BIO 100 Exam 3

Name some cell types and relate their overall shape and internal structure to their special functions.

Identify on a cell model or diagram the three major cell regions (nucleus, cytoplasm, and plasma membrane)

Identify the organelles on a cell model or describe them and indicate the major function of each.

Describe the structure and function of the cell nucleus and its contents.

Describe where and how DNA is stored within the cell

Identify the structure and molecular makeup of DNA

List the similarities and differences between the various nucleic acid molecules.

Summarize how DNA is replicated in a semi conservative way

Explain how errors in replication can lead to mutations

an error can pair an incorrect nucleotide

* if not fixed, could affect transcription of RNA and in turn affect translation of amino acid and protein

can lead to mutations and variations in strains of disease & living things

raw material of evolution by natural selection

* but most mutations are harmful

if Proofreading does not occur when an incorrect nucleotide is added, then there will be a mutation

Investigate how differences in DNA sequences can be used in DNA profiling

DNA Profiling - set of lab techniques that allows you to determine with certainty whether 2 samples of DNA are from the same individual

* compare small regions of DNA that are known to vary among the population - short tandem repeats (STR)

STRs are sites where a short nucleotide sequence is repeated many times in a row

* location of theses sites and the sequences are identical from person to person

* number of repeats vary

* compare # of repeats

Examine how the structure of DNA fits in the central dogma

starts in the nucleus

goes through a nuclear pore

translation occurs in the ribosome

protein is synthesized in the cytoplasm

Identify and describe the unique function of the organelles involved in protein synthesis.

Nucleus -houses DNA

* site of transcription

* RNA carries the instructions for making proteins from the nucleus to the cytoplasm

Endoplasmic Reticulum (ER) - networks of passageways and sacs

* Rough - contains ribosomes that will produce proteins (site of translation)

* Smooth - lacks ribosomes

Ribosome

* RNA's info is used by ribosomes to make a specific protein

* some ribosomes are attached to the rough ER membrane, some float freely in cytoplasm

Describe the process of protein synthesis, including how the genetic information is transferred during transcription and translation.

Transcription (DNA -> RNA) - sequence of DNA is copied to make a complementary RNA sequence in the nucleus

* newly made RNA molecule carries instructions for making a protein from the nucleus to the cytoplasm

Translation (RNA -> proteins) - information contained in the RNA is used to produce amino acids which are strung together to make proteins

* this process occurs in the ribosomes which are found in the rough ER

Summarize the process of PCR and Compare it to DNA Replication

Describe the early discoveries in molecular biology including PCR and DNA sequencing

PCR - common lab technique used to make copies of a specific region of DNA

* goal is to make enough of the target region of the DNA within the larger DNA molecule so it can be analyzed

* Process - DNA Polymerase (enzyme) binds to primers (short single-stranded DNA molecules complementary to sequences at each end of the target sequence) and synthesize new DNA nucleotides using free nucleotides floating around

STR Analysis - comparing the lengths of short tandem repeat or STR sequences at 13 predefined sites within human genome

* relies on PCR

* PCR can produce large quantities of STR for comparison

* STR sites vary widely so no two human have the same number of repeats at all 13 sites

DNA Sequencing - process of determining the precise order of nucleotides within a DNA molecule

Illustrate how these discoveries were applied into technologies

Whole-Genome Shotgun Method

* DNA is obtained from one or more individuals

* DNA is digested with restriction enzymes, which cut up DNA into small segments

* Sequence of DNA fragment is determined through an automated sequencing machine

* Computer programs use overlapping regions from each fragment to determine original order of sequences

* Complete genome is uploaded to database

Describe how scientists can analyze DNA profiles and how this information is applied

after PCR prepares STR analysis sample, gel electrophoresis allows scientists to visualize DNA samples based on their lengths

Gel Electrophoresis Process

* DNA is loaded into one end of the gel

* electrical current is applied

* negatively charged DNA molecules will migrate through the gel towards the positive pole

* smaller pieces of DNA migrate faster show in the bands on the gel

* staining shows the location of bands

Evaluate how we utilize biotechnology in law, health, and science

law - DNA profiling

Science - DNA sequencing

Science? - PCR

Health - Producing GMOs

Describe how scientists manipulate DNA to produce genetically modified products.

