PHYSIO EXAM 1

What is defined as the smallest unit of inheritance that codes for specific protein chains?

Gene

What is the term for a three-base sequence that codes for a specific amino acid or a regulatory function?

Codon

What chemical components constitute a nucleoside?

A nitrogenous base attached to a carbohydrate (sugar) with no phosphate.

How does a nucleotide differ structurally from a nucleoside?

A nucleotide is a nucleoside that has one or more phosphate groups attached.

Which two nitrogenous bases belong to the purine family in DNA?

Adenine ($A$) and Guanine ($G$).

Which two nitrogenous bases belong to the pyrimidine family in DNA?

Cytosine ($C$) and Thymine ($T$).

What structural feature characterizes a purine molecule?

A pyrimidine ring fused to an imidazole ring.

What structural feature characterizes a pyrimidine molecule?

A heterocyclic aromatic organic compound containing two nitrogen atoms.

Which specific carbohydrate is found in the nucleotides of RNA?

Ribose.

Which specific carbohydrate is found in the nucleotides of DNA?

Deoxyribose.

What type of chemical bond joins nucleotides together in a DNA chain?

$3'-5'$ phosphodiesterase linkages.

In what direction is DNA always read, replicated, and transcribed?

The $5'

ightarrow 3'$ direction.

Which nitrogenous base pairs with Adenine in DNA?

Thymine.

Which nitrogenous base pairs with Guanine in DNA?

Cytosine.

How many hydrogen bonds connect a Thymine-Adenine base pair?

Two.

How many hydrogen bonds connect a Cytosine-Guanine base pair?

Three.

What three factors stabilize the DNA double helix structure?

Van der Waals interactions, hydrophobic properties of nitrogen bases, and hydrogen bonds.

What are the names of the exposed sections of the DNA double helix that interact with proteins?

Major and minor grooves.

What are the four core histone proteins involved in DNA packaging?

$H2A$, $H2B$, $H3$, and $H4$.

What is the basic organizing unit of chromatin, consisting of eight histone molecules with DNA wrapped around them?

Nucleosome.

What structure is formed when strings of nucleosomes are wound into helical, tubular coils?

Solenoid structures.

Which nitrogenous base is unique to RNA, replacing Thymine?

Uracil (U).

What are the three major types of RNA found in living organisms?

Messenger RNA (mRNA), Transfer RNA (tRNA), and Ribosomal RNA (rRNA).

When RNA hybridizes with DNA, which base pairs with Adenine?

Uracil.

The process of copying DNA into RNA is called _____.

Transcription

The process of decoding transcribed RNA into proteins is called _____.

Translation

According to the Central Dogma, where in the cell does transcription primarily occur?

The nucleus.

According to the Central Dogma, where in the cell does translation primarily occur?

The cytoplasm or Rough Endoplasmic Reticulum (ER).

What enzyme uses DNA as a template to synthesize a complementary RNA molecule?

RNA polymerase.

Which region of RNA polymerase clamps around the DNA template to hold it in place?

The Jaws.

Which region of RNA polymerase allows free ribonucleoside triphosphates to enter the active site?

The ribonucleoside triphosphate tunnel.

What occurs at the 'active site' of RNA polymerase?

The addition of ribonucleoside triphosphates to the growing RNA molecule.

In what direction is a new RNA molecule synthesized during transcription?

The 5'

ightarrow 3'$ direction.

Why is there not a one-to-one correspondence between a single nucleotide and an amino acid during translation?

There are only 4 different nucleotides but 20 different amino acids.

How many different reading frames can an RNA sequence be translated into?

Three.

What is the physical manifestation of an organism's genetic information called?

Phenotype.

What term refers to the genetic information for an organism?

Genotype.

What is the term for a form of a gene that occurs at the same locus on homologous chromosomes?

Allele.

What is the definition of a 'locus' in genetics?

The specific location of allelic genes on a chromosome.

What term describes the existence of two or more different phenotypes resulting from two or more alleles?

Polymorphism.

What are the two primary forms of spontaneous DNA mutations?

Depurination and Deamination.

What is the consequence of depurination during DNA replication?

The replication machinery may skip the missing base, producing a nucleotide deletion.

Spontaneous Mutation: Deamination

Definition: The conversion of a Cytosine base into Uracil.

When the replication machinery encounters Uracil due to deamination, which base does it incorrectly insert into the new strand?

Adenine.

How do X-rays induce DNA mutations?

By exciting water to generate hydroxyl radicals that structure-alter bases or cause double-strand breaks.

What specific type of DNA damage is caused by ultraviolet (UV) light?

The formation of pyrimidine (thymine) dimers.

What is the mechanism by which Benzo[a]pyrene causes DNA mutations?

It is oxidized by cytochrome $P450$ and forms bulky adducts with guanine residues.

What is a point mutation?

A mutation that causes a change in a single nucleotide in the DNA sequence.

Mutation Type: Missense Mutation

Result: A codon that codes for a different amino acid than originally intended.

Mutation Type: Nonsense Mutation

Result: The creation of a premature stop codon.

How do insertions or deletions typically affect the translation of a gene?

They change the reading frame, resulting in a frameshift mutation.

