNA replication

What is genetics?

how genes control expression fo traits, how traits are inherited, and how genetic variation affects population diversity

Molecular genetics

interested in the structure and function of genes; how DNA is replicated, expressed, etc.

lagging strand

is behind the leading strand and synthesized in fragments

Describe the structure of the origin of replication (oriC) in E.coli

it creates a bubble that starts with a primer in the middle that has the starting point of replication and moves from 5' to 3'. This starts the leading strand that is synthesized in small pieces called "ozaki fragments"

what is the function of the lac repressor (lacl)?

lac repressor is responsible for if the lac gene will be expressed or not depending on if it is activated or not

DNA polymerase II

mismatch repair

gyrase

move ahead of replication fork, making and resealing breaks in double DNA to release torque from unwinding

Does the entire DNA in a chromosome contain genes

no

Does the entire DNA in a chromosome contain genes?

no

inheritance/hereditary

transmission of genetics traits from generation to generation

helicase

unwinds DNA at replication fork

what is a polycistronic RNA?

RNA synthesized from multiple genes. Carries information for synthesis of multiple proteins.

DNA replication is extremely accurate. Explain the mechanisms that contribute to the high fidelity (accuracy) of DNA replication in E. coli.

- Accurate selection of dNTPs by DNA polymerase (Rarely makes mistakes (like A → G rarely happens)) - Proofreading - Mismatch pair (Only done once DNA synthesis is complete)

What are the major features of the DNA double helix?

- Antiparallel orientation (makes DNA more flexible, and makes replication process easy) - The precise nucleotides/bases carries the genetic information - Has a major and minor group - Has a uniform size (thickness is 2 nm and the spacing between the bases is 0.34 nm) - The bases are on the inside and the sugar phosphate backbone is on the outside

What is the difference between DNA and RNA?

- DNA doesn't have a hydroxyl group on the second Carbon - DNA is mostly double stranded (RNA is single stranded) - RNA incorporates uracil while DNA uses thyosil

Describe how the RNA genome of retroviruses (such as HIV) and coronaviruses (e.g., COVID-19) replicate.

- HIV attaches to the host CD4 protein and fuses. - RNA enters the cell - RNA is reverse transcribed to a DNA - The DNA integrates to to the host chromosome - Expressed using the host transcription machinery. New viruses assemble.

What is telomerase? How is telomerase different from DNA polymerase?

- Telomerase adds complementary RNA bases to the 3′ end of the DNA strand. Once the 3′ end of the lagging strand template is sufficiently elongated, DNA polymerase adds the complementary nucleotides to the ends of the chromosomes; thus, the ends of the chromosomes are replicated. - DNA polymerase cannot replicate and repair DNA molecules at the ends of linear chromosomes. ... The telomerase enzyme attaches to the end of the chromosome; complementary bases to the RNA template are added on the 3′ end of the DNA strand

rRNA

- associated with specific ribosomes to form proteins; components of ribosomes

What did Thomas Hunt Morgan discover in his experiment?

- genes are carried on chromosomes - traits for eye color in fruit flies are carried on x-chromsomes - eye color is x-linked

what are the important features of a model genetic organism?

- grow fast - large number of offspring - small in size - easy to grow in a lab environment - have huge genetic variation

Why do we study genetics?

- helps us understand causes of many different diseases/disorders - genetics helps us improve crops and animals - genetic knowledge allows us to develop drugs to treat diseases

What are the required ingredients for DNA replication?

- template strand - substrates (raw materials) - primers - DNA polymerase - other proteins

What are the properties of the A, B, and Z forms of DNA and why do they form?

----

What is the rate of DNA replication in E. coli?

1,000 nucleotides per second

List the major research labs that worked on the structure of DNA.

1. The Biophysics Research Unite at King's College 2. The Cavendish Lab at Cambridge University

What are Chargaff's rules?

1. The amount of A=T and amount of G=C in DNA. A pairs with T and G pairs with C. 2. The amount of A, T, G, and C varies between species (suggesting the DNA sequence between species is diverse)

What are the three major branches (divisions) of genetics?

1. molecular 2. Mendelian (transmission) 3. population

Why does DNA replication proceed in a 5ʹ to 3ʹ direction?

Cannot happen 3 → 5 because 3' has OH and S has phosphate. Phosphate has to join...in the 3'OH of the other strand.

what are the components of the core RNA polymerase and the RNA polymerase holoenzyme in bacteria?

Core RNA polymerase: two alpha, one beta, one beta prime, and an omega holoenzyme: same thing but is joined by a sigma factor The core enzyme catalyzes RNA synthesis. The sigma factor joins to the core to form the holoenzyme, which binds to the promoter and initiates transcription.

There are hundreds of thousands of different biological molecules in our cells, including proteins, carbohydrates, and lipids. What makes DNA the hereditary molecule but not others?

DNA can replicate and make copies of itself. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. This is critical when cells divide because each new cell needs to have an exact copy of the DNA present in the old cell

what is the difference between the template and non template DNA strand in transcription?

DNA is double-stranded, but only one strand serves as a template for transcription at any given time. This template strand is called the noncoding strand. The non template strand is referred to as the coding strand because its sequence will be the same as that of the new RNA molecule.

When does DNA replicate?

DNA replicates only during cell division Bacteria: fision Eukaryotes: mitosis and meiosis

Why is transcription (RNA synthesis) necessary? In other words, why don't cells use DNA directly for protein synthesis?

If DNA is replicated it will damage and can't be throw away as easy

Compare DNA packaging in eukaryotes and prokaryotes such as bacteria.

In eukaryotes they wrap around histones proteins that are called nucleosomes. These nucleosomes coil to form a fiber. This fiber then creates long loops which are tightly coiled to form chromosomes. In bacteria contains a single circular chromosome and does not contain histones or nucleosomes. Instead they loop 10 fold and form supercoiled DNA.