Genetically Modified Organisms have acquired one or more genes through artificial means

Transgenic Organism - organism acquires a gene from another species

Transgenic Plants

* produced by inserting a desired gene into a plasmid, which is a small, circular, independently replicating DNA piece that was originally isolated from a bacterium

* plasmids temporarily carry the DNA with the desired gene that can be inserted into a genome of a plant

* transfers a gene into the plant which expresses the trait from the newly inserted gene

Transgenic Animal

* genetic modification to food animals to make them healthier or more productive

* pharmaceutical companies produced GMOs that secrete medically useful human protein

Outline the process of DNA to RNA to protein.

Compare and contrast transcription and translation

Define cancer

a disease caused when cells divide uncontrollably and spread into surrounding tissues

tumors are caused by uncontrolled cell division

* if it doesn't spread to other tissue it is benign (not cancerous)

* if it spreads to other tissues it is malignant and is considered cancerous

Outline the cell cycle and its relation to cancer

a cell cycle control system regulates the timing of cell duplication

Proto-oncogenes - code for proteins that properly regulate the cell cycle

Growth Factors - (a type of proto-oncogene) code for proteins that make cell replication "go" when it is appropriate

Tumor-Suppressor Genes - code for proteins that "stop" cell replication when something is wrong (at checkpoints) - when cell replication is stopped, the cell undergoes cell death

Differentiate between different types of mutations

mutation is any change to the genetic information of a cell or virus

* mainly cause harm but could lead to improvement

* occur spontaneously due to error during DNA replication

Point Mutation - mutation that only changes one nucleotide base

* Silent Mutation - does not change the amino acid produced because some amino acids are encoded by more than one RNA codon (or it changes non-coding DNA)

* Missense Mutation - produces a different amino acid from the original resulting in a mutant protein (may be nearly identical or substantially different)

*Nonsense Mutation - changes an amino acid codon to a stop codon which will shorten an amino acid and in turn, produce a shortened protein that is almost always defective

Frameshift Mutations - a change that throws off the reading frame

* Insertions - mutations that add nucleotides

* Deletions - mutation that remove nucleotides

Codons

group of three nucleotide bases in DNA or RNA that code for a specific amino acid

* multiple codons can code an amino acid

Describe and contrast tumor suppressor genes and oncogenes

Mutations cause DNA to code for abnormal proteins in the cell cycle control system that cannot properly regulate cell duplication

Oncogenes - mutated proto-oncogenes that produce abnormal proteins that fail to regulate the cell cycle

Mutated Growth Factors - a type of oncogene that produces proteins that promote, or allow cell division to "go" even when it's not appropriate

Mutated Tumor-Suppressor Genes - produce proteins that fail to stop the cell cycle, even when something goes wrong

Identify and describe the cause(s) of cancer

Spontaneous mutations - result from abnormalities in cellular and other biological processes

* can't be prevented

Induced mutations - result from contact with environmental agents that alter DNA structure

* Mutagens - physical & chemical factors in the environment that interacts with DNA and causes a mutation

* can be prevented

Identify methods of cancer treatment and prevention

some cancer-causing mutations can't be prevented because they're inherited or happen spontaneously

most cases are caused by carcinogens (factors in the environment that cause mutations or damage DNA)

Prevention methods

* healthy diet

* not smoking

* sun protection

* regular screenings

* exercising regularly

Treatment

* "Slash" - surgery which can physically remove a tumor (benign or malignant; malignant can't be treated just with surgery but also other treatments)

* "Burn" - radiation therapy which exposes parts of the body to high-energy radiation which disrupts cell division that can slow down or kill cancer cells but it also can damage normal body cells