What mechanism causes trinucleotide expansion mutations?

Slippage during DNA replication followed by incorrect re-annealing.

Which clinical disease is specifically associated with a trinucleotide expansion mutation?

Huntington disease.

Chromosomal Mutation: Translocation

Definition: The breakage of a DNA segment from one chromosome and its attachment to a different chromosome.

What term describes the reversal of a piece of DNA within a chromosome?

Inversion.

What is the chromosomal mutation called when there is a production of one or more extra copies of a DNA piece?

Duplication.

What are the two major categories of DNA damage that require repair?

Single nucleotide defects and double-stranded breaks.

Which DNA repair process is most commonly used to fix a deamination event?

Base excision repair.

What is the first step in nucleotide excision repair?

Specific repair endonucleases cleave the abnormal chain and remove the damaged region.

Which enzyme joins the newly synthesized segment to the remainder of the original DNA strand during repair?

DNA ligase.

In base excision repair, what is the role of DNA glycosylase?

It cleaves the N-glycosidic bond joining the damaged base to the deoxyribose.

When is Mismatch Repair typically active in the cell cycle?

During DNA replication.

What is the most common mechanism in somatic cells for repairing double-strand breaks?

Non-homologous end joining (NHEJ).

Why is Non-homologous end joining (NHEJ) considered a 'quick and dirty' repair mechanism?

It does not use a template and often results in the loss of some nucleotides at the break site.

Which double-strand break repair method is considered error-free?

Homologous recombination.

What is required for homologous recombination to occur?

The presence of a homologous chromosome to be used as a template.

Ionizing radiation (X-rays) most often causes which type of DNA damage?

Double-strand breaks.

How many pairs of autosomal chromosomes do humans have?

22 pairs.

What does autosomal inheritance imply regarding gender distribution?

Alleles are passed equally to both males and females.

What defines a dominant allele in terms of phenotypic expression?

Only one allele of a pair is required to manifest the phenotype.

What defines a recessive allele in terms of phenotypic expression?

Both alleles must be the same for the phenotype to be expressed.

Term: Homozygous

Definition: A state where both alleles for a particular gene are the same.

Term: Heterozygous

Definition: A state where the two alleles for a particular gene are different.

What are the four classifications of Mendelian inheritance patterns?

Autosomal Dominant, Autosomal Recessive, X-Linked Recessive, and X-Linked Dominant.

In Autosomal Dominant inheritance, do unaffected persons typically transmit the trait?

No, unaffected persons do not transmit the trait to their children.

How does the phenotype usually change if an individual has two mutant alleles in an Autosomal Dominant disorder?

The phenotype is generally more severe.

What is the typical status of the parents of a child with an Autosomal Recessive disorder?

They are usually phenotypically normal heterozygous carriers.

What is the average probability that a sibling in a carrier mating for an Autosomal Recessive trait will be affected?

One fourth ($25\%$).

If a rare recessive trait is found in a pedigree, what parental history is often suspected?

A marriage between close relatives (consanguinity).

What is the distinguishing feature of X-linked dominant disorders regarding 'carriers'?

There are no carriers; the disease is expressed in both males and females.

To whom will an affected male transmit an X-linked dominant mutant allele?

To all of his daughters, but none of his sons.

In X-linked inheritance, why can't a father pass the mutant allele to his son?

A father passes his $Y$ chromosome to his son, not his $X$ chromosome.

How many histone molecules make up the core of a nucleosome?

Eight (two copies each of H2A, H2B, H3, and H4).

In DNA replication, what occurs at the $3'$ end of the growing strand?

New nucleotides are added by forming phosphodiester bonds with the existing hydroxyl group.

What happens to the reading frame in a deletion mutation involving one nucleotide?

It shifts, altering all subsequent codons in the sequence.

Which chromosomal mutation involves the unequal crossing over during meiosis?

Recombination.

Mutation: Deamination of Cytosine

Conversion: Cytosine becomes Uracil, which then pairs with Adenine during replication.

Which specific DNA repair pathway uses DNA polymerase to fill a 'gap' created by an endonuclease at a baseless sugar-phosphate site?

Base excision repair.

What is the role of 'branch point migration' in homologous recombination?

It allows the base pairs holding the duplexes together to break and reform as the invading strand elongates.

What is the definition of immune tolerance?

The lack of responsiveness to a specific antigen that could otherwise elicit an immune response.

What is the most common example of antigen tolerance in normal physiology?

The host's normal absence of response to "self" antigens.

What condition results when the body's immune tolerance mechanism fails?

Autoimmunity.

The cross-reactivity of a pathogen and self-cells is known as _____.

Molecular mimicry

Why are females generally at a higher risk for developing autoimmune disorders?

Genetic factors play a role in increasing susceptibility for females.

Which specific HLA allotype is associated with the highest relative risk (> 150) for Ankylosing spondylitis?

$B27$

Which HLA allotype is associated with a relative risk of > 40 for Narcolepsy?

$DQ6$

Which HLA allotypes are associated with Celiac disease?

$DQ2$ and $DQ8$.

Rheumatoid arthritis is primarily associated with which HLA allotype?

$DR4$