Explain the main events at each of the three stages of DNA replication in E. coli (initiation, elongation, and termination).

Initiation - the double strand unwinds at the origin of replication Elongation - the primer grows, one base at a time Termination - the last primer sequence is removed from the end of the lagging strand and the nick is sealed

In eukaryotes, the origin-recognition complex (ORC) and the replication-licensing factor (MCM) synchronize DNA replication. ORC and MCM make sure that DNA replicates only once when the cell divides. Explain how these systems control DNA replication.

Initiation of DNA replication in eukaryotes involves two distinct steps: ORC and MCM. The origin of recognition complex (ORC) binds to the origin and initiates unwinding of the double strand The replication-licensing factor, known as MCM (minichromosome maintenance), approves (license) DNA replication It controls the timing of replication and makes sure that the origin does not signal multiple replications MCM contains a DNA helicase

what are the three steps of transcription? Describe the major events i each step.

Initiation: RNA polymerase binds to the promoter and unwinds the double stand Elongation: RNA polymerase uses one of the DNA strands as a template (template strand or antisense strand) and assembles complementary RNA nucleotides in a 5' → 3' direction Termination: transcription stops when RNA polymerase reaches the terminator (terminator signal)

The basic unit (monomer) of a nucleic acid is a nucleotide. Explain the components of a nucleotide. What types of nucleotides are present in DNA?

Just like in DNA, RNA is made of monomers called nucleotides. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar called ribose, and a phosphate group. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA)

Explain the mechanisms of how the following human disorders are caused by errors in DNA replication: (a) mitochondrial ataxia neuropathy, (b) premature aging (Werner syndrome), and cancer.

Mitochondrial ataxia neuropathy - Caused by a mutation in the y-polymerase (POLG) gene of the mitochondrial DNA Premature aging (Werner syndrome) - shortening of telomeres because of non-functional telomerase Cancer - uncontrolled cell division due to very active telomerase

Do all RNAs in our cells code for proteins?

No, mRNA is referred to as noncoding because they do not encode for proteins

What is the difference between non-coding RNA and messenger RNA (mRNA)?

Noncoding RNA doesn't code for proteins or genes. mRNA carries the info for coding in the polypeptide chain for proteins.

What is the difference between a nucleotide and a nucleotide triphosphate?

Nucleotides are nucleosides with a variable number of phosphate groups connected to the 5' carbon. Nucleoside triphosphates are a specific type of nucleotide.

How does RNA pol distinguish the template strand from the non-template strand during transcription?

One has a promoter on a non template strand but reads the template strand.

150 years ago, humans had different views about how traits are passed from parents to offspring. Explain how pangenesis, preformationism, inheritance of acquired characteristics, and blending inheritance differ from Mendelian inheritance.

Pangenesis: genetic information travels from different paths of the body to reproductive organs (incorrect) Preformationism: miniature organisms reside in sex cells; thus all traits are inherited from one parent (incorrect) Inheritance of acquired characteristics: acquired traits become incorporated into hereditary information (incorrect) Blending inheritance: genes blend and mix (incorrect) Mendelian inheritance: parents pass on discrete heritable units (particles) to offspring according to principles proposed by Mendel (correct)

Coronaviruses have a positive sense RNA genome. What is a positive sense RNA (ssRNA+)?

RNA that is directly used for protein synthesis

there are two major mechanisms of transcription termination in E. coli: rho-dependent and rho-independent terminations. What is the difference between the two?

Rho-dependent: requires rho protein for termination Rho-independent: contains inverted repeats and a series of A nucleotides. The repeats form a hairpin structure in RNA

chromosome

threadlike structures that are composed of DNA and proteins

Briefly describe Meselson and Stahl's experiment and the result they obtained.

The presence of two bands of DNA (one intermediate density and one light density) after two rounds of replication confirmed semiconservative DNA replication. Used centrifuge density gradient

Explain what information Watson and Crick used to build the model of DNA.

They used Franklin's x-ray data (without her knowledge) and the base composition study of Chargaff to build the DNA model from paper cut outs Purine + purine = too wide Pyrimidine + pyrimidine = too narrow Purine + pyrimidine = width consistent with x-ray data

Why is the leading DNA strand synthesized continuously whereas the lagging strand is synthesized discontinuously?

This lagging strand is synthesized in pieces because the DNA polymerase can only synthesize in the 5′ to 3′ direction, and so it constantly encounters the previously-synthesized new strand. The pieces are called Okazaki fragments, and each fragment begins with its own RNA primer.

Describe X-ray crystallography. How did this technique allow determination of the structure of DNA?

X-ray diffraction provided the information about the structure of DNA. (see study guide for image)

single strand binding proteins

attach to single stranded DNA and prevents secondary structures from forming

initiator proteins

binds to the origin, separates strands of DNA to initiate

tRNA

carrie specific amino acids to the ribosome, aiding the translation; carries amino acids during protein synthesis

What will be the problem if telomerase is nonfunctional?

chromosomes will get shorter in each generation

5' and 3' exonuclease activity

cuts DNA/RNA at the end one base at a time, in the 5' to 3' direction

substrates (raw materials)

deoxyribonucleoside triphosphates (dNTPs)

Why is DNA replication described as semiconservative?

each helix that is created contains one strand from the helix from which it was copied.

DNA polymerase III

elongates DNA

population genetics

explores the genetic variation in a population over time

DNA primase

synthesizes a short RNA primer to provide a 3' OH attachment of DNA nucleotide

leading strand

the main strand that is synthesized continuously and starts at the origin/primer

why are model organisms important?

they are important because it is impossible to study all organisms. We use model organisms to study specific biological processes.