* "Poison" - chemotherapy which uses drugs that disrupt cell division by passing through the bloodstream, so they affect cells throughout the body but has negative side effects

Compare the structure of prokaryotic and eukaryotic chromosomes

Eukaryotic

* chromosome is a very long piece of DNA wrapped around proteins

* DNA is contained within membrane-bound nucleus

* DNA is bound to proteins called histones that is wound up into chromosome

* each cell has 46 chromosomes except gametes

Prokaryotic

* DNA is not contained within any structure but is found freely in the cytoplasm (in the nucleoid)

* DNA is circular

* not bound with proteins, so no chromatin formed

Compare the functions, cellular processes, and cellular products of asexual and sexual reproduction

Sexual Reproduction - formation of genetically unique offspring

* egg and sperm cells formed via cell division from adult cells in ovaries & testes

* fertilization - sperm + egg = zygote (half of zygote chromosomes from mother and half from father)

* development - zygote develops into an embryo after repeated rounds of cell division developing fetus -> baby -> adult consisting of countless somatic cells with identical DNA

* growth and repair - throughout life, cell division provides new cells to expand tissues and organs, and replace damaged cells

Asexual Reproduction - formation of new genetically identical individual by a single parent without sperm or egg cell

* only one set of chromosomes passed down

* binary fission - one cell divides creating two genetically identical offspring; single-celled organisms reproduce this way

* plant reproduction - some plants sprout or send out runners that humans cut off to grow new plans

* regeneration - some animals can regenerate lost limbs

Describe the basic structure of a chromosome, including how it is packaged into an elaborate, multilevel system of coiling and folding

Chromosome - long piece of DNA wound up around a protein called a histone and tightly organized in a nucleus

Chromatin - DNA and protein

* non-dividing nucleus -> uncondensed chromatin fibers

* dividing nucleus -> condensed chromatin fibers

Describe key events of each phase of mitosis, and recognize the phases of mitosis from diagrams and micrographs

The nucleus and its duplicated chromosomes divide and it distributed to the two offspring cells

Interphase - cell performs normal functions and duplicates the chromosomes within the nucleus

* most of cell's lifetime

* comes before mitosis

* early - chromosomes are in an uncondensed state and loosely arranged in the nucleus. Cell carries out its normal functions

* middle - chromosomes duplicate - as cell prepares to divide in mitosis, each chromosome is duplicated

* end - each chromosome in the nucleus has a duplicate, attached to it at the centromere. (still uncondensed)

Prophase - (Chromosomes Condense) nuclear membrane dissolves; protein tracks called mitotic spindles laid to organize chromosomes

Metaphase - (Chromosomes Align) duplicated chromosomes line up in the center of the cell, with each chromosome attached to a separate track of the mitotic spindle

Anaphase - (Chromosomes Split) sister chromatids are separated as the spindles retreat towards opposite ends of the cell

Telophase - (Nucleus Reforms) nuclear membrane reforms with the nucleus duplicated into two nuclei, each with a full set of original chromosomes; chromosomes uncondense

Compare cytokinesis in animal and plant cells

Cytokinesis - distribution of cytoplasm to the two offspring cells

Animal Cell

* distributed through cleavage process - as cells separate, cleavage furrow contracts, deepening the furrow. Eventually the parent cell is pinched in two, leaving two independent offspring cells

Plant Cell

* different than animal cell due to stiff cell wall

* a cell plate (strip of membrane and cell wall materials that forms along the center of the cell) builds up and eventually fuses with membrane, separating the two offspring cells

Distinguish between the following pairs of terms, including structure and function of each: sex chromosomes versus autosomes, somatic cells versus gametes, and diploid versus haploid cells

Sex Chromosomes vs. Autosomes

* sex chromosomes have 1 pair on the 23 chromosomes pairs determining sex while autosomes have 22 pairs of chromosomes other than the sex chromosomes

Somatic Cells vs Gametes

* somatic cells are body cells (cells in the rest of the body othan than gametes) and have diploids which have 46 chromosomes while gametes are sex cells (egg & sperm cells) that have haploid which each gamete contains 23 chromosomes

Diploid - two sets of chromosomes (2n)

Haploid - single set of chromosomes (n)

Homologous Pairs of Chromosomes - two different chromosomes that contain same gene loci but may have different alleles of a particular gene

Sister Chromatids - identical copies produced during DNA replication and held together via centromere

Compare the processes and products of meiosis I, meiosis II, and mitosis, explaining how the independent assortment of chromosomes during meiosis, random fertilization, and crossing over contribute to genetic diversity in offspring

Meiosis occurs in gametes which contain only 23 chromosomes

Gametes produced via meiosis are haploid

Produces 4 daughter cells

Meiosis I

* Prophase I - nuclear membrane dissolves

* Metaphase I - chromosomes condense and line up by homologous pairs along the centerline of the cell (aligned chromosomes may swap pieces with each other)

* Anaphase I - homologous pairs of chromosomes separate and each chromosome still consists of two joined sister chromatids

* Telophase I - nuclear membrane reforms

* Cytokinesis - cell divides into 2 cells

Meiosis II

* Prophase II - in each of the 2 cells condensed by meiosis I, chromosomes (still duplicated with sister chromatids) condense

* Metaphase II - chromosomes line up in the center of the cell

* Anaphase II - sister chromatids split apart

* Cytokinesis II - each cell splits, producing 4 cells, each with half the number of chromosomes as the starting cell

* Telophase II - nuclear membrane reform & chromosomes condense

Mitosis

* occurs in somatic cells

* produces diploid somatic cells

* produces 2 daughter cells

Predict the consequences of nondisjunction in autosomes and sex chromosomes

Chromosomes fail to separate properly during cell division, resulting in daughter cells with unusual numbers of chromosomes

* if abnormal gamete is involved in fertilization, the resulting zygote will have abnormal number of chromosomes and cannot develop into viable embryo

* can affect both sex chromosomes and autosomes

Describe evidence that might be used to determine whether a species has historically reproduced sexually or asexually

Compare the advantages and disadvantages of sexual and asexual reproduction.

Sexual

* Advantage - more variation among offspring because it inherits from two parents

* Disadvantage - requires finding another mate and more energy

Asexual

* Advantage - time efficient as there is no need to search for a mate and requires less energy

* Disadvantages - no variation

Compare Meiosis and Mitosis and how meiosis relates to the inheritance of Cancer

Mitosis produces two genetically identical "daughter" cells from a single "parent" cell. Meiosis produces cells that are genetically unique from the parent and contain only half as much DNA.

Mitosis - mutations can cause uncontrolled cell division

* proto-oncogenes produce proteins that control cell cycle

* mutation may turn proto-oncogene into an oncogene which produces a protein that fails to regulate cell cycle (uncontrolled cell growth)

* accumulation of mutations in proto-oncogenes produce oncogene

Meiosis - cancer-causing mutation can be passed down

* BRCA gene

Several mutations are needed (Accumulation of genes) for a cell to become malignant

Identify and Summarize the ways sexual reproduction leads to genetic variation

every organism produced through sexual reproduction is genetically unique

Random Fertilization - one chromosome pair (out of 23 pairs) in an adult cell has an equal chance of giving a red or blue chromosome to the gamete

* 23 chromosomes are given, so 23 random combinations per gamete

* two gametes are needed for offspring so 46 different chromosomes

Independent Assortment - during Meiosis 1 (1st round of gamete formation), chromosomes line up by homologous pair (1 maternal, 1 paternal) and not in a specific order so over 8 million possibilities

Crossing Over - when homologous chromosomes line up during Meiosis, the maternal and paternal chromosomes swap pieces

* produces hybrid chromosomes that are partially maternal, partially paternal which is a new combination of genes that may be produced and passed onto offspring

Explain the Central Dogma of Molecular Biology

DNA is separated -> transcribed into mRNA -> translated into amino acids -> multiple amino acids make proteins -> proteins are needed for cells to function

Define gene expression and describe how it relates to a cell's function and phenotype

Through Gene Regulation cells control Gene Expression

Gene Expression - flow of genetic information from DNA to RNA to protein

* genes "expressed" into proteins

* every cell has the same DNA but look and act different due to how they differently express genes

* they control which genes are or are not expressed through gene regulation

Gene Regulation - mechanisms that turn on certain genes while keeping other genes turned off (transcription factors must be bound to DNA) in a particular cell

* turning off a gene means that gene expression is not being completed

* each cell expresses the DNA specific to itself and turns off those that aren't necessary

* several points along the path from DNA to RNA to protein that can be regulated

Control of RNA

before leaving the nucleus, RNA transcribed from a gene can be altered in several ways

* noncoding regions (introns) are spliced out, and remaining protein-coding regions (exons) are pasted together

* because different exons may be included or cut out each time, several different mRNA molecules may be produced from a single gene

* small RNA molecules called microRNAs bind to mRNA molecules, preventing them from producing protein

Protein Control

initiation, activation, breakdown

Translation (process of RNA -> proteins) plays a role in gene regulation

Barr Body

condensed, inactive X chromosome in a female

Illustrate a signal transduction pathway and predict what would happen to the cell's function if specific proteins were mutated

A series of relay molecules that convey the message from outside the cell into the cell's interior cytoplasm and eventually to the nucleus

receptor protein receives growth signal -> signal protein 1 -> transcription factor protein -> DNA in the nucleus -> mRNA -> new protein -> [Signal Protein 2 -> Cell Division] OR [Signal Protein 3 -> Cell Death]

signal usually results in the turning on or off of one or more genes

Describe the types of mutations that must occur for a tissue to become cancerous

Distinguish between a zygote, and embryo, and a fetus

Zygote - one single fertilized egg cell

* fused sperm and egg

Embryo - multiple unspecialized cells

* divided zygote

Fetus - specific levels of cell specialization

Define the following terms: fertilization, cleavage, blastocyst, gastrula, placenta, umbilical cord, amnion

Outline the development of a human from fertilization to birth

Identify which trimester of pregnancy you would expect mitosis to occur most rapidly

List the structures of the nucleus, and explain its function

Nuclear Envelope - double layered membrane that regulates what goes in and out of the nucleus

Nuclear Pore - opening in the membrane that lets substances enter and exit the nucleus

Nucleolus - DNA directs the production of ribosomal RNA (rRNA), which exits the nucleus and joins with protein to form ribosomes (which manufacture proteins)

Chromosomes - tightly packed DNA and protein

* chromatin (material that makes up chromosomes) is usually very loose in the nucleus, but coils tightly during cell division

Autosomal DOMINANT Inheritance

males and females have the trait at similar frequency (and either parent can transmit the trait)

each person with the trait has at least 1 parent with the trait

if neither parent has the trait, none of the children have it

affected parents (both) can have unaffected children

Autosomal RECESSIVE Inheritance

males and females have the trait at similar frequency (and either parent can transmit the trait)

if neither parent has the trait, some of the children can still have it

if both parents are affected, all the children are affected

Sex-Linked Inheritance

X-linked RECESSIVE Inheritance

* more males affected than females

* Hallmark - unaffected mothers have affected sons and unaffected daughters

* affected fathers have unaffected children

* affected mothers have all affected sons

X-linked DOMINANT Inheritance

* Hallmark - all daughters of affected fathers are affected and none of the sons are

* affected mothers can have both affected sons and daughters

Discuss what actually happens when a pregnant woman's "water breaks"

____ is the self-replicating material present in nearly all living organisms; it is the main constituent of chromosomes and the carrier of genetic information

DNA

____ is used in all steps of protein synthesis and carries the genetic information of many viruses

RNA

The ____ is the most prominent membrane-bound organelle in eukaryotic cells, and it houses most of a cell's DNA

Nucleus

The ______ ______ is the two-layered membrane that encases the nucleus of an eukaryotic cell, separating the nucleus from the cytoplasm.

nuclear envelope

A protein-lined channel in the nuclear envelope that regulates the transportation of molecules between the nucleus and the cytoplasm is called a ______ ______.

nuclear pore

The round body that sits inside the nucleus of a eukaryotic cell and makes ribosomal subunits from proteins and ribosomal RNA is known as the ______

nucleolus

______ are tightly coiled bundles of DNA and protein found in the nucleus of most living cells

Chromosomes

What part of a nucleotide molecule in DNA encodes genetic information?

the base - genetic information is encoded in the four-letter alphabet that corresponds to the four bases: adenine, guanine, cytosine, thymine

Phosphate Group

a chemical group that consists of a phosphorus atom bonded to 4 oxygen atoms

Deoxyribose

a central five-carbon sugar

Hydrogen Bond

Nitrogenous Base

Nucleotide

Base Pairs in DNA

A & T

C & G

After DNA replication, ______

each of the two daughter DNA molecules contains one strand from the original DNA molecule and one newly synthesized strand

How are DNA and RNA different?

DNA contains the bases A, G, C, and T; RNA contains the bases A, G, C, and U

If DNA directs the production of RNA, what does RNA make?

RNA makes protein

What is used to construct a molecule of DNA

nucleotides

What component of DNA gives it a negative charge?

phosphate group

Place the following steps of DNA replication in the proper order: DNA fragments are fused together; double helix is pulled apart; new strands of DNA are synthesized.

Double helix is pulled apart, new strands of DNA are synthesized, and DNA fragments are fused together

A drug that inhibits DNA ligase but not DNA polymerase is added to a cell. Explain how DNA replication would be affected as a result of the drug.

The new DNA fragments would not be fused together and the backbone of the DNA would be incomplete

What characteristics would indicate that a nucleic acid is RNA and not DNA

presence of uracil, but no thymine

presence of ribose, but no deoxyribose

what is the order of protein, DNA, and RNA

DNA -> RNA -> protein

Translation converts the information stored in _____ into ______

RNA; a protein

A series of three nucleotides that specifies an amino acid is a(n) _____

codon

What are the molecules and processes involved in the flow of genetic information through a cell?

Starts in the nucleus

- DNA -> (transcription) - > RNA

enters the cytoplasm by escaping through the nuclear pore and into the ribosome for translation then into the cytoplasm

- RNA-> translation -> protein

The principle role of ____ is to act as a messenger carrying instructions from DNA out of the nucleus for the synthesis of protein

RNA (role)

_____ is the first step of gene expression, during which a particular segment of DNA is converted into RNA

Transciption

A _____ is made up of hundreds or thousands of smaller units called amino acids, attached to one another in long chains

protein

_____ is the process in which mRNA codons are converted into an amino acid sequence

Translation

A _____ serves as the site of protein synthesis in the cytoplasm

ribosome

_____ is a long linear polymer found in the nucleus of a cell, shaped like a double helix, and associated with the transmission of genetic information

DNA (shape)

Plant Cell Wall role in the cell

strong, protective structure made from cellulose fibrils

Central Vacuole role in the cell

Regulates cytoplasm composition, creates internal pressure and stores cell compounds

Chloroplasts role in the cell

makes food by converting light energy into chemical energy

Mitochondrion role in the cell

Converts chemical fuel into molecules with high chemical energy content (ATP) that can power the cell

Golgi Apparatus role in the cell

modifies and packages proteins

Nucleus’s role in the cell

stores the genetic information of the cell

Lysosome role in the cell

break down macromolecules using digestive enzymes

Ribosome role in the cell

works with mRNA to synthesize proteins

Smooth ER role in the cell

site of lipid synthesis

What exists only in animal cells?

lysosome

What exists only in plant cells

cell wall

chloroplast

central vacuole

Steps of polymerase chain reaction (PCR)

start with a sample of double-stranded DNA

heat sample to separate DNA strands

DNA polymerase duplicates DNA strands

Cool sample to allow DNA double helices to form